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| Status |
Public on Mar 27, 2021 |
| Title |
mES RNAseq - rep2 |
| Sample type |
SRA |
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| Source name |
mES
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| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic
disease: none
cell type: embryonic stem cell
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| Growth protocol |
Cell lines were cultured under recommended culturing conditions.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with Maxwell LEV Simply RNA isolation kit. RNA quality was assessed with BioAnalyzer.
Poly(A) RNA enrichment and library preparation was performed with TruSeq kit v2 according to manufacturer’s instructions and sequenced on HiSeq2500, paired end 75 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
INCLUSION_LEVELS_FULL-Mm25.tab.gz
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| Data processing |
Raw reads of U-2 OS and HeLa samples were mapped to GRCm38 using the NF-CORE RNA-seq pipeline (v1.4.2)
Raw RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 2.2.2 (Tapial et al., (2017)), which is available on github (https://github.com/vastgroup/vast-tools), in combination with the Mm2 and Hs2 VastDB versions released on Dec. 20, 2019.
From primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Each event was required to pass filtering in at least 50% of replicates.
Genome_build: Human (GRCm38) (HeLa, U-2 OS)
Supplementary_files_format_and_content: INCLUSION_LEVELS_FULL-Hs23.tab.gz and INCLUSION_LEVELS_FULL-Mm25.tab.gz are primary vast-tools output files for human and mouse samples in tab-delimited format, respectively. See https://github.com/vastgroup/vast-tools#combine-output-format.
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| Submission date |
Mar 26, 2021 |
| Last update date |
Mar 27, 2021 |
| Contact name |
Gabrijela Dumbovic |
| E-mail(s) |
gabrijela.dumbovic@colorado.edu, gabrijela.dumbovic@gmail.com
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| Organization name |
University of Colorado
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| Department |
BioFrontiers
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| Lab |
John Rinn lab
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| Street address |
3415 Colorado avenue
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| City |
Boulder |
| State/province |
Colorado |
| ZIP/Postal code |
80303 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE169743 |
Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention |
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| Relations |
| BioSample |
SAMN18510184 |
| SRA |
SRX10457644 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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