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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
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
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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