|
Status |
Public on May 14, 2023 |
Title |
IVT_IFRD2_del_ex4-10_UT |
Sample type |
SRA |
|
|
Source name |
In vitro transcription
|
Organism |
synthetic construct |
Characteristics |
cell line: In vitro transcription treatment: untreated
|
Extracted molecule |
other |
Extraction protocol |
Qiagen miRNeasy kit (RNA-seq and NET-seq of U2 snRNA knockdown), Qiazol extraction (RNA-seq motor neurons), Trizol extraction (DMS-MaPseq) SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (RNA-seq motor neurons), KAPA mRNA HyperPrep kit (RNA-seq), NET-seq protocol (Mayer & Churchman Nature Protocols 2016) or xGen Broad-range RNA Library Prep Kit (DMS-MaPseq)
|
|
|
Library strategy |
RNA-Seq |
Library source |
other |
Library selection |
cDNA |
Instrument model |
Illumina iSeq 100 |
|
|
Data processing |
Adapter trimming (Cutadapt) Alignment (STAR for RNAseq and NETseq, bowtie for DMS-MaPseq) Differential splicing analysis with rMATS (RNAseq) DREEM (DMS-MaPseq) featureCounts (NETseq) Assembly: GRCh38 Supplementary files format and content: RNAseq_control_vs_U2_KD_rMATS_stat_intron_retention.txt: intron-exon junction counts for every annotated intron in each RNAseq sample and statistical testing between control and U2 snRNA using rmats-stats Supplementary files format and content: RNAseq_control_vs_U2_KD_SE.MATS.JC.txt: RNAseq rMATS output for skipped exons (SE) between all control and U2 snRNA knockdown replicates Supplementary files format and content: *vienna.txt: DMS reactivities for every nucleotide in the in vitro transcribed RNAs used for DMS-MaPseq Supplementary files format and content: *ER_counts.txt or *PR_counts.txt: featureCounts output from NET-seq data for the gene body region (ER, +300 nt from TSS to end of gene) or promoter region (PR -30 to + 300nt from TSS) of all genes
|
|
|
Submission date |
Jul 14, 2022 |
Last update date |
May 14, 2023 |
Contact name |
Karine Choquet |
E-mail(s) |
karine.choquet@usherbrooke.ca
|
Organization name |
Université de Sherbrooke
|
Department |
Biochemistry and Functional Genomics
|
Street address |
3201 rue Jean-Mignault
|
City |
Sherbrooke |
State/province |
Québec |
ZIP/Postal code |
J1E 4K8 |
Country |
Canada |
|
|
Platform ID |
GPL32483 |
Series (2) |
GSE208197 |
pre-mRNA splicing order is defined and maintains splicing fidelity across multi-intronic transcripts [I] |
GSE232455 |
pre-mRNA splicing order is defined and maintains splicing fidelity across multi-intronic transcripts |
|
Relations |
BioSample |
SAMN29751582 |
SRA |
SRX16239232 |