GSE180686
GSE GEOTranscriptome-wide identification of RNA binding protein binding sites using seCLIP-seq
Organism:
Homo sapiens
Platform:
GPL24676
Samples:
4
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Jul 23 2021
Last Updated:
May 09 2022
Status:
Public on Feb 07 2022
Contact:
Gene,,Yeo (UCSD)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA749175
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP329582
Summary
Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP:RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency, and scalability.
Overall Design
Identification of PRPF39 targets using transcriptome-wide seCLIP-seq in HepG2 cells.
Analysis (20 steps)
View Data Processing
Processing steps for GSE180686
- Raw reads were processed using the eCLIP pipeline v0.7.0
- Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0).
- Args: --random-seed 1 --bc-pattern NNNNNNNNNN
- Reads were then trimmed with cutadapt (1.14).
- Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA1/Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
- Reads were then trimmed again with cutadapt (1.14) to remove double-ligation events.
- Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA1/Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
- Trimmed and filtered reads were then mapped with STAR (2.7.6a) against a repeat element database (RepBase 18.05).
Showing first 8 steps.
Supplementary Files (2)
GEO Samples (4)
Dataset Citations (1)
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.
PMID 35322209
· 2022
· Nature protocols
Steven M Blue, Brian A Yee, Gabriel A Pratt, Jasmine R Mueller, Samuel S Park, Alexander A Shishkin, Anne C Starner, Eric L Van Nostrand, Gene W Yeo
SRA Experiments (4) and Runs (4)
Total: 2615 MBGSM5468035: PRPF39 clip, rep1; Homo sapiens; RIP-Seq
Sample: SRS9565856
BioProject: PRJNA749175
BioSample: SAMN20356338
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HepG2
antibody catalog: PA5-21627
antibody lot: UC2743613B
antibody manufacturer: Thermo Fisher Scientific
antibody: polyclonal, IgG, affinity purified
rnase i fragmentation condition: 10 ul 1:25 RNase I @ 37deg C for 5 minutes
inline barcode1: InvRNA1
Original files (1)
HepG2
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR15222627 | 22099417 | 2232041117 | 684.82 | 4114_CLIP1_S39_L002_R1_001.fastq.gz, SRR15222627, SRR15222627.lite | SRA |
GSM5468036: PRPF39 size-matched input, rep1; Homo sapiens; RIP-Seq
Sample: SRS9565857
BioProject: PRJNA749175
BioSample: SAMN20356337
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HepG2
antibody catalog: PA5-21627
antibody lot: UC2743613B
antibody manufacturer: Thermo Fisher Scientific
antibody: polyclonal, IgG, affinity purified
rnase i fragmentation condition: 10 ul 1:25 RNase I @ 37deg C for 5 minutes
inline barcode1: Ril19
Original files (1)
HepG2
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR15222628 | 21225810 | 2143806810 | 655.69 | 4114_INPUT1_S38_L002_R1_001.fastq.gz, SRR15222628, SRR15222628.lite | SRA |
GSM5468037: PRPF39 clip, rep2; Homo sapiens; RIP-Seq
Sample: SRS9565858
BioProject: PRJNA749175
BioSample: SAMN20356336
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HepG2
antibody catalog: PA5-21627
antibody lot: UC2743613B
antibody manufacturer: Thermo Fisher Scientific
antibody: polyclonal, IgG, affinity purified
rnase i fragmentation condition: 10 ul 1:25 RNase I @ 37deg C for 5 minutes
inline barcode1: InvRNA1
Original files (1)
HepG2
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR15222629 | 20719241 | 2092643341 | 645.16 | 4114_CLIP2_S41_L002_R1_001.fastq.gz, SRR15222629, SRR15222629.lite | SRA |
GSM5468038: PRPF39 size-matched input, rep2; Homo sapiens; RIP-Seq
Sample: SRS9565859
BioProject: PRJNA749175
BioSample: SAMN20356335
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HepG2
antibody catalog: PA5-21627
antibody lot: UC2743613B
antibody manufacturer: Thermo Fisher Scientific
antibody: polyclonal, IgG, affinity purified
rnase i fragmentation condition: 10 ul 1:25 RNase I @ 37deg C for 5 minutes
inline barcode1: Ril19
Original files (1)
HepG2
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR15222630 | 20445182 | 2064963382 | 629.82 | 4114_INPUT2_S40_L002_R1_001.fastq.gz, SRR15222630, SRR15222630.lite | SRA |
Linked Publications (1)
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.
Nature protocols · 2022
Data Files (5)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | 4114_CLIP1_S39_L002_R1_001.fastq.gz | RIP-Seq | 684.8 MB | link | |||
| — | 4114_CLIP2_S41_L002_R1_001.fastq.gz | RIP-Seq | 645.2 MB | link | |||
| — | 4114_INPUT1_S38_L002_R1_001.fastq.gz | RIP-Seq | 655.7 MB | link | |||
| — | 4114_INPUT2_S40_L002_R1_001.fastq.gz | RIP-Seq | 629.8 MB | link | |||
| — | SRR15222630.lite | RIP-Seq | 629.8 MB | link |