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| Status |
Public on Apr 26, 2012 |
| Title |
DG75-eGFP, 60 min nascent RNA, Rep.1 |
| Sample type |
SRA |
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| Source name |
DG75-eGFP, 60 min nascent RNA
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| Organism |
Homo sapiens |
| Characteristics |
cell line: DG75
cell type: B-cells
plasmid: eGFP
celluar rna type: nascent RNA
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| Treatment protocol |
500 uM 4sU added for 5 to 60 min, isolation of total cellular RNA using Trizol (Invitrogen), separation of total cellular RNA into nascent and untagged pre-existing RNA as described in Dolken et al., RNA 2008.
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| Growth protocol |
RPMI 1640 medium, 10% fetal calf serum, 100 IU/ml Penicillin, 100 ug/ml Streptomycin and 2 mM L-Glutamin
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| Extracted molecule |
total RNA |
| Extraction protocol |
whole-transcriptome analysis (WTAK) protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 2.0 |
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| Description |
AY60E
w/o rRNA depletion
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| Data processing |
Reads were mapped in a 3-step process using the Bowtie alignment program (Langmead, et al., 2009). First, reads were aligned to pre-rRNA sequences (18S, 5.8S, 28S and spacer regions). The remaining unmapped reads were aligned to all Ensembl transcripts (Ensembl version 60) excluding pseudo-genes and haplotypes to identify exonic and exon-exon junction reads (aligned reads overlapping an exon-exon junction by at least 1 nt). Reads that remained unmapped after step two were aligned to the human reference genome (GRCh37/hg19) to identify intron and exon-intron junction reads (overlapping an exon-intron junction by at least 1 nt). For each read the best alignment location was used. Reads mapping equally well to two different locations were discarded. The following Bowtie settings were used: seed region = first 20 nt, 3 mismatches allowed in the seed, 5 in the whole alignment.
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| Submission date |
Aug 25, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Caroline Friedel |
| Organization name |
Ludwig-Maximilians-Universität München
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| Department |
Institut für Informatik
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| Street address |
Amalienstr. 17
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| City |
München |
| ZIP/Postal code |
80333 |
| Country |
Germany |
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| Platform ID |
GPL9138 |
| Series (1) |
| GSE31653 |
Ultra short and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution |
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| Relations |
| SRA |
SRX097567 |
| BioSample |
SAMN00718859 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM786005_AY60E.rpkm.gz |
6.6 Mb |
(ftp)(http) |
RPKM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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