|
| Status |
Public on Oct 02, 2008 |
| Title |
PolII_ChIP-Seq in NB4 |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin IP against Pol II
|
| Organism |
Homo sapiens |
| Characteristics |
NB4 cells
|
| Growth protocol |
NB4 cells were grown in RPMI media containing 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) K562 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Pol II antibody (Covance: MMS-126R), adapters were ligated to ChIP DNA and sequenced using Illumina Genome Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ChIP DNA prepared using RNA Pol II antibody
|
| 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. (See Rozowsky et al. submitted)
|
| |
|
| Submission date |
Oct 01, 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 (1) |
| GSE13008 |
Genome-wide mapping of RNA Polymerase II binding sites |
|
| Relations |
| SRA |
SRX001943 |
| BioSample |
SAMN02195689 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM325935_Yale_NB4_Pol2_eland_result_rep1_laneA_FC12037_112207_s_3.txt.gz |
151.2 Mb |
(ftp)(http) |
TXT |
| GSM325935_Yale_NB4_Pol2_eland_result_rep1_laneB_071115_HWI-EAS134_0011_s_1.txt.gz |
194.8 Mb |
(ftp)(http) |
TXT |
| GSM325935_Yale_NB4_Pol2_eland_result_rep1_laneC_FC12482_110107_s_4.txt.gz |
39.6 Mb |
(ftp)(http) |
TXT |
| GSM325935_Yale_NB4_Pol2_eland_result_rep2_laneA_071115_HWI-EAS134_0011_s_2.txt.gz |
135.7 Mb |
(ftp)(http) |
TXT |
| GSM325935_Yale_NB4_Pol2_eland_result_rep2_laneB_FC12169_111107_s_4.txt.gz |
62.6 Mb |
(ftp)(http) |
TXT |
| GSM325935_Yale_NB4_Pol2_eland_result_rep3_laneA_071115_HWI-EAS134_0011_s_3.txt.gz |
139.2 Mb |
(ftp)(http) |
TXT |
| GSM325935_Yale_NB4_Pol2_eland_result_rep3_laneB_FC12169_111107_s_8.txt.gz |
27.6 Mb |
(ftp)(http) |
TXT |
| GSM325935_Yale_NB4_Pol2_processed_peaks.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
