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| Status |
Public on Jan 06, 2021 |
| Title |
ATACseq_D4mDOXRep1 |
| Sample type |
SRA |
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| Source name |
Primordial hemogenic endothelium from H9
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Inducible SOX17 H9 ESC
treatment: DOX-
replicate: 1
description: CD31 MACs cell at D4
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| 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).
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| 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Nov 13, 2019 |
| Last update date |
Jan 06, 2021 |
| Contact name |
Igor I. Slukvin |
| Organization name |
University of Wisconsin
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| Street address |
1220 Capitol Court
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| City |
Madison |
| ZIP/Postal code |
53715 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE140341 |
Profiling of melocular mechanism of SOX17 effect during hematopoieisis of human ES cells |
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| Relations |
| BioSample |
SAMN13279935 |
| SRA |
SRX7135453 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4159483_ATACseq_D4mDOXRep1.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSM4159483_ATACseq_D4mDOXRep1.bw |
205.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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