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Sample GSM6338701 Query DataSets for GSM6338701
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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