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Status |
Public on Sep 03, 2013 |
Title |
RBM10.KD.72h_RNA-Seq |
Sample type |
SRA |
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Source name |
RBM10.KD.72h_RNA-Seq
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Organism |
Homo sapiens |
Characteristics |
cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines rna subset: poly A RNA
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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
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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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
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Organization name |
Technische Hochschule MIttelhessen
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Department |
MNI
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Street address |
Wiesenstraße 14
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City |
Gießen |
ZIP/Postal code |
35390 |
Country |
Germany |
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Platform ID |
GPL11154 |
Series (1) |
GSE44976 |
Global analysis of alternative splicing regulated by RBM10 |
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Relations |
SRA |
SRX248565 |
BioSample |
SAMN01974949 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1095136_HEK293.RNA-Seq.KD.72h.F.tab.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
GSM1095136_HEK293.RNA-Seq.KD.72h.R.tab.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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