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Sample GSM1427067 Query DataSets for GSM1427067
Status Public on Jan 01, 2015
Title SUZ12
Sample type SRA
 
Source name Human primary fetal liver proerythroblasts (ProEs), SUZ12 ChIP
Organism Homo sapiens
Characteristics tissue: fetal liver
cell type: CD34+ HSPC-derived proerythroblasts
chip antibody: SUZ12 (Abcam ab12073; Active Motif 39357, lot 29111002)
Treatment protocol NA
Growth protocol Primary maturing fetal liver erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq analysis using the Illumina HiSeq 2000, 10-20 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer's protocol. Raw ChIP-seq data were processed using the Illumina software pipeline. Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC hg18) were retained for downstream data analysis.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description ChIP DNA
Data processing Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file.
 
Submission date Jul 03, 2014
Last update date May 15, 2019
Contact name Jian Xu
E-mail(s) Jian.Xu@UTSouthwestern.edu
Phone 214-648-6125
Organization name UT Southwestern Medical Center
Department Children's Research Institute
Street address 6000 Harry Hines Blvd. NL12.138B
City Dallas
State/province TX
ZIP/Postal code 75235
Country USA
 
Platform ID GPL11154
Series (2)
GSE59087 ChIP-seq analysis of PRC2 core subunits in primary human erythroid progenitor cells
GSE59090 ChIP-seq and RNA-seq analysis of PRC2 core subunits in primary human erythroid progenitor cells
Relations
BioSample SAMN02902826
SRA SRX646126
Named Annotation GSM1427067_SUZ12-F.bed.gz
Named Annotation GSM1427067_SUZ12-F.wig.gz
Named Annotation GSM1427067_SUZ12-F_peaks.bed.gz

Supplementary file Size Download File type/resource
GSM1427067_SUZ12-F.bed.gz 267.4 Mb (ftp)(http) BED
GSM1427067_SUZ12-F.wig.gz 44.2 Mb (ftp)(http) WIG
GSM1427067_SUZ12-F_peaks.bed.gz 346.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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