|
| Status |
Public on Nov 28, 2018 |
| Title |
F3D6 |
| Sample type |
SRA |
| |
|
| Source name |
fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSCs
Stage: day 6
replicate: 2
|
| Treatment protocol |
no treatment
|
| Growth protocol |
hiPSCs and hESCs were grown in E8 media on Matrigel
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: mRNA was extracted using the miRNEASY kit from Qiagen. ChIP-seq: Cells were crosslinked with formalin.
Bulk RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina. Single-cell RNA-seq: SMARTer Ultra Low RNA Kit for the Fluidigm C1 Nextera XT DNA Sample Preparation Kit. Gene edited lines RNA-seq: Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion PI™ Hi-Q™ Sequencing 200 Kit. ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Processed data file: CMdiffgenes.txt
Bulk RNA-seq
|
| Data processing |
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.9.3
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1 was used to generate bigwig files
AltAnalyze 2.0.9.3 was used to generated a table of RPKM values
Genome_build: Ensembl GRCh38, UCSC hg19
Supplementary_files_format_and_content: RNA-Seq: RPKM files
Supplementary_files_format_and_content: ChIP-Seq: bw files
|
| |
|
| Submission date |
Jun 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jared Churko |
| E-mail(s) |
jchurko@stanford.edu
|
| Organization name |
Stanford
|
| Department |
Radiology
|
| Street address |
265 Campus Dr G1105 SIM1
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE81585 |
Transcriptome signatures of human induced pluripotent stem cell-derived cardiomyocytes classify cardiomyocyte subtype populations |
|
| Relations |
| BioSample |
SAMN05195211 |
| SRA |
SRX1814998 |
