|
Status |
Public on Nov 06, 2023 |
Title |
isoseq_naive_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: Naive time: Naive
|
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.
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|
|
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
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|
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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 |
SAMN29921304 |
SRA |
SRX16527876 |