GSE180686

GSE GEO

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Transcriptome-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)

GSE180686_4114_CLIP1_rep1.vs.4114_CLIP2_rep2.bed.gz Download

GSE180686_RAW.tar Download

GEO Samples (4)

GSM5468035 GSM5468036 GSM5468037 GSM5468038

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 MB

SRX11528578 SRP329582 RIP-Seq SINGLE

GSM5468035: 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

SRX11528579 SRP329582 RIP-Seq SINGLE

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

SRX11528580 SRP329582 RIP-Seq SINGLE

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

SRX11528581 SRP329582 RIP-Seq SINGLE

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

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.

Nature protocols · 2022

Data Files (9)

Accession	File Name	Stored Type	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
—	SRR15222627_GSM5468035	RIP-Seq	684.0 MB	link
—	SRR15222628_GSM5468036	RIP-Seq	655.0 MB	link
—	SRR15222629_GSM5468037	RIP-Seq	645.0 MB	link
—	SRR15222630_GSM5468038	RIP-Seq	629.0 MB	link
—	SRR15222630.lite	RIP-Seq	629.8 MB	link