|
| Status |
Public on Jun 13, 2013 |
| Title |
kitneg_3_FPKM |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblast transduced with Gata2+cFos+Gfi1b+Etv6, kitneg, day 35
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype: huCD34/H2BGFP
cell type: embryonic fibroblasts
age: E14.5
transduction: Gata2+cFos+Gfi1b+Etv6
time: day 35
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted by FACS and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with up to 1 ug of total RNA for the construction of sequencing libraries according to Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA-seq
GFP+CD45+kitneg
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite.
Alignment to mm9 using Tophat release 1.4.1 and Bowtie release 0.12.7.
Differential expression performed with Cufflinks release 1.3.0 and Mus musculus mm9 reference annotation.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Cufflinks cuffdiff differential expression genes. fpkm_tracking output tab-delimited file. See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.
|
| |
|
| Submission date |
May 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Betty Chang |
| E-mail(s) |
[email protected]
|
| Organization name |
Mount Sinai School of Medicine
|
| Street address |
1425 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE47497 |
Induction of a hemogenic program in mouse fibroblasts |
|
| Relations |
| BioSample |
SAMN02183167 |
| SRA |
SRX287411 |
