|
| Status |
Public on Jun 20, 2015 |
| Title |
MDA-MB-231 cells HNRNPA2B1 knockdown_RNA-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231_HNRNPA2B1_KD
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
|
| Treatment protocol |
stable knockdown of the indicated gene was achieved using lentival particles and puromycin selection
|
| Growth protocol |
Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Cells were lysed using LB1 buffer, the nuclear fraction was then lysed with M-PER (Thermo Scientific) buffer and diluted 10-fold in dilution buffer before the immunoprecipitation. Rabbit α-m6A antibody (Synaptic Systems) and rabbit IgG control bound to protein A Dynabeads were used for the immunoprecipitations. The immunoprecipitated RNA was eluted with N6-methyladenosine (Sigma-Aldrich), ethanol precipitated and resuspended in water.
RNA was barcoded using ScriptSeq V2 kit (Epicentre) and sent for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Single-end reads were trimmed (cutadapt version 1.8) and alighned to human transcriptome (hg19) using Tophat-2.0.12.
Transcript abundance was quantified using Cuffilnks-2.0.2.
Aligned reads were combined from replicates and MISO (Misopy-0.5.2) was used to compare lternative splicing events (skipped exons, first alternative exon, last alternative exon and intron retention).
Genome_build: hg19
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Claudio Alarcon |
| E-mail(s) |
calarcon@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Department |
Systems Cancer Biology
|
| Lab |
Sohail Tavazoie
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE70061 |
Nuclear HNRNPA2B1 HITS-CLIP and RNA-seq |
|
| Relations |
| BioSample |
SAMN03783563 |
| SRA |
SRX1067122 |
