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Sample GSM832321 Query DataSets for GSM832321
Status Public on Feb 10, 2012
Title Runx1_thymocyte_control_ChIPseq
Sample type SRA
Source name Runx1_thymocyte_control_ChIPseq
Organism Mus musculus
Characteristics cell type: primary thymocyte
strain: Runx1f/f on C57BL/6 background
mouse age: 5-8 weeks
Treatment protocol For induced L8057 cells, 50 nM TPA was added to induced maturation of the cells for 72 hrs. L8057 cells and primary thymocytes were fixed with formaldehyde before sonicated for ChIP.
Growth protocol L8057 cells were grown in 38.5% IMDM + 38.5% RPMI + 20% FCS + %2 Pen/strep + 1% L-Glutamine,
Extracted molecule genomic DNA
Extraction protocol The purified DNA was prepared for sequencing on a Beckman Coulter SPRI-TE following manufacturer’s instructions. The seq-prepped DNA was PCR amplified using Illumina primers for 18 cycles. Samples were sequenced on either the Illumina Genome Analyzer II or Illumina Hi-Seq 2000 following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Alignment: Raw ChIP-Seq data were processed using the Illumina software pipeline. Only ChIP-Seq reads that aligned to exactly one location in the reference mouse genome were retained (UCSC, mm9)
Peaks:The MACS algorithm (Zhang et al., 200b) was used to identify bound regions by comparing the enrichment of the IP sample against a control IgG IP for background correction. MACS version 1.4.0rc2 was run with all parameters at their default settings.
Submission date Nov 13, 2011
Last update date May 15, 2019
Contact name Tali Mazor
Organization name MIT
Street address 77 Massachusetts Ave
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platform ID GPL13112
Series (2)
GSE33653 Direct Recruitment of Polycomb Repressive Complex 1 (PRC1) to Chromatin by Core Binding Transcription Factors (ChIP-Seq)
GSE33660 Direct Recruitment of Polycomb Repressive Complex 1 (PRC1) to Chromatin by Core Binding Transcription Factors
SRA SRX105456
BioSample SAMN00752613
Named Annotation GSM832321_Runx1_thymo_control_peaks.bed.gz
Named Annotation GSM832321_Runx1_thymo_control.bed.gz

Supplementary file Size Download File type/resource
GSM832321_Runx1_thymo_control.bed.gz 120.5 Mb (ftp)(http) BED
GSM832321_Runx1_thymo_control_peaks.bed.gz 13.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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