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GSE164666

GSE GEO
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Integrative RNA-omics discovers GNAS alternative splicing as a phenotypic driver of splicing factor mutant neoplasms

Organism: Homo sapiens
Platform: GPL20301
Samples: 29
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Jan 12 2021
Last Updated: Dec 29 2021
Status: Public on Sep 17 2021
Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA691525 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP301413

Summary

Mutations in splicing factors (SFs) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of mis-splicing by mutant U2AF1 and SRSF2, we performed RNA-Seq and eCLIP in human hematopoietic stem/progenitor cells (HSPCs) derived from isogenic induced pluripotent stem cell (iPSC) models. Integrative analyses of alternative splicing and differential binding converged on a long isoform of GNAS (GNAS-L), promoted by both mutant factors. MDS population genetics, functional and biochemical analyses support that GNAS-L is a driver of MDS and encodes a hyperactive long form of the stimulatory G protein alpha subunit, Gas-L, that activates ERK/MAPK signaling. SF-mutant MDS cells have activated ERK signaling and consequently are sensitive to MEK inhibitors. Our findings highlight an unexpected and unifying mechanism by which SF mutations drive oncogenesis with potential therapeutic implications for MDS and other SF-mutant neoplasms.

Overall Design

Isogenic iPSCs derived with CRISPR genome editing to insert heterozygous point mutations in SRSF2 and U2AF1 and insertion of a FLAG tag a the endogeneous were differentiated into heatopoietic stem and progenitor cells (HSPCs). eCLIP-Seq of each splicing factor and RNA-Seq were performed on the HSPCs.

Analysis (4 steps)

View Data Processing
Processing steps for GSE164666
  1. Library strategy: eCLIP-Seq
  2. For eCLIP-seq, and RNA-seq, raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
  3. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences.
  4. Remaining reads were mapped to the appropriate genome build using STAR aligner. eCLIP peaks were called with CLIPPER and normalized to size-matched input sample

Supplementary Files (2)

GSE164666_RAW.tar Download
GSE164666_counts_matrix.csv.gz Download
GEO Samples (29)
GSM5016575 GSM5016576 GSM5016577 GSM5016578 GSM5016579 GSM5016580 GSM5016581 GSM5016582 GSM5016583 GSM5016584 GSM5016585 GSM5016586 GSM5016587 GSM5016588 GSM5016589 GSM5016590 GSM5016591 GSM5016592 GSM5016593 GSM5016594 GSM5016595 GSM5016596 GSM5016597 GSM5016598 GSM5016599 GSM5016600 GSM5016601 GSM5016602 GSM5016603

Dataset Citations (1)

Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.
PMID 34620690 · 2022 · Cancer discovery
Emily C Wheeler, Shailee Vora, Daniel Mayer, Andriana G Kotini, Malgorzata Olszewska, Samuel S Park, Ernesto Guccione, Julie Teruya-Feldstein, Lewis Silverman, Roger K Sunahara, Gene W Yeo, Eirini P Papapetrou

SRA Experiments (29) and Runs (29)

Total: 67220 MB
SRX9832975 SRP301413 OTHER SINGLE
GSM5016575: U2AF1_hpc.WT-1_INPUT; Homo sapiens; OTHER
Sample: SRS8015358
BioProject: PRJNA691525
BioSample: SAMN17294103
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416253 43567149 3267536175 1213.76 U2AF1_hpc.WT-1_INPUT_R1_001.fastq.gz, SRR13416253, SRR13416253.lite SRA
SRX9832976 SRP301413 OTHER SINGLE
GSM5016576: U2AF1_hpc.WT-1_IP; Homo sapiens; OTHER
Sample: SRS8015359
BioProject: PRJNA691525
BioSample: SAMN17294102
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416254 55617614 4171321050 1528.66 U2AF1_hpc.WT-1_IP_R1_001.fastq.gz, SRR13416254, SRR13416254.lite SRA
SRX9832977 SRP301413 OTHER SINGLE
GSM5016577: U2AF1_hpc.WT-2_INPUT; Homo sapiens; OTHER
Sample: SRS8015361
BioProject: PRJNA691525
BioSample: SAMN17294101
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416255 45664741 3424855575 1274.28 U2AF1_hpc.WT-2_INPUT_R1_001.fastq.gz, SRR13416255, SRR13416255.lite SRA
SRX9832978 SRP301413 OTHER SINGLE
GSM5016578: U2AF1_hpc.WT-2_IP; Homo sapiens; OTHER
Sample: SRS8015360
BioProject: PRJNA691525
BioSample: SAMN17294100
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416256 50201232 3765092400 1390.06 U2AF1_hpc.WT-2_IP_R1_001.fastq.gz, SRR13416256, SRR13416256.lite SRA
SRX9832979 SRP301413 OTHER SINGLE
GSM5016579: U2AF1_hpc.S34F-1_INPUT; Homo sapiens; OTHER
Sample: SRS8015362
BioProject: PRJNA691525
BioSample: SAMN17294099
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416257 46300646 3472548450 1306.25 U2AF1_hpc.S34F-1_INPUT_R1_001.fastq.gz, SRR13416257, SRR13416257.lite SRA
SRX9832980 SRP301413 OTHER SINGLE
GSM5016580: U2AF1_hpc.S34F-1_IP; Homo sapiens; OTHER
Sample: SRS8015364
BioProject: PRJNA691525
BioSample: SAMN17294098
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416258 71936044 5395203300 2010.47 U2AF1_hpc.S34F-1_IP_R1_001.fastq.gz, SRR13416258, SRR13416258.lite SRA
SRX9832981 SRP301413 OTHER SINGLE
GSM5016581: U2AF1_hpc.S34F-2_INPUT; Homo sapiens; OTHER
Sample: SRS8015363
BioProject: PRJNA691525
BioSample: SAMN17294097
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416259 52081468 3906110100 1451.64 U2AF1_hpc.S34F-2_INPUT_R1_001.fastq.gz, SRR13416259, SRR13416259.lite SRA
SRX9832982 SRP301413 OTHER SINGLE
GSM5016582: U2AF1_hpc.S34F-2_IP; Homo sapiens; OTHER
Sample: SRS8015365
BioProject: PRJNA691525
BioSample: SAMN17294096
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416260 42188436 3164132700 1182.2 U2AF1_hpc.S34F-2_IP_R1_001.fastq.gz, SRR13416260, SRR13416260.lite SRA
SRX9832983 SRP301413 OTHER SINGLE
GSM5016583: SRSF2_hpc.WT-1_INPUT; Homo sapiens; OTHER
Sample: SRS8015366
BioProject: PRJNA691525
BioSample: SAMN17294095
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416261 32813897 2461042275 912.16 SRSF2_hpc.WT-1_INPUT_R1_001.fastq.gz, SRR13416261, SRR13416261.lite SRA
SRX9832984 SRP301413 OTHER SINGLE
GSM5016584: SRSF2_hpc.WT-1_IP; Homo sapiens; OTHER
Sample: SRS8015367
BioProject: PRJNA691525
BioSample: SAMN17294094
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416262 26729185 2004688875 741.64 SRSF2_hpc.WT-1_IP_R1_001.fastq.gz, SRR13416262, SRR13416262.lite SRA
SRX9832985 SRP301413 OTHER SINGLE
GSM5016585: SRSF2_hpc.WT-2_INPUT; Homo sapiens; OTHER
Sample: SRS8015369
BioProject: PRJNA691525
BioSample: SAMN17294093
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416263 27249632 2043722400 760.0 SRSF2_hpc.WT-2_INPUT_R1_001.fastq.gz, SRR13416263, SRR13416263.lite SRA
SRX9832986 SRP301413 OTHER SINGLE
GSM5016586: SRSF2_hpc.WT-2_IP; Homo sapiens; OTHER
Sample: SRS8015368
BioProject: PRJNA691525
BioSample: SAMN17294092
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416264 26447082 1983531150 744.39 SRSF2_hpc.WT-2_IP_R1_001.fastq.gz, SRR13416264, SRR13416264.lite SRA
SRX9832987 SRP301413 OTHER SINGLE
GSM5016587: SRSF2_hpc.P95L-1_INPUT; Homo sapiens; OTHER
Sample: SRS8015371
BioProject: PRJNA691525
BioSample: SAMN17294091
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416265 23610742 1770805650 658.91 SRSF2_hpc.P95L-1_INPUT_R1_001.fastq.gz, SRR13416265, SRR13416265.lite SRA
SRX9832988 SRP301413 OTHER SINGLE
GSM5016588: SRSF2_hpc.P95L-1_IP; Homo sapiens; OTHER
Sample: SRS8015370
BioProject: PRJNA691525
BioSample: SAMN17294090
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416266 33347619 2501071425 945.72 SRSF2_hpc.P95L-1_IP_R1_001.fastq.gz, SRR13416266, SRR13416266.lite SRA
SRX9832989 SRP301413 OTHER SINGLE
GSM5016589: SRSF2_hpc.P95L-2_INPUT; Homo sapiens; OTHER
Sample: SRS8015372
BioProject: PRJNA691525
BioSample: SAMN17294089
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: none (input)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416267 30632498 2297437350 853.65 SRSF2_hpc.P95L-2_INPUT_R1_001.fastq.gz, SRR13416267, SRR13416267.lite SRA
SRX9832990 SRP301413 OTHER SINGLE
GSM5016590: SRSF2_hpc.P95L-2_IP; Homo sapiens; OTHER
Sample: SRS8015373
BioProject: PRJNA691525
BioSample: SAMN17294088
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
antibody: anti-FLAG (Sigma F1804)
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416268 33476673 2510750475 932.7 SRSF2_hpc.P95L-2_IP_R1_001.fastq.gz, SRR13416268, SRR13416268.lite SRA
SRX9832991 SRP301413 RNA-Seq PAIRED
GSM5016591: WT-1-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015374
BioProject: PRJNA691525
BioSample: SAMN17294087
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: WT
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416240 48377851 9675570200 3737.15 WT-1-rnaseq_R1.fastq.gz, WT-1-rnaseq_R2.fastq.gz, SRR13416240, SRR134… SRA
SRX9832992 SRP301413 RNA-Seq PAIRED
GSM5016592: WT-2-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015375
BioProject: PRJNA691525
BioSample: SAMN17294086
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: WT
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416241 45320732 9064146400 3507.73 WT-2-rnaseq_R1.fastq.gz, WT-2-rnaseq_R2.fastq.gz, SRR13416241, SRR134… SRA
SRX9832993 SRP301413 RNA-Seq PAIRED
GSM5016593: WT-3-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015376
BioProject: PRJNA691525
BioSample: SAMN17294085
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: WT
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416242 48792366 9758473200 3770.52 WT-3-rnaseq_R1.fastq.gz, WT-3-rnaseq_R2.fastq.gz, SRR13416242, SRR134… SRA
SRX9832994 SRP301413 RNA-Seq PAIRED
GSM5016594: WT-4-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015378
BioProject: PRJNA691525
BioSample: SAMN17294084
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: WT
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416243 53466686 10693337200 4170.68 WT-4-rnaseq_R1.fastq.gz, WT-4-rnaseq_R2.fastq.gz, SRR13416243, SRR134… SRA
SRX9832995 SRP301413 RNA-Seq PAIRED
GSM5016595: WT-5-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015377
BioProject: PRJNA691525
BioSample: SAMN17294083
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: WT
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416244 46400467 9280093400 3547.3 WT-5-rnaseq_R1.fastq.gz, WT-5-rnaseq_R2.fastq.gz, SRR13416244, SRR134… SRA
SRX9832996 SRP301413 RNA-Seq PAIRED
GSM5016596: WT-6-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015379
BioProject: PRJNA691525
BioSample: SAMN17294082
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: WT
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416245 53414879 10682975800 4053.73 WT-6-rnaseq_R1.fastq.gz, WT-6-rnaseq_R2.fastq.gz, SRR13416245, SRR134… SRA
SRX9832997 SRP301413 RNA-Seq PAIRED
GSM5016597: U2AF1-S34F-1-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015380
BioProject: PRJNA691525
BioSample: SAMN17294081
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416246 59113595 11822719000 4596.1 U2AF1-S34F-1-rnaseq_R1.fastq.gz, U2AF1-S34F-1-rnaseq_R2.fastq.gz, SRR… SRA
SRX9832998 SRP301413 RNA-Seq PAIRED
GSM5016598: U2AF1-S34F-2-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015381
BioProject: PRJNA691525
BioSample: SAMN17294080
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416247 50449645 10089929000 3811.5 U2AF1-S34F-2-rnaseq_R1.fastq.gz, U2AF1-S34F-2-rnaseq_R2.fastq.gz, SRR… SRA
SRX9832999 SRP301413 RNA-Seq PAIRED
GSM5016599: U2AF1-S34F-3-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015382
BioProject: PRJNA691525
BioSample: SAMN17294107
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: U2AF1 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416248 42477337 8495467400 3572.8 U2AF1-S34F-3-rnaseq_R1.fastq.gz, U2AF1-S34F-3-rnaseq_R2.fastq.gz, SRR… SRA
SRX9833000 SRP301413 RNA-Seq PAIRED
GSM5016600: SRSF2-P95L-1-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015383
BioProject: PRJNA691525
BioSample: SAMN17294076
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416249 50152975 10030595000 3887.73 SRSF2-P95L-1-rnaseq_R1.fastq.gz, SRSF2-P95L-1-rnaseq_R2.fastq.gz, SRR… SRA
SRX9833001 SRP301413 RNA-Seq PAIRED
GSM5016601: SRSF2-P95L-2-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015384
BioProject: PRJNA691525
BioSample: SAMN17294079
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416250 37660061 7532012200 3114.62 SRSF2-P95L-2-rnaseq_R1.fastq.gz, SRSF2-P95L-2-rnaseq_R2.fastq.gz, SRR… SRA
SRX9833002 SRP301413 RNA-Seq PAIRED
GSM5016602: SRSF2-P95L-3-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015386
BioProject: PRJNA691525
BioSample: SAMN17294078
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416251 52186103 10437220600 4003.21 SRSF2-P95L-3-rnaseq_R1.fastq.gz, SRSF2-P95L-3-rnaseq_R2.fastq.gz, SRR… SRA
SRX9833003 SRP301413 RNA-Seq PAIRED
GSM5016603: SRSF2-P95L-4-rnaseq_R1; Homo sapiens; RNA-Seq
Sample: SRS8015385
BioProject: PRJNA691525
BioSample: SAMN17294077
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPSC-HSPCs
genotype: SRSF2 mutation
cell type: iPSC-HSPCs
cell culture: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)
selection: CD34+/CD45+
day of differentiation: 11 - 13
Original files (1)
iPSC-HSPCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13416252 46183888 9236777600 3540.58 SRSF2-P95L-4-rnaseq_R1.fastq.gz, SRSF2-P95L-4-rnaseq_R2.fastq.gz, SRR… SRA

Linked Publications (1)

Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.
Cancer discovery · 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.

Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.
Cancer discovery · 2022

Data Files (60)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— SRR13416253_GSM5016575 OTHER 1.2 GB link
— SRR13416254_GSM5016576 OTHER 1.5 GB link
— SRR13416255_GSM5016577 OTHER 1.2 GB link
— SRR13416256_GSM5016578 OTHER 1.4 GB link
— SRR13416257_GSM5016579 OTHER 1.3 GB link
— SRR13416258_GSM5016580 OTHER 2.0 GB link
— SRR13416259_GSM5016581 OTHER 1.4 GB link
— SRR13416260_GSM5016582 OTHER 1.2 GB link
— SRR13416261_GSM5016583 OTHER 912.0 MB link
— SRR13416262_GSM5016584 OTHER 741.0 MB link
— SRR13416263_GSM5016585 OTHER 760.0 MB link
— SRR13416264_GSM5016586 OTHER 744.0 MB link
— SRR13416265_GSM5016587 OTHER 658.0 MB link
— SRR13416266_GSM5016588 OTHER 945.0 MB link
— SRR13416267_GSM5016589 OTHER 853.0 MB link
— SRR13416268_GSM5016590 OTHER 932.0 MB link
— SRSF2_hpc.P95L-1_INPUT_R1_001.fastq.gz OTHER 658.9 MB link
— SRSF2_hpc.P95L-1_IP_R1_001.fastq.gz OTHER 945.7 MB link
— SRSF2_hpc.P95L-2_INPUT_R1_001.fastq.gz OTHER 853.6 MB link
— SRSF2_hpc.P95L-2_IP_R1_001.fastq.gz OTHER 932.7 MB link
— SRSF2_hpc.WT-1_INPUT_R1_001.fastq.gz OTHER 912.2 MB link
— SRSF2_hpc.WT-1_IP_R1_001.fastq.gz OTHER 741.6 MB link
— SRSF2_hpc.WT-2_INPUT_R1_001.fastq.gz OTHER 760.0 MB link
— SRSF2_hpc.WT-2_IP_R1_001.fastq.gz OTHER 744.4 MB link
— U2AF1_hpc.S34F-1_INPUT_R1_001.fastq.gz OTHER 1.3 GB link
— U2AF1_hpc.S34F-1_IP_R1_001.fastq.gz OTHER 2.0 GB link
— U2AF1_hpc.S34F-2_INPUT_R1_001.fastq.gz OTHER 1.4 GB link
— U2AF1_hpc.S34F-2_IP_R1_001.fastq.gz OTHER 1.2 GB link
— U2AF1_hpc.WT-1_INPUT_R1_001.fastq.gz OTHER 1.2 GB link
— U2AF1_hpc.WT-1_IP_R1_001.fastq.gz OTHER 1.5 GB link
— U2AF1_hpc.WT-2_INPUT_R1_001.fastq.gz OTHER 1.2 GB link
— U2AF1_hpc.WT-2_IP_R1_001.fastq.gz OTHER 1.4 GB link
— SRR13416240_GSM5016591 RNA-Seq 3.6 GB link
— SRR13416241_GSM5016592 RNA-Seq 3.4 GB link
— SRR13416241.lite RNA-Seq 3.4 GB link
— SRR13416242_GSM5016593 RNA-Seq 3.7 GB link
— SRR13416243_GSM5016594 RNA-Seq 4.1 GB link
— SRR13416244_GSM5016595 RNA-Seq 3.5 GB link
— SRR13416245_GSM5016596 RNA-Seq 4.0 GB link
— SRR13416246_GSM5016597 RNA-Seq 4.5 GB link
— SRR13416247_GSM5016598 RNA-Seq 3.7 GB link
— SRR13416248_GSM5016599 RNA-Seq 3.5 GB link
— SRR13416249_GSM5016600 RNA-Seq 3.8 GB link
— SRR13416250_GSM5016601 RNA-Seq 3.0 GB link
— SRR13416251_GSM5016602 RNA-Seq 3.9 GB link
— SRR13416252_GSM5016603 RNA-Seq 3.5 GB link
— SRSF2-P95L-1-rnaseq_R1.fastq.gz RNA-Seq 3.8 GB link
— SRSF2-P95L-2-rnaseq_R1.fastq.gz RNA-Seq 3.0 GB link
— SRSF2-P95L-3-rnaseq_R1.fastq.gz RNA-Seq 3.9 GB link
— SRSF2-P95L-4-rnaseq_R1.fastq.gz RNA-Seq 3.5 GB link
— U2AF1-S34F-1-rnaseq_R1.fastq.gz RNA-Seq 4.5 GB link
— U2AF1-S34F-2-rnaseq_R1.fastq.gz RNA-Seq 3.7 GB link
— U2AF1-S34F-3-rnaseq_R1.fastq.gz RNA-Seq 3.5 GB link
— WT-1-rnaseq_R1.fastq.gz RNA-Seq 3.6 GB link
— WT-2-rnaseq_R1.fastq.gz RNA-Seq 3.4 GB link
— WT-3-rnaseq_R1.fastq.gz RNA-Seq 3.7 GB link
— WT-4-rnaseq_R1.fastq.gz RNA-Seq 4.1 GB link
— WT-5-rnaseq_R1.fastq.gz RNA-Seq 3.5 GB link
— WT-6-rnaseq_R1.fastq.gz RNA-Seq 4.0 GB link
— WT-6-rnaseq_R2.fastq.gz RNA-Seq 4.0 GB link