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GSE230097

GSE GEO
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Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Organism: Homo sapiens
Platform: GPL24676
Samples: 16
Experiment Types:
Other
Submitted: Apr 19 2023
Last Updated: Mar 05 2024
Status: Public on Mar 04 2024
Contact: Akshay,,Bhinge (Living Systems Institute, University of Exeter)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA957458

Summary

RNA processing is a fundamental mode of gene regulation that is perturbed in a variety of diseases including cancer and neurodegenerative disorders. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions such as CLIP rely on purifying single proteins at a time. Methods to identify transcriptome wide binding of RBPs without purifying individual RBPs are gaining interest. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale in an RBP agnostic manner. Our method allows precise mapping of the 5’ end of the RBP binding site and uncovers RBPs that are differentially activated during cell fate transitions.

Overall Design

ePRINT analysis of HEK293T cells transfected with an siRNA against FUS or a scrambled control siRNA. ePRINT analysis of motor neuron progenitors and differentiated motor neurons.

Analysis (6 steps)

View Data Processing
Processing steps for GSE230097
  1. Adapters were removes using cutadapt and reads were mapped to hg19 using STAR.
  2. Initial peak calling was performed for each sample by CLIPper using only the r1 reads.
  3. Peaks with genomic overlap in at least two ePRINT samples were identified and their genomic coordinates merged to define the candidate peak superset using HOMER.
  4. These peaks were then filtered using the input retaining those significantly enriched in the ePRINT samples in comparison to the corresponding input samples.
  5. The remaining high confidence peaks were then input to DESEQ2 for differential analysis.
  6. Bedgraph files were generated from the r1 reads using bedtools

Supplementary Files (1)

GSE230097_RAW.tar Download
GEO Samples (16)
GSM7186916 GSM7186917 GSM7186918 GSM7186919 GSM7186920 GSM7186921 GSM7186922 GSM7186923 GSM7186924 GSM7186925 GSM7186926 GSM7186927 GSM7186928 GSM7186929 GSM7186930 GSM7186931

SRA Experiments (16) and Runs (16)

Total: 13889 MB
SRX20015711 SRP433437 RNA-Seq PAIRED
GSM7186916: ep 293T siNeg R1; Homo sapiens; RNA-Seq
Sample: SRS17357614
BioProject: PRJNA957458
BioSample: SAMN34254260
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: control siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219264 16109671 1643186442 520.03 10249_sample1_r1.fq.gz, 10249_sample1_r2.fq.gz, SRR24219264, SRR24219… SRA
SRX20015712 SRP433437 RNA-Seq PAIRED
GSM7186917: ep 293T siNeg R2; Homo sapiens; RNA-Seq
Sample: SRS17357615
BioProject: PRJNA957458
BioSample: SAMN34254259
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: control siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219263 19477938 1986749676 623.75 10249_sample2_r1.fq.gz, 10249_sample2_r2.fq.gz, SRR24219263, SRR24219… SRA
SRX20015713 SRP433437 RNA-Seq PAIRED
GSM7186918: ep 293T siFUS R1; Homo sapiens; RNA-Seq
Sample: SRS17357616
BioProject: PRJNA957458
BioSample: SAMN34254258
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: FUS siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219262 24845634 2534254668 806.23 10249_sample3_r1.fq.gz, 10249_sample3_r2.fq.gz, SRR24219262, SRR24219… SRA
SRX20015714 SRP433437 RNA-Seq PAIRED
GSM7186919: ep 293T siFUS R2; Homo sapiens; RNA-Seq
Sample: SRS17357617
BioProject: PRJNA957458
BioSample: SAMN34254257
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: FUS siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219261 33892248 3457009296 1096.05 10249_sample4_r1.fq.gz, 10249_sample4_r2.fq.gz, SRR24219261, SRR24219… SRA
SRX20015715 SRP433437 RNA-Seq PAIRED
GSM7186920: input 293T siNeg R1; Homo sapiens; RNA-Seq
Sample: SRS17357618
BioProject: PRJNA957458
BioSample: SAMN34254256
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: control siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219260 16159755 1648295010 518.68 10249_sample5_r1.fq.gz, 10249_sample5_r2.fq.gz, SRR24219260, SRR24219… SRA
SRX20015716 SRP433437 RNA-Seq PAIRED
GSM7186921: input 293T siNeg R2; Homo sapiens; RNA-Seq
Sample: SRS17357619
BioProject: PRJNA957458
BioSample: SAMN34254255
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: control siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219259 25355825 2586294150 812.08 10249_sample6_r1.fq.gz, 10249_sample6_r2.fq.gz, SRR24219259, SRR24219… SRA
SRX20015717 SRP433437 RNA-Seq PAIRED
GSM7186922: input 293T siFUS R1; Homo sapiens; RNA-Seq
Sample: SRS17357622
BioProject: PRJNA957458
BioSample: SAMN34254254
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: FUS siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219258 17751288 1810631376 567.28 10249_sample7_r1.fq.gz, 10249_sample7_r2.fq.gz, SRR24219258, SRR24219… SRA
SRX20015718 SRP433437 RNA-Seq PAIRED
GSM7186923: input 293T siFUS R2; Homo sapiens; RNA-Seq
Sample: SRS17357621
BioProject: PRJNA957458
BioSample: SAMN34254253
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
cell type: Human embryonic Kidney
genotype: WT
treatment: FUS siRNA
geo_loc_name: missing
collection_date: missing
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219257 18461582 1883081364 593.43 10249_sample8_r1.fq.gz, 10249_sample8_r2.fq.gz, SRR24219257, SRR24219… SRA
SRX20015719 SRP433437 RNA-Seq PAIRED
GSM7186924: ep MNP R1; Homo sapiens; RNA-Seq
Sample: SRS17357620
BioProject: PRJNA957458
BioSample: SAMN34254252
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: Motor neuron progenitors
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219256 63748286 6502325172 2062.44 10249_sample9_r1.fq.gz, 10249_sample9_r2.fq.gz, SRR24219256, SRR24219… SRA
SRX20015720 SRP433437 RNA-Seq PAIRED
GSM7186925: ep MNP R2; Homo sapiens; RNA-Seq
Sample: SRS17357624
BioProject: PRJNA957458
BioSample: SAMN34254251
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: Motor neuron progenitors
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219255 45733368 4664803536 1461.54 10249_sample10_r1.fq.gz, 10249_sample10_r2.fq.gz, SRR24219255, SRR242… SRA
SRX20015721 SRP433437 RNA-Seq PAIRED
GSM7186926: ep MN R1; Homo sapiens; RNA-Seq
Sample: SRS17357623
BioProject: PRJNA957458
BioSample: SAMN34254250
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: motor neurons
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219254 20936394 2135512188 675.57 10249_sample11_r1.fq.gz, 10249_sample11_r2.fq.gz, SRR24219254, SRR242… SRA
SRX20015722 SRP433437 RNA-Seq PAIRED
GSM7186927: ep MN R2; Homo sapiens; RNA-Seq
Sample: SRS17357625
BioProject: PRJNA957458
BioSample: SAMN34254249
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: motor neurons
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219253 17786869 1814260638 566.69 10249_sample12_r1.fq.gz, 10249_sample12_r2.fq.gz, SRR24219253, SRR242… SRA
SRX20015723 SRP433437 RNA-Seq PAIRED
GSM7186928: Input MNP R1; Homo sapiens; RNA-Seq
Sample: SRS17357626
BioProject: PRJNA957458
BioSample: SAMN34254248
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: Motor neuron progenitors
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219252 29435065 3002376630 946.74 10249_sample13_r1.fq.gz, 10249_sample13_r2.fq.gz, SRR24219252, SRR242… SRA
SRX20015724 SRP433437 RNA-Seq PAIRED
GSM7186929: Input MNP R2; Homo sapiens; RNA-Seq
Sample: SRS17357627
BioProject: PRJNA957458
BioSample: SAMN34254247
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: Motor neuron progenitors
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219251 33479906 3414950412 1069.37 10249_sample14_r1.fq.gz, 10249_sample14_r2.fq.gz, SRR24219251, SRR242… SRA
SRX20015725 SRP433437 RNA-Seq PAIRED
GSM7186930: Input MN R1; Homo sapiens; RNA-Seq
Sample: SRS17357628
BioProject: PRJNA957458
BioSample: SAMN34254246
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: motor neurons
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219250 19877566 2027511732 645.57 10249_sample15_r1.fq.gz, 10249_sample15_r2.fq.gz, SRR24219250, SRR242… SRA
SRX20015726 SRP433437 RNA-Seq PAIRED
GSM7186931: Input MN R2; Homo sapiens; RNA-Seq
Sample: SRS17357629
BioProject: PRJNA957458
BioSample: SAMN34254245
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-derived
cell line: iPSC-derived
cell type: motor neurons
genotype: WT
treatment: differentiation into motor neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
iPSC-derived
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR24219249 28669426 2924281452 923.75 10249_sample16_r1.fq.gz, 10249_sample16_r2.fq.gz, SRR24219249, SRR242… SRA

Linked Publications (1)

ePRINT: exonuclease assisted mapping of protein-RNA interactions.
Genome biology · 2024

Data Files (16)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 10249_sample10_r1.fq.gz RNA-Seq 1.4 GB link
— 10249_sample11_r1.fq.gz RNA-Seq 675.6 MB link
— 10249_sample12_r1.fq.gz RNA-Seq 566.7 MB link
— 10249_sample13_r1.fq.gz RNA-Seq 946.7 MB link
— 10249_sample14_r1.fq.gz RNA-Seq 1.0 GB link
— 10249_sample15_r1.fq.gz RNA-Seq 645.6 MB link
— 10249_sample16_r1.fq.gz RNA-Seq 923.8 MB link
— 10249_sample1_r1.fq.gz RNA-Seq 520.0 MB link
— 10249_sample2_r1.fq.gz RNA-Seq 623.8 MB link
— 10249_sample3_r1.fq.gz RNA-Seq 806.2 MB link
— 10249_sample4_r1.fq.gz RNA-Seq 1.1 GB link
— 10249_sample5_r1.fq.gz RNA-Seq 518.7 MB link
— 10249_sample6_r1.fq.gz RNA-Seq 812.1 MB link
— 10249_sample7_r1.fq.gz RNA-Seq 567.3 MB link
— 10249_sample8_r1.fq.gz RNA-Seq 593.4 MB link
— 10249_sample9_r1.fq.gz RNA-Seq 2.0 GB link