|
| Status |
Public on May 01, 2024 |
| Title |
TIG120_OSKL_day5 (bulkRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Human dermal fibroblasts infected with SeV-OSKL and sampled at day5
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human dermal fibroblasts
gender: Female
|
| Growth protocol |
Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö+Y medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA or total RNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Human dermal fibroblasts infected with SeV-OSKL and sampled at day5
|
| Data processing |
FASTQ files were generated from bcl files using bcl2fastq v2.17.1.14 (illumina) and processed using ENCODE long-rna-seq-pipeline v2.3.4.
Sequenced reads were mapped to the human reference genome (GRCh38) using TopHat 2.1.1 or STAR 2.5.1b with GENCODE v24 gene annotations.
Normalized gene expression data was calculated using RSEM 1.2.23.
Gene count data was obtained using featureCounts bundled in Subread 1.5.1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.
|
| |
|
| Submission date |
Feb 07, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Akira Kunitomi |
| E-mail(s) |
akira.kunitomi@gladstone.ucsf.edu
|
| Organization name |
The J. David Gladstone Institutes
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE224698 |
Gene expression profiles of human dermal fibroblasts and human pluripotent stem cells analyzed by bulk RNA-seq |
| GSE224850 |
H1FOO-DD promotes efficiency and uniformity in reprogramming to naive pluripotency |
|
| Relations |
| BioSample |
SAMN33185261 |
| SRA |
SRX19301588 |
