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Sample GSM7855190 Query DataSets for GSM7855190
Status Public on Jan 18, 2024
Title WTC-11, 3CHIR, rep3, ATACseq
Sample type SRA
 
Source name WTC-11
Organism Homo sapiens
Characteristics cell line: WTC-11
cell type: human iPSCs
genotype: WT
treatment: 3 uM CHIR
Treatment protocol WTC-11 hiPSCs were seeded onto a 24-well plate at a density of 150k cells per well. Cells were differentiated at day 0 under 1 µM CHIR, 1 µM CHIR+50 µM Tranilast, 3 µM CHIR, and 3 µM CHIR+50 µM Tranilast in the presence of 500 µg/mL BSA and 213 µg/mL AA.
Extracted molecule genomic DNA
Extraction protocol The samples were processed following protocol described in Corces et al. (DOI: 10.1038/nmeth.4396).
The sequencing libraries were generated following protocol described in Corces et al. (DOI: 10.1038/nmeth.4396)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Data processing The quality of raw sequencing data (fastq files) was assessed using FastQC (v 0.11.8)
Bowtie2 was used for alignment
Picard tools was used to mark and remove duplicates
SAMtools was used to sort and obtain high-quality mapped reads and to remove reads from the mitochondrial chromosome
Peak calling was performed using the MACS2 callpeak command
Assembly: hg38
Supplementary files format and content: bw files and txt files
 
Submission date Oct 23, 2023
Last update date Jan 18, 2024
Contact name Nathan J. Palpant
Organization name University of Queensland
Street address 306 Carmody Road
City Birsbane
State/province QLD
ZIP/Postal code 4067
Country Australia
 
Platform ID GPL30173
Series (2)
GSE246078 Dose escalation of Wnt stimulation during the exit from pluripotency identifies tranilast as a small molecule regulator of cardiac mesoderm differentiation (ATAC-Seq)
GSE246081 Dose escalation of Wnt stimulation during the exit from pluripotency identifies tranilast as a small molecule regulator of cardiac mesoderm differentiation
Relations
BioSample SAMN37932947
SRA SRX22186336

Supplementary file Size Download File type/resource
GSM7855190_C3_S11.bw 314.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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