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Sample GSM1167172 Query DataSets for GSM1167172
Status Public on Dec 20, 2013
Title RBM10 CLIP-Seq Replicate 1
Sample type SRA
 
Source name HeLa cells
Organism Homo sapiens
Characteristics cell line: HeLa
antibody: Sigma Aldricht RBM10 (HPA034972) antibody
Growth protocol HeLa cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.
Extracted molecule total RNA
Extraction protocol HeLa cells were grown in 150mm plates, rinsed once with ice-cold PBS and placed in a Stratalinker without the cover plate and irradiated once with an energy of 400mJ/cm. Cells were then scraped off the palte and centrifuged at 2500rpm for 5 min at 4°C and the pellet re-suspended in 3x the cells volume of PBS and distributed in two separate eppendorf tubes. Each tube of crosslinked lysate was resuspended in 700 μl of 1X PXL (PBS (tissue culture grade without Mg++ or Ca++) 0.1% SDS 0.5% deoxycholate 0.5% NP-40, supplemented with protease inhibitors and with 15 μl RNAsin (Promega)) and kept on ice for 10 min. 30 μl of RQ1 DNAse (Promega, M6101) were added to each tube and extracts were incubated at 37° for 5 min, centrifuged at 1000 rpm, followed by an incubation at 37° for 5 minutes with RNAse I. Extracts were the centrifuged at 12000 rpm for 10’ and then clarified on protein A Dynabeads for 2 hours at 4°C, before immunoprecipitation using protein A pre-adsorbed with either rabbit IgGs or EWS antibody (5μg) at 4 °C under constant rotation. After incubation for 3 hours, stringent washes were performed with ice-cold buffers as follows: 2 washes with 1X PXL, 2 washes with 5X PXL (High-salt Wash Buffer) and 2 washes with PNK Buffer (50 mM Tris-Cl pH 7.4 10 mM MgCl2 0.5% NP-40). Alkaline phosphatase (Roche) treatment (3μl) was performed at 37°C for 20’ in Thermomixer, followed by 4 washes in PNK buffer (one wash including 20mM EGTA). 3’ RNA linker ligation was carried out overnight at 16°C on beads using T4 RNA ligase (Fermentas) and radioactively-labeled linkers. Beads were extensively washed (1x PXL buffer, 1x 5XPXL buffer, 3x PNK buffer), before and after PNK treatment (T4, NEB, [40 units]) for 20’ at 37°C. Finally, beads were resuspended in 30ml of PNK buffer, supplemeted with Novex loading buffer and loaded on a Novex NuPAGE 10% Bis-Tris gel. The gel was run at 175V in the cold room and subsequently transfered to nitrocellulose using the Novex wet transfer apparatus, for 1 h at 30V in NuPAGE Transfer Buffer with 10% methanol. After transfer, the nitrocellulose filter was rinsed in 1X PBS, and exposed to autoradiogram. The radioactively labeled RNA-protein complexes were excised and proteinase K treatment was performed (20’ at 37°C) before RNA extraction with Phenol-Chloroform and preciiptation overnight with 3M NaOAc pH 5.2, glycogen (Ambion, 9510) and 1:1 EtOH:isopropanol.
The RNA was resuspended in RNase free water and 5’ end linker ligation (containing also barcode sequences) was carried out with T4 RNA ligase at 16°C for 5 hours. RNAs were reverse-transcribed, PCR amplified with barcoded primers and sequenced using Solexa (Illumina) technology.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina Genome Analyzer IIx
 
Data processing Basecalling was performed using Illumina pipeline versions 1.6.0 within within SCS 2.6 for the RBM6 and RBM10 data, Illumina pipeline versions 1.7.0 within within SCS 2.8 for the RBM5 data.
Reads were mapped to the human genome using GEM (Marco-Sola et al. 2013), allowing for up to 2 mismatches and retaining only sequences that mapped uniquely to the genome.
All the unmapped reads were then trimmed 1 base from the 3’ end and remapped. This sequential trimming and mapping was continued up to 21nt length reads (15 bases of trimming).
Additional filtered datasets and analysis description can be found here: http://regulatorygenomics.upf.edu/Data/RBMs/
Genome_build: hg18
Supplementary_files_format_and_content: BED files containing all mapped reads.
 
Submission date Jun 18, 2013
Last update date May 15, 2019
Contact name Endre Sebestyén
Organization name Semmelweis University
Department 1st Department of Pathology and Experimental Cancer Research
Street address Üllői út 26.
City Budapest
ZIP/Postal code 1085
Country Hungary
 
Platform ID GPL10999
Series (1)
GSE48066 Regulation of NUMB alternative splicing by RBM5, RBM6 and RBM10 controls cancer cell proliferation (CLIP-Seq)
Relations
BioSample SAMN02207431
SRA SRX309728

Supplementary file Size Download File type/resource
GSM1167172_RBM10_rep1_halfopen.bed.gz 22.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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