|
| 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 |
