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  1. Software for "MetaLIMS, A Simple Open-Source Laboratory Information Management System for Small Metagenomic Labs"

    ID: doi:10.5524/100293

    Release Date: 04-01-2017

    Description: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of ...

  2. Supporting data for "The Healthy Brain Network Serial Scanning Initiative"

    ID: doi:10.5524/100259

    Release Date: 12-30-2016

    Description: Although typically measured during the resting state, a growing literature is illustrating the ability to map intrinsic connectivity in task and natur...

  3. Supporting data for "Stepwise Distributed Open Innovation Contests for Software Development - Acceleration of Genome-Wide Association Analysis"

    ID: doi:10.5524/100264

    Release Date: 12-23-2016

    Description: The association of differing genotypes with disease related phenotypic traits offers great potential to both help identify new therapeutic targets and...

  4. Supporting data for "Genome sequencing of the winged midge, Parochlus steinenii, from the Antarctic Peninsula"

    ID: doi:10.5524/100256

    Release Date: 12-07-2016

    Description: In the Antarctic, only two species of Chironomidae occur naturally—the wingless midge, Belgica antarctica, and the winged midge, Parochlus steinenii...

  5. Supporting data for "Calculating quality of public high-throughput sequencing data to obtain suitable subset for reanalysis from the Sequence Read Arc...

    ID: doi:10.5524/100304

    Release Date: 04-17-2017

    Description: It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing num...

  6. De novo sequencing of Ginkgo biloba

    ID: doi:10.5524/100209

    Release Date: 11-15-2016

    Description: Ginkgo biloba is one of the world’s most ancient plants, a living fossil that has remained essentially unchanged in terms of gross morphology for m...

  7. Supporting data for "Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets"

    ID: doi:10.5524/100204

    Release Date: 06-10-2016

    Description: Bioinformatics software often requires human-generated tabular text files as input and have specific requirements for how those data are formatted. Us...

  8. Supporting data for "ReGaTE, Registration of Galaxy Tools in Elixir"

    ID: doi:10.5524/100287

    Release Date: 03-14-2017

    Description: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work, and have been guided in their choices by a number o...

  9. NeuroView: a customizable browser-base utility

    ID: doi:10.5524/100237

    Release Date: 10-24-2016

    Description: The amount of data acquired for an fMRI experiment dimension wise is very large and a challenge for neuroscience studies, in particular for data analy...

  10. Supporting data for "Sequencing, de novo assembly, and annotation of a pink bollworm larval midgut transcriptome"

    ID: doi:10.5524/100203

    Release Date: 05-24-2016

    Description: The pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is one of the world's most important pests of cotton. Insecticide spr...

  11. A cortical surface-based geodesic distance package for Python

    ID: doi:10.5524/100232

    Release Date: 10-24-2016

    Description: The human cerebral cortex, whether tracing it through phylogeny or ontogeny, emerges through expansion and progressive differentiation into larger and...

  12. Facilitating big data meta-analyses for clinical neuroimaging through ENIGMA wrapper scripts

    ID: doi:10.5524/100231

    Release Date: 10-24-2016

    Description: A vast number of clinical disorders may involve changes in brain structure that are correlated with cognitive function and behavior (e.g., depression,...

  13. Nipype interfaces in CBRAIN

    ID: doi:10.5524/100226

    Release Date: 10-24-2016

    Description: We aim at the large-scale, automatic sharing of software tools between neuroimaging processing platforms, which will increase the relevance of such pl...

  14. Supporting data for "Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper"

    ID: doi:10.5524/100196

    Release Date: 10-04-2016

    Description: The five-pacer viper (Deinagkistrodon acutus) is a venomous snake living in Southern China, characterized by a triangular head and upturned rostral. I...

  15. Software and supporting material for: "RES-Scanner: a software package for genome-wide identification of RNA-editing sites"

    ID: doi:10.5524/100211

    Release Date: 08-15-2016

    Description: High-throughput sequencing (HTS) provides a powerful resolution for the genome-wide identification of RNA-editing sites. However, it remains a great c...

  16. Dataset collection from the 2015 Brainhack Proceedings

    ID: doi:10.5524/100215

    Release Date: 08-23-2016

    Description: Brainhack - a novel conference model for the open neuroscience research community - exploded in 2015. With three-day events in Honolulu (June), Montr...

  17. Optimized implementations of voxel-wise degree centrality and local functional connectivity density mapping in AFNI

    ID: doi:10.5524/100219

    Release Date: 10-20-2016

    Description: Degree centrality (DC) and local functional connectivity density (lFCD) are statistics calculated from brain connectivity graphs that measure how impo...

  18. Supporting data for the draft genome of the Northern snakehead, Channa argus

    ID: doi:10.5524/100279

    Release Date: 03-03-2017

    Description: The Northern snakehead (Channa argus), a member of Channidae family in Perciformes, is an economically important freshwater fish with its main distrib...

  19. Supporting data for "MinION nanopore sequencing of environmental metagenomes: a synthetic approach"

    ID: doi:10.5524/100278

    Release Date: 02-06-2017

    Description: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon ...

  20. Generating music with resting-state fMRI data

    ID: doi:10.5524/100224

    Release Date: 10-24-2016

    Description: Resting-state fMRI (rsfMRI) data generates time courses with unpredictable hills and valleys. People with musical training may notice that, to some de...

  21. Supporting data for "Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis".

    ID: doi:10.5524/100168

    Release Date: 12-08-2015

    Description: Human epidermis from three patients underwent single-target immunofluorescence labelling against: calmodulin, β1 integrin, β4 integrin, keratin-10, ...

  22. Supporting data for "Multi-platform microRNA profiling of hepatoblastoma patients using formalin fixed paraffin embedded archival samples".

    ID: doi:10.5524/100180

    Release Date: 11-26-2015

    Description: Formalin fixed paraffin embedded (FFPE) samples are a valuable resource in cancer research and have the potential to be extensively used. However, the...

  23. Supporting data for the "Draft genome of the Chinese mitten crab, Eriocheir sinensis"

    ID: doi:10.5524/100186

    Release Date: 01-12-2016

    Description: Chinese mitten crab, Eriocheir sinensis, has been one of the most famous representatives of crustacean in China. Its transition from swimming type to ...

  24. GigaDB promoting data dissemination and reproducibility

    ID: doi:10.5524/2014GGBNCIH

    Release Date: 06-23-2014

    Description: GigaDB promoting data dissemination and reproducibility.

  25. Supporting material for "High throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multi-transcripto...

    ID: doi:10.5524/100169

    Release Date: 04-07-2016

    Description: The venom of predatory marine cone snails mainly contains a diverse array of unique bioactive peptides commonly referred to as conopeptides or conotox...

  26. Supporting materials for: "VirAmp: A Galaxy-based viral genome assembly pipeline".

    ID: doi:10.5524/100113

    Release Date: 04-21-2015

    Description: We have developed a multi-step viral genome assembly pipeline named VirAmp, that combines existing tools and techniques and presents them to end users...

  27. Supporting data for the dynamics and stabilization of the Human gut microbiome during the first year of life.

    ID: doi:10.5524/100145

    Release Date: 05-14-2015

    Description: Here we performed metagenomic shotgun sequencing on fecal samples from 98 full-term Swedish infants (new born, 4-months and 12-months old) and their m...

  28. Supporting data for "Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment"

    ID: doi:10.5524/100144

    Release Date: 10-21-2015

    Description: There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specia...

  29. Supporting data for "Addressing health disparities in Hispanic breast cancer: Accurate and inexpensive sequencing of BRCA1 and BRCA2"

    ID: doi:10.5524/100154

    Release Date: 08-26-2015

    Description: Germline mutations in the BRCA1 and BRCA2 genes account for 20 to 25% of inherited breast cancer and about 10% of all breast cancer cases. Detection o...

  30. 3-dimensional microCT reconstructions of brooding brittle stars

    ID: doi:10.5524/100130

    Release Date: 09-24-2015

    Description: Brooding brittle stars have a special reproduction mode of retaining their eggs and juveniles inside respiratory body-sacs called bursae. In the past,...

  31. Supporting material for: "Free breathingly acquired myocardial perfusion data sets for performance analysis of motion compensation algorithms"

    ID: doi:10.5524/100106

    Release Date: 10-22-2014

    Description: Perfusion quantification by using first-pass gadolinium-enhanced myocardial perfusion magnetic resonance imaging (MRI) has proved to be a reliable too...

  32. The genome of the saltwater crocodile (Crocodylus porosus)

    ID: doi:10.5524/100127

    Release Date: 10-29-2014

    Description: Saltwater crocodiles (Crocodylus porosus) are the largest reptilian species alive today and as the name suggests they shows a high tolerance to salini...

  33. Anguidae lizard (Ophisaurus gracilis) genome assembly data

    ID: doi:10.5524/100119

    Release Date: 03-25-2015

    Description: The evolutionary transition from a lizard-like body to a snake-like body form is one of the most important transformations in reptilian evolution. The...

  34. Validation Data For Capture-based whole genome promoter bisulfite-seq for 8 pairs of HCC tumor and non-tumor liver (NTL) samples

    ID: doi:10.5524/100120

    Release Date: 02-05-2015

    Description: Epigenetic alterations such as aberrant DNA methylation of promoter and enhancer regions that lead to atypical gene expression have been associated wi...

  35. Supporting material for: "Shared data for IMRT optimization research: the CORT dataset"

    ID: doi:10.5524/100110

    Release Date: 11-26-2014

    Description: Here we provide intensity modulation radiation therapy (IMRT) datasets for a prostate case, a liver case, a head and neck case, and a standard IMRT ph...

  36. Supporting data and materials for "Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural pr...

    ID: doi:10.5524/100151

    Release Date: 07-22-2015

    Description: The production of biogas takes place under anaerobic conditions and involves microbial decomposition of organic matter. Most of the participating micr...

  37. Data looking at methylation changes of intestinal genes in the neonatal period of preterm neonate pigs

    ID: doi:10.5524/100070

    Release Date: 09-01-2014

    Description: For this study, six term pigs were delivered close to full term (115–116 days gestation, by cesarean section) from two pregnant sows (Large White ×...

  38. Software and supporting material for: "SmileFinder: a resampling-based platform to evaluate signatures of selection from genome-wide sets of matching ...

    ID: doi:10.5524/100100

    Release Date: 11-05-2014

    Description: SmileFinder is a simple program that looks for the sweep patterns left by historic selection in genome-wide allele frequency datasets by evaluating th...

  39. Phylogenomic analyses data of the avian phylogenomics project

    ID: doi:10.5524/101041

    Release Date: 11-27-2014

    Description: Determining the evolutionary relationships of modern birds has been one of the biggest challenges in systematic biology. To address this challenge, we...

  40. Genomic data of the Great black cormorant (Phalacrocorax carbo)

    ID: doi:10.5524/101034

    Release Date: 04-22-2014

    Description: The Great Cormorant (Phalacrocorax carbo) is a widespread member of the cormorant family and is known by several different names around the world - th...

  41. Genomic data of the Northern Carmine bee-eater (Merops nubicus)

    ID: doi:10.5524/101029

    Release Date: 04-22-2014

    Description: The Northern Carmine Bee-eater (Merops nubicus) is part of the bee-eater family, Meropidae, and is also known as the Nubian bee-eater. It is a brightl...

  42. Genomic data of the Bald Eagle (Haliaeetus leucocephalus)

    ID: doi:10.5524/101040

    Release Date: 05-12-2014

    Description: The Bald Eagle (Haliaeetus leucocephalus(Linnaeus, 1766)) is the official emblem of the United States and it belongs to a group of birds known as fish...

  43. Whole-Genome Sequences of DA and F344 Rats with Different Susceptibilities to Arthritis, Autoimmunity, Inflammation and Cancer

    ID: doi:10.5524/100042

    Release Date: 05-29-2013

    Description: DA and F344 are two inbred rat strains with numerous dichotomous phenotypes, including susceptibility to autoimmune disease models and inflammatory r...

  44. Genomic data of Flax (Linum usitatissimum)

    ID: doi:10.5524/100081

    Release Date: 02-26-2014

    Description: Flax (Linum usitatissimum) is also known as linseed. It is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally releva...

  45. Genome data from foxtail millet (Setaria italica)

    ID: doi:10.5524/100020

    Release Date: 05-28-2013

    Description: Foxtail millet (Setaria italica) (2n=18), is an annual grass grown both as cereal crop (grain production) and as forage food. It is primarily grown i...

  46. Genomic data of the Anna's Hummingbird (Calypte anna)

    ID: doi:10.5524/101004

    Release Date: 05-12-2014

    Description: The Anna's Hummingbird (Calypte anna (Lesson, 1829)) is a medium-sized hummingbird native to the west coast of North America and is the only North Ame...

  47. Genomic data from Chinese cabbage (Brassica rapa)

    ID: doi:10.5524/100021

    Release Date: 05-28-2013

    Description: Available here is genomic data for the polyploid plant Brassica rapa ssp. pekinensis line Chiifu-401-42, a Chinese cabbage. As there are several oil ...

  48. Genomic data for the domestic cucumber (Cucumis sativus var sativus L)

    ID: doi:10.5524/100025

    Release Date: 05-28-2013

    Description: Here we present genomic data for the domestic cucumber (Cucumis sativus var. sativus L.). The cucumber is a member of the Cucurbitaceae or cucurbit f...

  49. De novo high-coverage sequencing and annotated assemblies of the budgerigar genome

    ID: doi:10.5524/100059

    Release Date: 07-22-2013

    Description: Background: Parrots are considered one of the most behaviorally advanced vertebrate groups. They have an advanced ability of vocal learning. Parrots c...

  50. Example files and supporting material for "EMPeror: An interactive analysis and visualization tool for high throughput microbial ecology datasets."

    ID: doi:10.5524/100068

    Release Date: 11-23-2013

    Description: EMPeror is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets. Due to...

  51. Resources for the MeDUSA (Methylated DNA Utility for Sequence Analysis) MeDIP-seq computational analysis pipeline for the identification of differenti...

    ID: doi:10.5524/100035

    Release Date: 05-28-2013

    Description: Here we present 18 genome-wide DNA methylation profiles of wild type and Thymine DNA glycosylase (Tdg) knockout cells, which serve as an excellent mur...

  52. Genomic data of the Speckled mousebird (Colius striatus)

    ID: doi:10.5524/101023

    Release Date: 04-22-2014

    Description: The Speckled Mousebird (Colius striatus) is the largest species of mousebird and named because of its overall mousey-brown colour. The bird can be fo...

  53. Bisulfite-PCR combined with cloning Sanger sequencing data for validating DNA methylation level in Trichinella spiralis

    ID: doi:10.5524/100043

    Release Date: 05-28-2013

    Description: Trichinella spiralis is the smallest nematode parasite of humans and is also infectious in the rat, pig and bear species. Responsible for the disease ...

  54. Genomic data from Triticum urartu - the progenitor of wheat A genome

    ID: doi:10.5524/100050

    Release Date: 05-28-2013

    Description: The wheat A genome, as a basic genome of bread wheat and other polyploid wheats, is centrally important to the evolution, domestication, and genetic i...

  55. Genomic data of the Chinese alligator (Alligator sinensis)

    ID: doi:10.5524/100077

    Release Date: 08-21-2014

    Description: The Chinese alligator (Alligator sinensis), a freshwater crocodilian endemic to China, is one of the most endangered crocodilian species. Currently, t...

  56. Genomic data of the Little egret (Egretta garzetta)

    ID: doi:10.5524/101002

    Release Date: 04-22-2014

    Description: The Little Egret (Egretta garzetta) is a small white heron. An adult's average size is 55–65 cm long with an 88–106 cm wingspan, and weighs 350–...

  57. The avian phylogenomic project data

    ID: doi:10.5524/101000

    Release Date: 05-08-2014

    Description: The evolutionary relationship of modern birds is one of the most challenging questions in systematic biology and has been debated for centuries. We pr...

  58. Genomic data of the Great-crested grebe (Podiceps cristatus)

    ID: doi:10.5524/101036

    Release Date: 04-22-2014

    Description: The Great Crested Grebe (Podiceps cristatus) is known for its elaborate mating display and is the largest member of the Grebe family in the Old World....

  59. Genomic data of the Bar-tailed trogon (Apaloderma vittatum)

    ID: doi:10.5524/101016

    Release Date: 04-22-2014

    Description: The Bar-tailed Trogon (Apaloderma vittatum) belongs to the Trogonidae family of birds and lives in forests at a preferred altitude of around 1600 metr...

  60. Genomic data of the Hoazin (Opisthocomus hoazin)

    ID: doi:10.5524/101011

    Release Date: 05-12-2014

    Description: The Hoazin (Opisthocomus hoazin (Müller, 1776)) is a pheasant-sized tropical bird found in swamps, forest and mangroves of the Amazon and Orinoco Del...

  61. Genomic data from the Chinese Rhesus macaque (Macaca mulatta lasiota)

    ID: doi:10.5524/100002

    Release Date: 05-28-2013

    Description: The Chinese rhesus macaque (Macaca mulatta lasiota) is a subspecies of rhesus macaques that mainly resides in western and central China. Due to their...

  62. Transcriptome from a lymphoblastoid cell line taken from the YH Han Chinese individual

    ID: doi:10.5524/100013

    Release Date: 05-28-2013

    Description: The transcriptome available here was generated from the same sample of peripheral blood mononuclear cells (PBMCs) from a consented donor (Homo sapiens...

  63. Genomic data from the polar bear (Ursus maritimus)

    ID: doi:10.5524/100008

    Release Date: 05-28-2013

    Description: The polar bear (Ursus maritimus) is one of the largest land carnivores, second only to the Alaskan brown bear. In an effort to adapt to the extremely...

  64. Genome sequence of YH: the first diploid genome sequence of a Han Chinese individual

    ID: doi:10.5524/100015

    Release Date: 05-28-2013

    Description: Genomic data from the YH (Homo sapiens) genome – first diploid genome sequence of a Han Chinese, a representative of the Asian population. The geno...

  65. Comparative analysis of the amorfrutin A and rosiglitazone (Rosi)-dependent hepatic transcriptomes in a mouse model of diet-induced obesity

    Keywords: whole liver

    Description: Male C57BL/6 mice at 6 weeks of age were fed a HFD (60% of calories as fat) for 12 weeks to induce obesity and insulin resistance. Subsequently mice w...

    ID: 10.1621/Iw9Fidj7Hn

  66. Analysis of the estrogen-related receptor β (ERRβ/ESRRB) and DY131-regulated transcriptome in human DU145 prostate cancer cells

    Keywords: epithelium DU145 cells

    Description: Human DU145 prostate cancer cells stably transfected with an ERRβ/ESRRB expression vector or an empty vector control were treated for 12 h with 3 µM...

    ID: 10.1621/KhoLDn0eUQ

  67. Chronic time course and dose-dependence analysis of the clofibrate (Clofib)-regulated transcriptome in rat liver

    Keywords: whole liver

    Description: Livers were isolated from rats treated for 4 - 29 d with or without 30 - 300 mg/kg bw/d Clofib.

    ID: 10.1621/N4Z6Zseri5

  68. Analysis of the 17β-estradiol (17βE2)-regulated transcriptome in rat trigeminal ganglia

    Keywords: trigeminal ganglia whole

    Description: Cultured trigeminal ganglia from 8 week old random cycling female rats were 17βE2-deprived then treated for 24 h with or without 1 nM 17βE2.

    ID: 10.1621/gWBqfhz6yG

  69. Comparative analysis of the 17β-estradiol (17βE2)-, genistein (Gen)-, and phytoestrogen (S-equol [Sequol] and liquiritigenin [Liquir])-regulated, es...

    Keywords: epithelium MCF-7 cells

    Description: Human MCF-7 breast cancer cells were infected for 72 h with (i) control adenovirus expressing β-gal; (ii) adenovirus expressing ERβ/ESR2; or (ii) ad...

    ID: 10.1621/0xZtJIMQg2

  70. Analysis of the Ssfa2-dependent transcriptome in mouse liver

    Keywords: whole liver

    Description: Liver was isolated from 32 week old C57BL6/J male Ssfa2 KO and WT mice fed a normal chow diet.

    ID: 10.1621/NCM4UKSDLs

  71. Analysis of the Bromo Adjacent Homology Domain Containing 1 (Bahd1)-dependent transcriptome in mouse E16.5 placenta and liver

    Keywords: whole liver

    Description: Placenta and liver tissue was isolated at embryonic day 16.5 from male and female Bahd1 knockout and wild-type mice.

    ID: 10.1621/FPygkhLBsO

  72. Tissue-specific expression patterns of nuclear receptor coregulators


    Description: C57/Bl6J and 129x1/SvJ male or female mice (n = 6) at 8-9 weeks of age from each strain were sacrificed at lights-on (ZT0) by halothane inhalation (Ha...

    ID: 10.1621/datasets.04002

  73. Acute time course and dose-dependence analysis of the clofibrate (Clofib)-regulated transcriptome in rat liver

    Keywords: whole liver

    Description: Livers were isolated from rats treated for 3 - 24 h with or without 30 mg - 300 mg/kg bw/d Clofib.

    ID: 10.1621/39jyLTZloo

  74. Analysis of the GW501516 (GW1516)-regulated transcriptome in primary human macrophages expressing constitutively active AMPK

    Keywords: myeloid lineage macrophages monocyte-derived

    Description: Primary human macrophages transduced with constitutively active (T172A) AMPK α1 variant were treated for 24 h with or without 100 nM GW1516.

    ID: 10.1621/2w9z81daL1

  75. Analysis of the dihydrotestosterone (DHT)-regulated transcriptome in human LNCaP-C4-2B prostate cancer cells

    Keywords: epithelium LNCaP-C4-2B cells

    Description: Human LNCaP-C4-2B prostate cancer cells were treated with for 16 h with or without 10 nM DHT.

    ID: 10.1621/mpN8PDaTeM

  76. Time course and dose dependence analysis of the bisphenol A (BPA)-regulated transcriptome in Ishikawa cells

    Keywords: endometrium epithelium Ishikawa cells

    Description: Human Ishikawa endometrial carcinoma cells were treated with or without 1 nM, 100 nM, 10 µM or 100 µM BPA for 8 h, 24 h or 48 h.

    ID: 10.1621/CwEZYldrxg

  77. Time course transcriptomic analysis of rosiglitazone (Rosi)-treated C3H/10T1/2 cells

    Keywords: WAT adipocytes C3H/10T1/2 cell-derived

    Description: Fully differentiated C3 h/10T1/2 adipocytes were cultured with 1 µM Rosi or vehicle for 1 h.

    ID: 10.1621/hLnw2RmSWG

  78. Mutational analysis of the peroxisome proliferator activated receptor-γ coactivator 1- β (PGC1β/Ppargc1b)-regulated transcriptome in mouse liver an...

    Keywords: whole liver

    Description: Liver and skeletal muscle were isolated from C5BL/6 wild type mice or mice expressing a mutant form of PGC1β/Ppargc1b lacking two out of the three LX...

    ID: 10.1621/d4Kt4gB72O

  79. Dose dependent analysis of the rosiglitazone (Rosi)-regulated liver and inguinal adipose tissue transcriptomes in the Leprdb null mutant mouse

    Keywords: whole liver

    Description: Liver or inguinal adipose tissue was collected from male BKS.Cg-m +/+ Leprdb/J mice treated with or without Rosi at a range of doses for 18 days. The...

    ID: 10.1621/9IFwN8xkBn

  80. Analysis of the 17β-estradiol (17βE2) dependent transcriptome in SUM44PE invasive lobular carcinoma breast cancer cell lines

    Keywords: epithelium SUM44PE cells

    Description: SUM44PE invasive lobular carcinoma breast cancer cell lines were treated with 1 nM 17βE2 or vehicle for 3 h and 24 h.

    ID: 10.1621/6ugTmHZK5X

  81. Transcriptomic analysis of progesterone (P4)-treated mouse ovary

    Keywords: Female reproductive ovary whole

    Description: Newborn Sprague-Dawley rat ovaries dissected from pups less than 8 h old, were cultured in the presence or absence of 1 µM P4 for 48 h.

    ID: 10.1621/lbPzmF6Pwq

  82. Analysis of the dexamethasone (Dex)- and testosterone (Test)-regulated transcriptomes in rat gastrocnemius muscle

    Keywords: gastrocnemius whole

    Description: Gastrocnemius muscle was isolated from male Wistar-Hannover rats treated with or without a combination of 0.7 mg/kg/d Dex and 28 mg/kg/d Test for 7 da...

    ID: 10.1621/9MncYfbHNA

  83. Analysis of the androgen receptor (AR) and dihydrotestosterone (DHT)-regulated transcriptomes in normal (LNCaP) and androgen-independent (LNCaP-abl) c...

    Keywords: epithelium LNCaP cells

    Description: Human LNCaP or LNCaP-abl prostate cancer cells were transfected with AR siRNA or scrambled control siRNA for 72 h. LNCaP-abl cells were also treated w...

    ID: 10.1621/UhiFZHfzQW

  84. Analysis of the Nur77/Nr4a1-regulated transcriptome in pyramidal neurons

    Keywords: hippocampus pyramidal neurons

    Description: After 10 days in culture, dissociated mouse hippocampal pyramidal neurons were infected with lentivirus expressing Nur77/Nr4a1 or GFP for 6 d.

    ID: 10.1621/pDfF4bWOiY

  85. Analysis of the GW4604-dependent transcriptome in the intestine of the Cyp27a1 null mutant mouse

    Keywords: other whole mucosa

    Description: 3-4 month Cyp27a1 knockout mice were treated with or without two doses of 100 mg/kg body weight GW4064 by oral gavage 12 h apart. Mice were sacrifice...

    ID: 10.1621/datasets.04008

  86. Dose-dependent transcriptomic analysis of the diethylhexylphthalate (DEHP)-treated rat neonatal cardiomyocytes

    Keywords: cardiac muscle cardiomyocytes 1° cells

    Description: Rat neonatal cardiomyocytes isolated from 2-day-old Sprague-Dawley rat pups were treated with or without a range of doses of DEHP for 72 h.

    ID: 10.1621/796eXQYCUb

  87. Comparative analysis of peroxisome proliferator-activated receptor-γ (PPARγ/Pparg)- and GW7845-regulated transcriptomes in rat pancreatic islets

    Keywords: islets whole

    Description: Rat pancreatic islets isolated from male Wistar rats were transduced with PPARγ/Pparg adenovirus or empty adenovirus for 32 h and treated for 16 h wi...

    ID: 10.1621/VMxZKKVCkB

  88. Analysis of the dihydrotestosterone (DHT)- and RTI 6413-018-dependent transcriptomes in LNCaP prostate cancer cells

    Keywords: epithelium LNCaP cells

    Description: Human LNCaP prostate cancer cells were treated with 10 nM DHT or 100 nM RTI 6413-018 for 6-24 h.

    ID: 10.1621/PG6srxDzNt

  89. Analysis of the p300/CBP interacting protein (pCIP/Ncoa3) dependent transcriptome in mouse embryonic stem cells

    Keywords: pluripotent ESCs E14 cells

    Description: Mouse E14 embryonic stem cells were transfected with two pCIP siRNAs or pooled non-specific siRNAs.

    ID: 10.1621/gMh9LUMTKF

  90. Analysis of the thyroid hormone receptor-α (TRα/THRA) and TRβ/THRB-regulated transcriptomes in human HepG2 hepatocellular carcinoma cells

    Keywords: epithelium HepG2 cells

    Description: Human HepG2 hepatocellular carcinoma cells stably expressing TRα/THRA, TRβ/THRB, or empty vector were treated with or without 100 nM T3 for 6 h.

    ID: 10.1621/OzD9WkdLYj

  91. Analysis of the all-trans retinoic acid (ATRA)-regulated, retinoid X receptor-α (RXRα/Rxra)-dependent transcriptome in mouse liver

    Keywords: whole liver

    Description: Liver was isolated from male C57BL/6 RXRα/Rxra knockout and wild-type (WT) mice fed a 150 mg/kg ATRA or normal chow diet for 7d.

    ID: 10.1621/VeCAnn9CdU

  92. Time course transcriptomic analysis of 17β-estradiol (17βE2)-treated MCF-7 cells

    Keywords: epithelium MCF-7 cells

    Description: Human MCF-7 breast carcinoma cells were treated with or without 100 nM 17βE2 for 10 min, 40 min or 160 min.

    ID: 10.1621/wAeixXWJin

  93. Analysis of the hepatocyte nuclear factor 4-α variant 2 (HNF4α/HNF4A-2)-dependent transcriptome in rat pancreatic beta cells

    Keywords: islets beta cells INS1 cells

    Description: Rat INS-1 pancreatic beta-cells were stably transfected with a vector encoding tetracycline inducible human HNF4α/HNF4A-2 and cultured in the absence...

    ID: 10.1621/fJ25BjavY5

  94. Analysis of the 17β-estradiol (17βE2)-dependent transcriptome in human vagina

    Keywords: whole vagina

    Description: Vaginal samples were retrieved from women treated with or without 0.05 mg/day 17βE2 for 3 months.

    ID: 10.1621/HudStqvikW

  95. Analysis of the Am580 and rosiglitazone (Rosi) dependent transcriptomes in human monocyte-derived dendritic cells

    Keywords: dendritic cells monocyte-derived

    Description: Human monocyte-derived dendritic cells were treated with 100 nM Am580, 2.5 µM Rosi, and 1 µM AGN193109 for 5 days.

    ID: 10.1621/HslyUoSYAs

  96. Analysis of the MEK1/2-regulated transcriptome in R5020-treated human T47D cells

    Keywords: epithelium T47D cells

    Description: Human T47D breast cancer cells were treated with or without a combination of (1) vehicle or (2) 10 µM U0126 (a MEK 1/2 kinase inhibitor) for 10 minut...

    ID: 10.1621/XGSeVZH1LR

  97. Analysis of the 1,25-dihydroxyvitamin D3 (125DVD3)-dependent transcriptome in human primary bronchial smooth muscle cells

    Keywords: smooth muscle bronchus 1° cells

    Description: Human primary bronchial smooth muscle cells were treated with or without 100 nM 125DVD3 for 24 h.

    ID: 10.1621/vmOkKoHIoi

  98. Transcriptomic analysis of WY 14,643 and thyroid hormone receptor-β (TRβ/Thrb) Δ337T cross-talk in mouse heart

    Keywords: whole heart

    Description: 4-6 month old male wild-type mice or mice with cardiomyocyte specific expression of human TRβ/Thrb1 Δ337T dominant negative point mutant were treate...

    ID: 10.1621/iawFmJZiMO

  99. Timecourse analysis of the 17β-estradiol (17βE2) dependent transcriptome in T47D, MCF-7 and BT-474 breast cancer cell lines

    Keywords: epithelium MCF-7 cells

    Description: Human T47D, MCF-7, and BT-474 breast cancer cells were treated with 10 nM 17βE2 or vehicle for 1-24 h. 

    ID: 10.1621/gKdplxXbTj

  100. Time course analysis of the all-trans retinoic acid (ATRA)-regulated transcriptome in multipotent P19-derived A404 cells

    Keywords: pluripotent P19 cells

    Description: Multiprotein A404 cells expressing puromycin-N-acetyltransferase under the smooth muscle α-actin promoter, were treated with or without 1 µM ATRA fo...

    ID: 10.1621/olv1cR29xi

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