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Sample GSM320734 Query DataSets for GSM320734
Status Public on Sep 16, 2008
Title PolII_ChIP-Seq in HeLa S3
Sample type SRA
Source name Chromatin IP against Pol II
Organism Homo sapiens
Characteristics HeLa S3 cells (ATCC/Snyder Lab)
growth properties: Suspension Morphology: epithelial
antibody: Pol II (Covance 8WG16) Cellular Condition: Normal
Growth protocol HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml.
Extracted molecule genomic DNA
Extraction protocol Purified ChIP and Input DNA samples from 2 x 10^8 cells were size-selected on agarose gels for fragments 120 to 350 bp prior to library preparation. RNA polymerase II ChIP DNA samples were prepared according to the same protocol as used for the STAT1 samples except that the cells were not stimulated prior to formaldehyde fixation. RNA Pol II-DNA complexes were isolated with the mouse monoclonal antibody 8WG16 (Covance). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Description Chromatin IP against Pol II
Data processing Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads (mapped against NCBI36) to the averaged sequenced DNA fragment size ~200bps and then accumulated into fragment density signal maps. Peaks in these maps are identified by comparison to a computer simulated null model for each Mb of each chromosome (accounting for the variability in mappability of sequence tags across the human genome. For potential target regions the number of sequenced tags is compared against the normalized number of sequence tags overlapping the region from the matching Input DNA reference sample. Fold enrichment ratios are computed from the ratio of these two sets of counts for each regions as well as p-value using the cumulative distribution function for the binomial distribution. P-value are corrected for multiple hypothesis testing using a Benjamini-Hochberg correction factor and a false discovery rate threshold of 0.05 is imposed.
Submission date Sep 15, 2008
Last update date May 15, 2019
Contact name Flora Vaccarino
Organization name Yale University
Department Child Study Center
Lab Vaccarino
Street address 230 South Frontage Road
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
Platform ID GPL9115
Series (2)
GSE12781 PolII transcription factor in Human HeLa S3
GSE12783 Genome-wide maps of transcription factor binding using ChIP-Seq for Human ENCODE
SRA SRX003801
BioSample SAMN02195757

Supplementary file Size Download File type/resource
GSM320734_HeLa_PolII_eland_results_rep1_laneB_FC201WVA_20080307_s_6.txt.gz 158.8 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep2_laneA_FC5817_s_3.txt.gz 61.3 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep2_laneB_FC5817_s_4.txt.gz 55.6 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep2_laneC_FC5817_s_8.txt.gz 92.3 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep2_laneD_FC201WVA_20080307_s_7.txt.gz 102.1 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep2_laneE_FC201WVA_20080307_s_8.txt.gz 112.3 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep3_laneA_FC4390_070107_s_1.txt.gz 36.3 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep3_laneB_FC201WVA_20080307_s_3.txt.gz 126.6 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep3_laneC_FC20B5RA_20080331_s_1.txt.gz 120.8 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_eland_results_rep3_laneD_FC20B5RA_20080331_s_2.txt.gz 121.2 Mb (ftp)(http) TXT
GSM320734_HeLa_PolII_peaks.txt.gz 691.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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