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Sample GSM2224546 Query DataSets for GSM2224546
Status Public on Feb 24, 2017
Title SMC1A_WT_ChIPseq
Sample type SRA
 
Source name hematopoietic stem/progenitor cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone Marrow
cell type: BM-derived Lin-Kit+ cells
Extracted molecule genomic DNA
Extraction protocol LK cells were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 300 to 500 bp. Protein-DNA complexes were isolated with specific antibodies.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description SMC1_i95
Data processing Basecalls performed using Illumina NextSeq 500
ChIP-Seq reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings
Data were filtered using the following specifications:only reads that pass Illumina's purity filter,aligned with no more than 2 mismatches,and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed.
peaks were called using SICER version 1.1 with the following setting:Threshold for redundancy allowed for ChIP reads(1),window size(200bp) ,FDR cutoff(1E-10)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file
 
Submission date Jul 01, 2016
Last update date May 15, 2019
Contact name Peng Zhang
E-mail(s) pxz36@miami.edu
Organization name University of Miami Miller School of Medicine
Lab Feng-Chun Yang
Street address 1011 NW 15th Street
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
 
Platform ID GPL19057
Series (2)
GSE83960 ASXL1 Interacts with the Cohesin Complex to Maintain Chromatid Separation and Gene Expression for Normal Hematopoiesis [ChIP-Seq]
GSE83962 ASXL1 Interacts with the Cohesin Complex to Maintain Chromatid Separation and Gene Expression for Normal Hematopoiesis
Relations
BioSample SAMN05341302
SRA SRX1892694

Supplementary file Size Download File type/resource
GSM2224546_11_2470IUPUI_WT_BM_SMC1_i95_uniqnorm_signal.bw 118.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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