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Displaying 50 of 601 results for " "
  1. GitHub repository gitter-lab/pria_lifechem software archive

    Description: Virtual screening on PriA-SSB and RMI-FANCM with the LifeChem library.

  2. genome-analysis-workflows CWL workflow definitions for executing MGI analysis pipelines

    Description: CWL and docker based pipelines for analysis of high-throughput sequence data on local or cloud compute

  3. Cerebral Cortex cloud platform example code

    Description: Example code that to demonstrate the capabilities of the Cerebral Cortex Kernel

  4. DEEPEST-Fusion

    Description: This is a statistical fusion detection algorithm particularly engineered for screening big RNA sequencing databases

  5. Tools and workflow to produce VCF files from BAM files using Google Cloud Pipelines

    Description: Although Google Cloud Genomics and Sentieon pipelines support robust tools to obtain high quality VCFs from BAM files, obtaining VCF files from these ...

  6. Processed ATAC-seq from dorsolateral-prefrontal cortex in adult brain

    Description: Processed data ATAC-seq data from 341 samples from dorsolateral-prefrontal cortex samples of individuals with schizophrenia and control

  7. iTextMine

    Description: iTextMine is an Integrated Text Mining System for Large Scale Knowledge Extraction from Literature. The system employs parallel processing for dockeri...

  8. OpenNeuro-processed

    Description: OpenNeuro dataset processed with various neuroimaging tools and pipelines

  9. Regtools software

    Description: Source code for the regtools application

  10. Protein Ontology (PRO)

    Description: Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships be...

  11. GTEx exon-exon-junction-level expression summary for Snaptron

    Description: GTEx exon-exon-junction-level expression summary from the Snaptron collection. Format is a tab-separated text file compressed and indexed using BGZip...

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. Tissue-specific expression patterns of nuclear receptor coregulators

    Keywords:

    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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. Transcriptomic analysis of (1) wild type peroxisome prolferator activated receptor-γ coactivator 1 (PGC1α/PPARGC1); (2) estrogen receptor related re...

    Keywords: epithelium HepG2 cells

    Description: Human HepG2 liver cancer cells were subjected to adenoviral infection with empty vector or vectors encoding: (1) wild type PGC1; (2) ERRα/Esrra-disru...

    ID: 10.1621/datasets.02004

  49. Analysis of the estrogen receptor-α (ERα/ESR1)-dependent transcriptome in MCF-7 breast cancer cells

    Keywords: epithelium MCF-7 cells

    Description: Human MCF-7 breast cancer cells were transfected with an ERα/ESR1 shRNA plasmid.

    ID: 10.1621/5F49JYoGXU

  50. Analysis of the 17β-estradiol (17βE2)-regulated transcriptome in mouse hippocampus

    Keywords: hippocampus whole

    Description: Four month old ovariectomized female C57BL/6 mice were treated with 0.2mg/kg 17βE2 for 1 h prior to removal of hippocampi.

    ID: 10.1621/u8t3ZH9qPV


Displaying 50 of 601 results for " "