|
| Status |
Public on Aug 28, 2013 |
| Title |
Mouse Embryonic Fibroblast 1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblast
genetic background: BALB/c
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Micro Kit. Poly A enrichment was performed with Oligo dT bead selection. The resulting poly-A+ RNA was fragmented and cDNA was synthesized using Superscript II and random primers. 500ng of total RNA was used for each library.
Libraries were prepared according to standard Illumina protocol, using the Illumina TruSeq mRNA Sample Prep Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence to 50bp and mapped to mm10 after removal of mouse rRNA sequences.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated after alignment to mm10 using SeqMap.
Genome_build: mm10
Supplementary_files_format_and_content: gene name and RPKM values for each Sample.
|
| |
|
| Submission date |
Apr 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Brady |
| Organization name |
Stanford University
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE46104 |
Global transcriptome profiling of Oct4/Klf4/Sox2 (3Factor, 3F) + IL6 iPS clones derived from mouse embryonic fibroblasts. |
|
| Relations |
| Reanalyzed by |
GSE80793 |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02046481 |
| SRA |
SRX265578 |
