|
| Status |
Public on Dec 01, 2010 |
| Title |
shLuc.1309;ROSA-rtTA (-dox) |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts (MEFs)
|
| Organism |
Mus musculus |
| Characteristics |
strain: shLuc.1309;ROSA-rtTA
|
| Growth protocol |
24 degrees C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol/Phenol Cholorofom extractions
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
small RNA sequencing
|
| Data processing |
The 36nt long Illumina reads were stripped of the 3’ linker and the resulting small RNA sequences were mapped to the Release 9 genome. Only reads matching the mouse genome 100% were used for further analysis. For annotation, we used UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs.
|
| |
|
| Submission date |
Dec 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Colin Dean Malone |
| E-mail(s) |
colin.malone@med.nyu.edu
|
| Phone |
708-602-2170
|
| Organization name |
NYU Medical Center
|
| Department |
Skirball Institute - Developmental Genetics
|
| Lab |
Lehmann Lab
|
| Street address |
NYUMC, Skirball Institute, 540 1st Ave, 4-10
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE19476 |
A rapid and scalable system for studying gene function in mice using conditional RNA interference |
|
| Relations |
| SRA |
SRX018689 |
| BioSample |
SAMN00010834 |
