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Status |
Public on Jul 17, 2020 |
Title |
RNAseq_III-3-WT |
Sample type |
SRA |
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Source name |
iPSC-CMs
|
Organism |
Homo sapiens |
Characteristics |
cell-type: iPSC-CMs day post-differentiation: day 40 genotype: isogenic line to III-3 to correct LMNA mutation
|
Treatment protocol |
iPSCs and hESCs 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 and hESC-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.
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Growth protocol |
iPSC lines and hESCs 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 |
total RNA |
Extraction protocol |
(RNA-seq) iPSC-CMs were detached from cell culture plates and RNA was extracted using a microRNeasy kit (QIAGEN). (ChIP-seq) Lysates were clarified from sonicated nuclei and LMNA-DNA complexes were isolated with antibody. (ATAC-seq) The samples were extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218) (RNA-seq) RNA libraries were prepared for sequencing using standard Illumina protocols. (ChIP-seq) ChIP-seq libraries were prepared for sequencing using The Ion Proton™ System protocols. (ATAC-seq) ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (illumina).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
(RNA-seq) FastQC 0.11.4 (RNA-seq) STAR 2.5.1b (RNA-seq) Cufflinks 2.2.1 (ChIP-seq) EDD (ATAC-seq) Cutadapt0.5 (ATAC-seq) Bowtie2.2.6 (ATAC-seq) Sambamba0.6.5 (ATAC-seq) Samtools1.2.0 (ATAC-seq) Deeptools2.0.0 Genome_build: human reference genome (hg19) Supplementary_files_format_and_content: (RNA-seq) tab-delimited text file (gene_exp) include gene expression and differential expression for each sample. (ChIP-seq) Bed and Bedgraphs for ChIP-seq.
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Submission date |
Jul 17, 2017 |
Last update date |
Jul 17, 2020 |
Contact name |
Joseph Wu |
Organization name |
Stanford University School of Medicine
|
Street address |
Stanford University School of Medicine
|
City |
Stanford |
State/province |
Carlifornia |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE101514 |
Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy |
|
Relations |
BioSample |
SAMN07357713 |
SRA |
SRX3009239 |