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Sample GSM3349778 Query DataSets for GSM3349778
Status Public on Jul 03, 2019
Title ATAC-seq_III-3-WT, rep1
Sample type SRA
 
Source name iPSC-CMs
Organism Homo sapiens
Characteristics cell type: iPSC-CMs
day post-differentiation: day 40
genotype/variation: LMNA WT/Corr-WT
Treatment protocol iPSCs were grown to 90% confluence and subsequently differentiated into beating cardiomyocytes, using a small-molecule-based monolayer method described previously. Ten days after cardiac differentiation, iPSC-CM monolayers were purified using RPMI-1640 without glucose (Life Technologies) with B27 supplement (Life Technologies). Non-glucose culture medium was changed every 2 days. After 5 days, iPSC-CMs were reseeded onto Matrigel-coated plates in a culture medium containing glucose.
Growth protocol iPSC lines were maintained in chemically defined medium Essential 8 (E8 medium) (Life Technologies) on Matrigel-coated (BD Bioscience, San Jose, CA) plates at 37°C with 5% (vol/vol) CO2.
Extracted molecule genomic DNA
Extraction protocol The samples were extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218).
ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (Illumina).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Description Isogenic line to III-3 to correct LMNA mutation
ATAC-seq Replicate #1
processed data file: PT3WT_ATAC_USPD16084651_HJ35WBBXX_L8_1.trim.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
Data processing ATAC-seq reads were mapped to hg19 genome: bowtie 2
Following QC to remove duplicate reads, average read intensities were calculated: deepTools and R/Bioconductor (v.3.2.1).
Genome_build: human reference genome hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig
 
Submission date Aug 21, 2018
Last update date Jul 03, 2019
Contact name Lei Tian
E-mail(s) tianlei@stanford.edu
Phone 6502388262
Organization name Stanford's Postdoctoral Scholar programs
Street address 1215 Welch Rd
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL21697
Series (2)
GSE118883 Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy [ATAC-seq]
GSE118885 Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy
Relations
BioSample SAMN09873846
SRA SRX4590592

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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