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Sample GSM4159483 Query DataSets for GSM4159483
Status Public on Jan 06, 2021
Title ATACseq_D4mDOXRep1
Sample type SRA
Source name Primordial hemogenic endothelium from H9
Organism Homo sapiens
Characteristics cell type: Inducible SOX17 H9 ESC
treatment: DOX-
replicate: 1
description: CD31 MACs cell at D4
Growth protocol Inducible SOX17 H9 ESC s were differentiated in ColIV coating plate. Singular Cells were plated 5,000 cells/cm2 to 10cm plates coated with ColIV (Sigma-Aldrich). After 1 day, media was changed to IF9S media with 50 ng/ml FGF, 2 mM LiCl, 15 ng/ml Activin A, and 50 ng/ml BMP4. On day 2, media was changed to IF9S media with 50 ng/ml VEGF, 2.5 uM SB431542 and 50 ng/ml FGF and D4 PHE cells were collected (1 X 106 cells).
Extracted molecule genomic DNA
Extraction protocol D4 PHE cell were CD31 MACs, and then cells were frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay.
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing ATAC-seq fragments were mapped to human genome by BWA with default settings. Human genome were divided into 32 bp bins and the number of reads in each bin was counted. In order to smooth the data, reads were extended to 200 bp. To normalize signals across ATAC-seq datasets, the number of reads in each dataset was reduced by random sampling to the smallest number of reads present in the datasets. ATAC-seq peaks were called by MACS2.
ChIP-seq fragments were aligned by BWA (version 0.7.15) with quality threshold at 5 for read trimming and all the other options in default settings. Normalized SOX17 ChIP-seq signals were calculated by MACS2 by using all the tags at the same loci.
RNA-seq fragments were aligned by STAR (version 2.5.2b) to human genome with gene annotations from GENCODE (version 27). Transcript expression levels were quantified by RSEM (version 1.3.0).
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq BED files contain peaks called by MACS2
Supplementary_files_format_and_content: ATAC-seq bigWig files contain normalized ATAC-seq signals as described in ATAC-seq data processing step
Supplementary_files_format_and_content: ChIP-seq bigWig files contain normalized SOX17 fold enrichment over IgG control calculated by MACS2
Supplementary_files_format_and_content: RNA-seq TSV files contain gene expression levels quantified by RSEM
Submission date Nov 13, 2019
Last update date Jan 06, 2021
Contact name Igor I. Slukvin
Organization name University of Wisconsin
Street address 1220 Capitol Court
City Madison
ZIP/Postal code 53715
Country USA
Platform ID GPL18573
Series (1)
GSE140341 Profiling of melocular mechanism of SOX17 effect during hematopoieisis of human ES cells
BioSample SAMN13279935
SRA SRX7135453

Supplementary file Size Download File type/resource
GSM4159483_ATACseq_D4mDOXRep1.bed.gz 1.8 Mb (ftp)(http) BED 205.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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