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Sample GSM1968334 Query DataSets for GSM1968334
Status Public on Dec 08, 2018
Title ASXL1_WT_ChIPSeq
Sample type SRA
 
Source name WT_BM-derived MSPCs
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Wild type
cell type: BM-derived Mesenchymal stem/progenitor cells (MSPCs)
cell type: BM-derived MSPCs
passages: 5-10
chip antibody: ASXL1 (Santa Cruz sc-85283)
Growth protocol Bone marrow–derived mesenchymal stem/progenitor cells were cultured with MSC medium (MesenCult basal media plus 20% of MesenCult Supplemental), and replated when the cultures reached 80-90% confluency.
Extracted molecule genomic DNA
Extraction protocol MSPCs were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 300 to 500 bp. Histone-DNA complexes were isolated with specific histone modification 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
 
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: tab-delimited text file format,it contains peaks position imformation such as chromosome,peaks start and end positions.
 
Submission date Dec 08, 2015
Last update date May 15, 2019
Contact name Caiying Zhu
E-mail(s) zhucaiying@ihcams.ac.cn
Phone 13622053408
Organization name Institute of Hematology & Blood Diseases Hospital
Street address NO. 288 Nanjing Road, Heping District, Tianjin
City Tianjin
ZIP/Postal code 300020
Country China
 
Platform ID GPL19057
Series (2)
GSE75786 Loss of Asxl1 Alters Mesenchymal Stem Cell Fate through H3K4me3 [ChIP-seq]
GSE75788 Loss of Asxl1 Alters Mesenchymal Stem Cell Fate through H3K4me3
Relations
SRA SRX1471726
BioSample SAMN04326717

Supplementary file Size Download File type/resource
GSM1968334_ASXL1_WT.peaks.txt.gz 175.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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