|
| Status |
Public on Feb 15, 2012 |
| Title |
mouse siSupt4h |
| Sample type |
SRA |
| |
|
| Source name |
striatal neural cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: striatal neural cells
genotype: HdhQ7/Q8
transfection: siSupt4h
|
| Treatment protocol |
mammalian cells were transfected with NC siRNA or siSupt4h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was purified by Dynabeads® mRNA Purification Kit from total RNA. Then they were fragmented and reverse-transcribed as double strand cDNA by Super-script double-stranded cDNA synthesis kit from Invitrogen (Cat. 11917-010). The DNA then was end-repaired. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 150bp-350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequencedfollowing the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
non-genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq
insert size is 150bp-350 bp
|
| Data processing |
Raw data were uploaded to https://dnanexus.com and RNA-Seq/Transcriptome-base quantification analyses were performed to the samples.
|
| |
|
| Submission date |
Nov 04, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Ning Deng |
| E-mail(s) |
ndeng@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics Department
|
| Lab |
Cohen Lab
|
| Street address |
300 Pasteur Drive, RmL-314
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE33497 |
The effects on transcriptome from absence of Spt4/Supt4h by RNA-seq |
|
| Relations |
| SRA |
SRX105289 |
| BioSample |
SAMN00752514 |
