|
| Status |
Public on Aug 21, 2013 |
| Title |
rnaseq ko1 |
| Sample type |
SRA |
| |
|
| Source name |
neonatal tail tip fibroblasts, Hotair knockout
|
| Organism |
Mus musculus |
| Characteristics |
strain: backcross to C57BL6 with over 97% similarity
cell type: neonatal tail tip fibroblasts
genotype/variation: Hotair knockout
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from cells was extracted with the TRIzol reagent (Invitrogen) and the RNeasy mini kit (Qiagen). Poly-A selected RNA was isolated from total RNA with MicroPoly(A)Purist Kit (Ambion) according to the manufacturer’s instruction.
RNA-seq libraries were prepared following the dUTP protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were aligned to the mouse reference sequence NCBI Build 37/mm9 with the TopHat algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq, per-gene RPKM was calculated for all RefSeq annotated genes submitted in the txt file.
|
| |
|
| Submission date |
Jun 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Dr. CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE48005 |
Targeted disruption of Hotair leads to homeotic transformation and de-repression of imprinted genes [RNA-Seq, ChIP-Seq] |
| GSE48007 |
Targeted disruption of Hotair leads to homeotic transformation and de-repression of imprinted genes |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02205118 |
| SRA |
SRX306684 |
