 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 03, 2013 |
| Title |
Ctrl_RBM10.KD.24h_RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Ctrl_RBM10.KD.24h_RNA-Seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines
rna subset: poly A RNA
|
| Treatment protocol |
siRNA transfections were performed in antibiotics free medium, i.e. DMEM with 10% final concentration FBS, using RNAiMAX (Invitrogen). RBM10 overexpression was induced with 10 ng/mL doxycycline for 16 hours
|
| Growth protocol |
The HEK293 T-REx Flp-In cells were cultured in a 37 °C incubator with 5 % CO2 and maintainence medium containing: High glucose DMEM (Gibco) supplemented with 10% final concentration FBS (heat inactivated, Gibco), 100 U/ml of penicillin and 100 μg/ml streptomycin (Gibco), 15 μg/ml blasticidin (InvivoGen) and 100 μg/ml zeocin (InvivoGen). The stable cell lines were maintained in selective medium containing: DMEM with 10% final concentration of FBS, 100 U/ml of penicillin and 100 μg/ml streptomycin, 100 μg/ml hygromycin and 15 μg/ml blasticidin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.
RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).
processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.
Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.
Genome_build: hg19
|
| |
|
| Submission date |
Mar 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Andreas Gogol-Döring |
| E-mail(s) |
andreas.gogol-doering@mni.thm.de
|
| Organization name |
Technische Hochschule MIttelhessen
|
| Department |
MNI
|
| Street address |
Wiesenstraße 14
|
| City |
Gießen |
| ZIP/Postal code |
35390 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44976 |
Global analysis of alternative splicing regulated by RBM10 |
|
| Relations |
| SRA |
SRX248556 |
| BioSample |
SAMN01974931 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1095127_HEK293.RNA-Seq.Ctrl_KD.24h.F.tab.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
| GSM1095127_HEK293.RNA-Seq.Ctrl_KD.24h.R.tab.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
