|
| Status |
Public on Nov 06, 2023 |
| Title |
isoseq_48H_activated_noDiv_WT |
| Sample type |
SRA |
| |
|
| Source name |
Spleens and lymph nodes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleens and lymph nodes
Sex: male
genotype: WT
cell division: 0
time: 48h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol isolated high-quality RNA samples (>500 ng total RNA)
Three SMRTbell libraries (Naive, 48h activated 0 division and 2 divisions) from Trizol isolated high-quality RNA samples (>500 ng total RNA) were sequenced on a Sequel SMRT Cells 1M for a general survey of full-length isoforms in a transcriptome with moderate to high expression levels.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Sequel |
| |
|
| Data processing |
Consensus sequences (.ccs) were generated from your raw subread data by using ccs (--min-rq 0.9). Full-length reads were generated after primer removal and demultiplexing using lima --ccs.
Then we removed polyA tails and artificial concatemers with isoseq3 refine (--require-polya --min-polya-length 20) and clustered consensus sequences to generate transcriptome fastas with isoseq3 cluster (--use-qvs).
High-Quality Full-Length Polished Isoforms were mapped to the genome and collapsed into transcripts based on genomic mapping using pbmm2 align (--preset ISOSEQ).
We then used isoseq3 collapse to generate fastq and gff files. Transcripts were annotated using SQANTI3 (v0.1) (Tardaguila et al., 2018) (--aligner_choice minimap2) and providing liste of mouse polyA motifs retrieved from PolyASite database (https://polyasite.unibas.ch/atlas), transcript abundance from isoseq3 output and CAGE peaks from Fantom5 (https://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_latest/extra/CAGE_peaks/).
Assembly: mm10 / Mus_musculus.GRCm38.94
Supplementary files format and content: gtf files containing collapsed transcripts
|
| |
|
| Submission date |
Jul 23, 2022 |
| Last update date |
Nov 06, 2023 |
| Contact name |
Denis Seyres |
| E-mail(s) |
denisseyres1@gmail.com
|
| Organization name |
UniversitatSpital Basel
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24198 |
| Series (2) |
| GSE209603 |
Dynamic 3'UTR changes during naïve CD4+ T cell activation and proliferation are reverted in the effector/memory state [Iso-Seq] |
| GSE209604 |
Dynamic 3'UTR changes during naïve CD4+ T cell activation and proliferation are reverted in the effector/memory state |
|
| Relations |
| BioSample |
SAMN29921303 |
| SRA |
SRX16527877 |
