|
| Status |
Public on May 13, 2019 |
| Title |
het_2h_2 |
| Sample type |
SRA |
| |
|
| Source name |
human fibroblast/mouse ES cells
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: human fibroblast/mouse ES cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was obtained using Rneasy purification kit
Libraries were prepared according to Illumina's instructions accompanying the Tru-Seq V2 kit (RS-122-2001). Briefly, Poly-A+ RNA was isolated from total RNA using oligo-dT magnetic beads (Illumina TruSeq V2). Following first (Superscript III, Life Technologies) and second strand synthesis, cDNA libraries were constructed according to standard Illumina protocols. RNA and DNA integrity and quality was measured using an Agilent Bioanalyzer 2100.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using Illunima HiSeq 2000 or Nextseq 500
RNA-seq reads were mapped to a concatenated genome sequence of human GRCh38/hg38 and mouse GRCm38/mm10 annotations using STAR/2.4.2a.
Following mapping, human and mouse transcript abundance were individually quantified using rsem/1.2.21.
Expression levels were normalized by transcripts per million (TPM).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: text file with expected count, TPM and FPKM.
|
| |
|
| Submission date |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Thach Mai |
| E-mail(s) |
tamai@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
269 Campus Dr
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL16512 |
| Series (2) |
| GSE103509 |
Transcription factor NKX3-1 is required for reprogramming to pluripotency and can replace OCT4 in mouse and human iPSC induction [RNA-seq] |
| GSE103536 |
Transcription factor NKX3-1 is required for reprogramming to pluripotency and can replace OCT4 in mouse and human iPSC induction |
|
| Relations |
| BioSample |
SAMN07606031 |
| SRA |
SRX3161733 |
