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Title: modENCODE_Lieb and White Lab: unltra-deep sequencing data of genomic DNA, chromatin input, and ChIP of Su(Hw) and H3K36me3 from S2 cells on Illumina Genome Analyzer      
dateReleased:
03-04-2011
description:
This is a dataset generated by the modENCODE Project. It contains both the pair-end and single-end sequencing data of genomic DNA, chromatin input and the ChIP of the factors Su(Hw) and H3K36me3 from Drosophila S2 cells and it was generated on Illumina Genome Analyzer. The goal was to sequence ~120M tags of each sample and used this ultra-deep dataset to systematically evaluate both experimental and computational factors that influence the results of ChIP-seq experiments. For data usage terms and conditions, please refer to and S2 cells from the modENCODE batch were amplified before transferring to the plates. 15 plates were put in culture until the cells reached the appropriate concentration. Cells were harvested from 2 plates to extract the genomic DNA. The remaining 13 plates were then treated with formaldehyde at the same time and the chromatin were extracted. 3 plates were used to produce an Input sample corresponding to the chromatin DNA of the treated cells. Each plate corresponding to an eppendorff tube of chromatin, ChIP experiments were performed on 5 tubes for H3K36me3 and on 5 tubes for Su(Hw). ChIP and DNA extraction were performed independently on each tube. After the purification of the DNA, the tubes corresponding to the same sample (Su(Hw), H3K36me3, Input and gDNA) were pooled together. After mixing, each sample was aliquoted again into 5 tubes. 1 aliquot of each was used for ChIP-chip on Affymetrix tiling arrays for quality control, 1 aliquot was used for single-end sequencing at the University of Chicago HGAC, 1 aliquot was used for single-end sequencing at UNC, 1 aliquot was used for paired-end sequencing at UNC and the remaining aliquot was kept as a back-up of the original samples. For each sample, >100M single-end tags were produced (~5 runs), along with the tags from 1 lane of paired-end sequencing experiment. Besides several experimental factors, the performance of multiple peak callers were evaluated at different sequencing depths.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-27679
refinement:
raw
alternateIdentifiers:
27679
keywords:
functional genomics
dateModified:
05-03-2014
availability:
available
types:
gene expression
name:
Drosophila melanogaster
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27679/E-GEOD-27679.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27679/E-GEOD-27679.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27679
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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