GSE78507
GSE GEOEnhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [eCLIP-Seq]
Organism:
Homo sapiens
Platform:
GPL16791
Samples:
10
Experiment Types:
Other
Submitted:
Feb 25 2016
Last Updated:
May 15 2019
Status:
Public on Apr 07 2016
Contact:
Gene,,Yeo (UCSD)
Relations
SubSeries of: GSE78509
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313162
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP070818
Summary
Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using a recently developed enhanced UV crosslinking and immunoprecipitation (eCLIP) approach, we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad region- and binding site-level IMP1 and IMP2 show reproducible binding to a large and overlapping set of 3'UTR-enriched targets. RNA Bind-N-Seq applied to recombinant full-length IMP1 and IMP2 reveals CA-rich motifs that are enriched in eCLIP-defined binding sites. We observe that IMP1 loss in hPSCs recapitulates IMP1 phenotypes, including a reduction in cell adhesion and an increase in cell death. For cell adhesion, in hPSCs we find IMP1 maintains levels of integrin mRNA, specifically regulating RNA stability of ITGB5. Additionally, we show IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles.
Overall Design
eCLIP-seq was performed in biological replicate for IGF2BP1/IMP1 and IGF2BP2/IMP2, as well as one replicate each for IGF2BP3/IMP3, RBFOX2, and an IgG control. Each sample has a size-matched input control for analysis
Analysis (33 steps)
View Data Processing
Processing steps for GSE78507
- Library strategy: eCLIP-Seq
- Takes output from raw files.
- Run to trim off both 5â and 3â adapters on both reads.
- Command: quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
- Takes output from cutadapt round 1.
- Run to trim off the 3â adapters on read 2, to control for double ligation events.
- Command: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
- Takes output from cutadapt round 2.
Showing first 8 steps.
Supplementary Files (1)
GSE78507_RAW.tar
Download
GEO Samples (10)
Dataset Citations (1)
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
PMID 27068461
· 2016
· Cell reports
Anne E Conway, Eric L Van Nostrand, Gabriel A Pratt, Stefan Aigner, Melissa L Wilbert, Balaji Sundararaman, Peter Freese, Nicole J Lambert, Shashank Sathe, Tiffany Y Liang, Anthony Essex, Severine Landais, Christopher B Burge, D Leanne Jones, Gene W Yeo
SRA Experiments (10) and Runs (17)
Total: 3943 MBGSM2071742: IMP1_CLIP_biosample1; Homo sapiens; OTHER
Sample: SRS1310219
BioProject: PRJNA313162
BioSample: SAMN04516103
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: IMP1
antibody manufacturer: antibody manufacturer:MBL
antibody_catalog_number: MBL_RN007P
Original files (1)
H9 embryonic stem cell line
GSM2071743: IMP2_CLIP_biosample1; Homo sapiens; OTHER
Sample: SRS1310218
BioProject: PRJNA313162
BioSample: SAMN04516104
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: IMP2
antibody manufacturer: antibody manufacturer:MBL
antibody_catalog_number: MBL_RN008P
Original files (1)
H9 embryonic stem cell line
GSM2071744: Size-matched_Input_biosample1; Homo sapiens; OTHER
Sample: SRS1310220
BioProject: PRJNA313162
BioSample: SAMN04516105
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: null
antibody manufacturer: -
antibody_catalog_number: -
Original files (1)
H9 embryonic stem cell line
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR3187404 | 17420962 | 1672657212 | 772.28 | Stefan-1to25-Input_S15_R1.unassigned.randomer.fastq.gz, Stefan-1to25-… | SRA |
GSM2071745: IMP1_CLIP_biosample2; Homo sapiens; OTHER
Sample: SRS1310216
BioProject: PRJNA313162
BioSample: SAMN04516106
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: IMP1
antibody manufacturer: antibody manufacturer:MBL
antibody_catalog_number: MBL_RN007P
Original files (1)
H9 embryonic stem cell line
GSM2071746: IMP2_CLIP_biosample2; Homo sapiens; OTHER
Sample: SRS1310217
BioProject: PRJNA313162
BioSample: SAMN04516107
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: IMP2
antibody manufacturer: antibody manufacturer:MBL
antibody_catalog_number: MBL_RN008P
Original files (1)
H9 embryonic stem cell line
GSM2071747: IMP3_CLIP_biosample2; Homo sapiens; OTHER
Sample: SRS1310215
BioProject: PRJNA313162
BioSample: SAMN04516108
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: IMP3
antibody manufacturer: antibody manufacturer:MBL
antibody_catalog_number: MBL_RN009P
Original files (1)
H9 embryonic stem cell line
GSM2071748: IgG_CLIP_biosample2; Homo sapiens; OTHER
Sample: SRS1310214
BioProject: PRJNA313162
BioSample: SAMN04516109
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: IgG isotype control
antibody manufacturer: antibody manufacturer:Thermo Fisher
antibody_catalog_number: antibody catalog#:02-6102
Original files (1)
H9 embryonic stem cell line
GSM2071749: Size-matched_Input_biosample2; Homo sapiens; OTHER
Sample: SRS1310213
BioProject: PRJNA313162
BioSample: SAMN04516110
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H9 embryonic stem cell line
target protein: antibody: null
antibody manufacturer: -
antibody_catalog_number: -
Original files (1)
H9 embryonic stem cell line
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR3187413 | 20465913 | 2148920865 | 708.19 | Stefan_Input_040915_GAGATTCC-ATAGAGGC_R1.unassigned.randomer.fastq.gz… | SRA |
GSM2071750: RBFOX2_CLIP; Homo sapiens; OTHER
Sample: SRS1310212
BioProject: PRJNA313162
BioSample: SAMN04516111
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H1 embryonic stem cell line
target protein: antibody: RBFOX2
antibody manufacturer: antibody manufacturer:Bethyl
antibody_catalog_number: antibody catalog#:A300-864A
Original files (1)
H1 embryonic stem cell line
GSM2071751: RBFOX2_size-matched_input; Homo sapiens; OTHER
Sample: SRS1310211
BioProject: PRJNA313162
BioSample: SAMN04516112
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: H1 embryonic stem cell line
target protein: antibody: null
antibody manufacturer: -
antibody_catalog_number: -
Original files (1)
H1 embryonic stem cell line
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR3187416 | 7805483 | 819575715 | 245.07 | SF3B4_H1_INPUT_ATTACTCG-CCTATCCT_L005_R1.unassigned.randomer.fastq.gz… | SRA |
Linked Publications (1)
Data Files (34)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | FOX2-H1ES_S9_R1.A01_RBFOX2_H1ES_1to25_RBFOX2.randomer.… | OTHER | 118.0 MB | link | |||
| — | FOX2-H1ES_S9_R1.A01_RBFOX2_H1ES_1to25_RBFOX2.randomer.… | OTHER | 118.0 MB | link | |||
| — | FOX2-H1ES_S9_R1.B06_RBFOX2_H1ES_1to25_RBFOX2.randomer.… | OTHER | 56.1 MB | link | |||
| — | FOX2-H1ES_S9_R1.B06_RBFOX2_H1ES_1to25_RBFOX2.randomer.… | OTHER | 56.1 MB | link | |||
| — | SF3B4_H1_INPUT_ATTACTCG-CCTATCCT_L005_R1.unassigned.ra… | OTHER | 245.1 MB | link | |||
| — | SF3B4_H1_INPUT_ATTACTCG-CCTATCCT_L005_R1.unassigned.ra… | OTHER | 245.1 MB | link | |||
| — | Stefan-1to25-Imp1_S16_R1.A01_Stefan_1to25_Imp1_IGF2BP1… | OTHER | 129.6 MB | link | |||
| — | Stefan-1to25-Imp1_S16_R1.A01_Stefan_1to25_Imp1_IGF2BP1… | OTHER | 129.6 MB | link | |||
| — | Stefan-1to25-Imp1_S16_R1.B06_Stefan_1to25_Imp1_IGF2BP1… | OTHER | 111.4 MB | link | |||
| — | Stefan-1to25-Imp1_S16_R1.B06_Stefan_1to25_Imp1_IGF2BP1… | OTHER | 111.4 MB | link | |||
| — | Stefan-1to25-Imp2_S17_R1.C01_Stefan_1to25_Imp2_IGF2BP2… | OTHER | 135.3 MB | link | |||
| — | Stefan-1to25-Imp2_S17_R1.C01_Stefan_1to25_Imp2_IGF2BP2… | OTHER | 135.3 MB | link | |||
| — | Stefan-1to25-Imp2_S17_R1.D08fixed_Stefan_1to25_Imp2_IG… | OTHER | 138.3 MB | link | |||
| — | Stefan-1to25-Imp2_S17_R1.D08fixed_Stefan_1to25_Imp2_IG… | OTHER | 138.3 MB | link | |||
| — | Stefan-1to25-Input_S15_R1.unassigned.randomer.fastq.gz | OTHER | 772.3 MB | link | |||
| — | Stefan-1to25-Input_S15_R1.unassigned.randomer.fastq.gz | OTHER | 772.3 MB | link | |||
| — | Stefan_IGF2BP1_040915_TCCGGAGA-ATAGAGGC_R1.A01_Stefan_… | OTHER | 270.4 MB | link | |||
| — | Stefan_IGF2BP1_040915_TCCGGAGA-ATAGAGGC_R1.A01_Stefan_… | OTHER | 270.4 MB | link | |||
| — | Stefan_IGF2BP1_040915_TCCGGAGA-ATAGAGGC_R1.B06_Stefan_… | OTHER | 210.2 MB | link | |||
| — | Stefan_IGF2BP1_040915_TCCGGAGA-ATAGAGGC_R1.B06_Stefan_… | OTHER | 210.2 MB | link | |||
| — | Stefan_IGF2BP2_040915_GAGATTCC-CCTATCCT_R1.C01_Stefan_… | OTHER | 234.8 MB | link | |||
| — | Stefan_IGF2BP2_040915_GAGATTCC-CCTATCCT_R1.C01_Stefan_… | OTHER | 234.8 MB | link | |||
| — | Stefan_IGF2BP2_040915_GAGATTCC-CCTATCCT_R1.D08fixed_St… | OTHER | 193.2 MB | link | |||
| — | Stefan_IGF2BP2_040915_GAGATTCC-CCTATCCT_R1.D08fixed_St… | OTHER | 193.2 MB | link | |||
| — | Stefan_IGF2BP3_040915_TCCGGAGA-TATAGCCT_R1.C01_Stefan_… | OTHER | 212.9 MB | link | |||
| — | Stefan_IGF2BP3_040915_TCCGGAGA-TATAGCCT_R1.C01_Stefan_… | OTHER | 212.9 MB | link | |||
| — | Stefan_IGF2BP3_040915_TCCGGAGA-TATAGCCT_R1.D08fixed_St… | OTHER | 200.7 MB | link | |||
| — | Stefan_IGF2BP3_040915_TCCGGAGA-TATAGCCT_R1.D08fixed_St… | OTHER | 200.7 MB | link | |||
| — | Stefan_IgG_040915_ATTACTCG-TATAGCCT_R1.A01_Stefan_IgG_… | OTHER | 117.9 MB | link | |||
| — | Stefan_IgG_040915_ATTACTCG-TATAGCCT_R1.A01_Stefan_IgG_… | OTHER | 117.9 MB | link | |||
| — | Stefan_IgG_040915_ATTACTCG-TATAGCCT_R1.B06_Stefan_IgG_… | OTHER | 88.6 MB | link | |||
| — | Stefan_IgG_040915_ATTACTCG-TATAGCCT_R1.B06_Stefan_IgG_… | OTHER | 88.6 MB | link | |||
| — | Stefan_Input_040915_GAGATTCC-ATAGAGGC_R1.unassigned.ra… | OTHER | 708.2 MB | link | |||
| — | Stefan_Input_040915_GAGATTCC-ATAGAGGC_R1.unassigned.ra… | OTHER | 708.2 MB | link |