|
| Status |
Public on Dec 25, 2019 |
| Title |
Input_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Epithelial cells
cell line: LNCaP
antibody: input
|
| Treatment protocol |
LNCAP cells growing at steady state were UV-crosslinked in PBS and harvested for CLIP. RNA-RBP complexes were isolated using an overnight pulldown with HNRNPM antibody (SC20001; SantaCruz), and further purified by PAGE electrophoresis. eCLIP library preparation was performed as described by Van Nostrand et al. (2016)
|
| Growth protocol |
LNCAP cells were maintained in in RPMI media supplemented with 10% fetal bovine serum (FBS; Lonza) 1mM sodium pyruvate (Gibco, 11360070), non-essential amino acids (Gibco; 11140050) and 50U/ml Penicillin-Streptomycin (Gibco, 15140163).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
LNCAP cells were grown on 150mm dishes were UV crosslinked (150mJ), using the UV Stratalinker 2400. Cell pellets were flash frozen in liquid nitrogen. RBP complex isolation and eCLIP library preparation was performed as described by Van Nostrand et al. (2016)
eCLIP libraries were prepared using the protocol described by Van Nostrand et al. (2016)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: eCLIP-seq
Basecalls performed using CASAVA
CLIP-seq reads treated with the protocol outlined in Van Nostrand et al. (2016) Briefly, reads were adapter-trimmed using cutadapt and aligned to the human hg19 genome using STAR version 2.4.2a
Mapped reads were then processed and peaks were called with scripts from the Yeo Lab
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were produced using bamCoverage in the deeptools package
|
| |
|
| Submission date |
Apr 27, 2018 |
| Last update date |
Dec 26, 2019 |
| Contact name |
Diana HP Low |
| E-mail(s) |
dlow@imcb.a-star.edu.sg
|
| Organization name |
Institute of Molecular and Cell Biology
|
| Lab |
Chromatin, Epigenetics & Differentiation
|
| Street address |
#03-06, 61 Biopolis Drive, Proteos
|
| City |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE113783 |
HNRNPM-regulated splicing dependencies in prostate cancer [eCLIP-Seq] |
| GSE113786 |
HNRNPM-regulated splicing dependencies in prostate cancer |
|
| Relations |
| BioSample |
SAMN08995375 |
| SRA |
SRX4004258 |
