|
| Status |
Public on Jul 17, 2020 |
| Title |
RNAseq_III-3-WT |
| Sample type |
SRA |
| |
|
| 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.
|
| 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).
|
| |
|
| 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.
|
| |
|
| 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 |
