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| Status |
Public on Dec 23, 2011 |
| Title |
K562_WCE_1 |
| Sample type |
SRA |
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| Source name |
K562-WCE
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| Organism |
Homo sapiens |
| Characteristics |
cell type: K562 erythrocytic leukaemia cells (ATCC CCL-243)
chip antibody: None
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| Growth protocol |
K562 erythrocytic leukaemia cells (ATCC CCL-243) were grown according to standard protocols in RPMI 1640 media (Invitrogen, 22400105) supplemented with 10% fetal bovine serum (FBS, Atlas Biologicals, F-0500-A) and 10% Penicillin/Streptomycin (Invitrogen, 15140122); H1 ES cells were grown in TeSR media on Matrigel (Cellular Dynamics), as described previously (Ernst, J., et al. (2011). Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries of CR ChIP samples were prepared according to a modified version of the Illumina Genomic DNA protocol, as described previously (Mikkelsen et al., 2007). Briefly, ChIP DNA was ligated to Illumina adaptors and subjected to 22 cycles of PCR amplification. Amplified products between 200 and 800 bp were purified on a 2% agarose gel. Roughly 5 picomoles of DNA library was then applied to each lane of the flow cell and sequenced on Illumina GAII sequencers according to standard Illumina protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
K562 ChIP Input Control
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| Data processing |
Alignment: Sequence reads were aligned to the human genome reference (hg19) using MAQ version 0.7.1 (Li et al., 2008, Genome Research 18, 1851-1858) with default parameters. Reads mapping to multiple positions in the genome were placed randomly at one of those locations.
Read Density Maps: BAM files were processed to WIG format using the 'count' command of igvtools (http://www.broadinstitute.org/igv/igvtools -- Robinson, et al. Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011)). Reads were extended to 200 bp using the -e parameter, otherwise defaults were used. The WIG files were then processed to BIGWIG format using the UCSC wigToBigWig utility (available here: http://hgdownload.cse.ucsc.edu/admin/exe/) with the -clip option specified.
Peak calling: Enriched intervals (binding sites) were identified using QuEST (Valouev et al., 2008, Nature methods 5, 829-834) and MACS (Zhang et al., 2008, Genome biology 9, R137). A control dataset derived by sequencing of at least two un-enriched input DNA samples (whole cell extract, WCE) was used to define a background model for binding assessment. These procedures yielded a list of enriched intervals for each CR, together with an estimate of statistical significance. As a first step, we retained all peaks with p < 10-8 or estimated FDR below 5%. We then applied a post-processing step, consolidating all the peaks called by the two algorithms, as described previously (Novershtern et al., 2011, Cell 144, 296-309). We call a peak only if it was found by either one method in at least two replicate ChIP-seq experiments, or by both methods in at least one replicate. We considered peaks to be overlapping if they are within a distance of 50bp.
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| Submission date |
Nov 10, 2011 |
| Last update date |
Nov 19, 2022 |
| Contact name |
Kevin Dong |
| Organization name |
Dana-Farber Cancer Institute
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| Street address |
360 Longwood Ave
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| City |
Boston |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE32509 |
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells |
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| Relations |
| SRA |
SRX116450 |
| BioSample |
SAMN00771258 |
| Named Annotation |
GSM831022_K562_WCE_K562_1.bw |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM831022_FC_30CLLAAXX_ln_7.sorted.K562_WCE_K562_1.aln.bed.gz |
101.0 Mb |
(ftp)(http) |
BED |
| GSM831022_K562_WCE_K562.seg.bed.gz |
147 b |
(ftp)(http) |
BED |
| GSM831022_K562_WCE_K562_1.bw |
168.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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