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GSE104949

GSE GEO
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RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

Organism: Homo sapiens
Platform: GPL15520
Samples: 6
Experiment Types:
Other
Submitted: Oct 13 2017
Last Updated: Jul 25 2021
Status: Public on Jul 27 2018
Contact: Shaun,Michael,Webb (University of Edinburgh)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA414217 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP119918

Summary

TRIM25 E3 ubiquitin ligase is a new RNA-binding protein. We present the first high-throughput analysis of the molecular interactomes of TRIM25. We show that TRIM25 is a bona fide RNA-binding protein that interacts with numerous coding and non-coding transcripts. This suggests that TRIM25 could play a role in the regulation of RNA metabolism.

Overall Design

We performed UV crosslinking and immunoprecipitations in HeLa cells transiently expressing T7-tagged TRIM25, followed by high-throughput sequencing of TRIM25-associated RNAs (CLIP-seq). This was done in three biological replicates. Please note that each processed data is genrated from Trim25 and Mock dataset pairs (e.g. e.g.Trim25_exp1_significant_clusters.gtf.gz generated from both Trim25 CLIP-seq exp1 and Mock CLIP-seq exp1 ) and linked to the corresponding Trim25 CLIP-seq sample records.

Analysis (9 steps)

View Data Processing
Processing steps for GSE104949
  1. library strategy: CLIP-seq
  2. novoindex
  3. Remove 3’adapter using flexbar
  4. collapse data and remove PCR duplicates using pyCRAC
  5. align using novalign
  6. Readcounter using pyCRAC
  7. calculate FDR using Mock sample using pyCRAC
  8. intersect fdr with reads using bedtools intersect
Showing first 8 steps.

Supplementary Files (1)

GSE104949_RAW.tar Download
GEO Samples (6)
GSM2810841 GSM2810842 GSM2810843 GSM2810844 GSM2810845 GSM2810846

Dataset Citations (1)

PubMed citation (PMID 29117863)

SRA Experiments (6) and Runs (6)

Total: 334 MB
SRX3280921 SRP119918 RIP-Seq SINGLE
GSM2810841: Trim25 CLIP-seq exp1; Homo sapiens; RIP-Seq
Sample: SRS2591732
BioProject: PRJNA414217
BioSample: SAMN07782122
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: Trim25 CLIP-seq
cell line: HeLa
genotype/variation: transiently expressing T7-tagged TRIM25
Original files (1)
Trim25 CLIP-seq
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6170072 12437431 214219477 149.37 Trim25_CLIP_exp1.fq.gz, SRR6170072, SRR6170072.sralite SRA
SRX3280922 SRP119918 RIP-Seq SINGLE
GSM2810842: Trim25 CLIP-seq exp2; Homo sapiens; RIP-Seq
Sample: SRS2591733
BioProject: PRJNA414217
BioSample: SAMN07782121
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: Trim25 CLIP-seq
cell line: HeLa
genotype/variation: transiently expressing T7-tagged TRIM25
Original files (1)
Trim25 CLIP-seq
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6170073 3645907 87428940 60.2 Trim25_CLIP_exp2.fq.gz, SRR6170073, SRR6170073.sralite SRA
SRX3280923 SRP119918 RIP-Seq SINGLE
GSM2810843: Trim25 CLIP-seq exp3; Homo sapiens; RIP-Seq
Sample: SRS2591734
BioProject: PRJNA414217
BioSample: SAMN07782120
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: Trim25 CLIP-seq
cell line: HeLa
genotype/variation: transiently expressing T7-tagged TRIM25
Original files (1)
Trim25 CLIP-seq
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6170074 5734940 133873280 89.79 Trim25_CLIP_exp3.fq.gz, SRR6170074, SRR6170074.sralite SRA
SRX3280924 SRP119918 RIP-Seq SINGLE
GSM2810844: Mock CLIP-seq exp1; Homo sapiens; RIP-Seq
Sample: SRS2591735
BioProject: PRJNA414217
BioSample: SAMN07782119
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: Mock CLIP-seq
cell line: HeLa
genotype/variation: mock-transfected
Original files (1)
Mock CLIP-seq
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6170075 551235 8513699 6.15 Mock_CLIP_exp1.fq.gz, SRR6170075, SRR6170075.sralite SRA
SRX3280925 SRP119918 RIP-Seq SINGLE
GSM2810845: Mock CLIP-seq exp2; Homo sapiens; RIP-Seq
Sample: SRS2591736
BioProject: PRJNA414217
BioSample: SAMN07782117
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: Mock CLIP-seq
cell line: HeLa
genotype/variation: mock-transfected
Original files (1)
Mock CLIP-seq
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6170076 643452 17732813 11.75 Mock_CLIP_exp2.fq.gz, SRR6170076, SRR6170076.sralite SRA
SRX3280926 SRP119918 RIP-Seq SINGLE
GSM2810846: Mock CLIP-seq exp3; Homo sapiens; RIP-Seq
Sample: SRS2591737
BioProject: PRJNA414217
BioSample: SAMN07782118
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: Mock CLIP-seq
cell line: HeLa
genotype/variation: mock-transfected
Original files (1)
Mock CLIP-seq
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6170077 938215 24783493 16.29 Mock_CLIP_exp3.fq.gz, SRR6170077, SRR6170077.sralite SRA

Linked Publications (1)

Transcriptome regulation by PARP13 in basal and antiviral states in human cells.
iScience · 2024

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Mock_CLIP_exp1.fq.gz RIP-Seq 6.1 MB link
— Mock_CLIP_exp2.fq.gz RIP-Seq 11.8 MB link
— Mock_CLIP_exp3.fq.gz RIP-Seq 16.3 MB link
— Trim25_CLIP_exp1.fq.gz RIP-Seq 149.4 MB link
— Trim25_CLIP_exp2.fq.gz RIP-Seq 60.2 MB link
— Trim25_CLIP_exp3.fq.gz RIP-Seq 89.8 MB link