|
| Status |
Public on Sep 11, 2014 |
| Title |
nSR100-iCLIP-hs |
| Sample type |
SRA |
| |
|
| Source name |
293T, dox-inducible
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T
antibody: FLAG
construct: dox-inducible lentiviruses expressing Flag-nSR100
|
| Treatment protocol |
A stable cell line was established by transducing cells with dox-inducible lentiviruses expressing Flag-nSR100 and selection with 2 ug/mL puromycin. For iCLIP experiments, cells were treated with 2 ug/mL dox and crosslinked (0.15 J/cm2) at 254 nm in a Stratalinker 1800
|
| Growth protocol |
N2A and 293T cell lines were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), sodium pyruvate, and non-essential amino acids. N2A and 293T cells that were transduced with lentiviruses were additionally cultured in the presence of 2ug/mL puromyocin to maintain selection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iCLIP was performed as described in Huppertz et. al, 2014, Methods.
iCLIP libraries were generated as described in Huppertz et. al, 2014, Methods
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
iCLIP barcode: NNTTAANNN. Antibody: anti-FLAG
|
| Data processing |
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences for all species were downloaded from Ensembl. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
PAR-iCLIP/iCLIP: Reads were collapsed, and the barcode and adaptor sequences were trimmed from the 5' and 3' ends respectively. Tags longer than 20 nucleotides were mapped to the human reference geneome hg19 or mouse reference genome mm9 using Bowtie by allowing a maximum of 2 mismatches, and only tags with less than or equal to five mapped locations were kept. Bedgraphs were generated using the BEDtools (v2.17.0) tool: genomecov
mm9, hg19
Genome_build: Bedgraphs of individual PAR-iCLIP/iCLIP tag densities are provided
|
| |
|
| Submission date |
Aug 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bushra Raj |
| E-mail(s) |
bushra.raj@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE57278 |
A global regulatory mechanism for activating an exon network required for neurogenesis |
|
| Relations |
| BioSample |
SAMN03003928 |
| SRA |
SRX685775 |
