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GSE126337

GSE GEO
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Musashi-1 is a master regulator of aberrant translation in Group 3 medulloblastoma

Organism: Homo sapiens
Platform: GPL11154
Samples: 6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Feb 09 2019
Last Updated: Jan 03 2023
Status: Public on Feb 01 2020
Contact: Sheila,,Singh (McMaster University)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA521634 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP185353

Summary

Transcripts regulated by Musashi-1 (MSI1) are explored through shRNA-mediated knockdown of MSI1 in SU_MB002 medulloblastoma cells.

Overall Design

SU_MB002, a treatment refractory pediatric medulloblastoma cell line is transduced with either a scrambled control or shMsi1 knockdown construct. The changes in transcriptomic profile is identified through RNA-sequencing

Analysis (3 steps)

View Data Processing
Processing steps for GSE126337
  1. Reads were mapped to GRCh38 using STAR (v2.4.2a) and Gencode v25 gene annotations
  2. STAR --genomeDir /STARgenomes/hg38_Gencode25 --outFileNamePrefix $sampleName"_" --readFilesIn /path/to/read1 /path/to/read2 --readFilesCommand zcat --runThreadN 8 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --sjdbGTFfile /path/to/gencode.v25.annotation.gtf
  3. Read counts from STAR were merged along with gene annotations using bespoke R script

Supplementary Files (2)

GSE126337_MKamedaRNASeq_ReadCounts_updatedAnnot_hg38.txt.gz Download
GSE126337_RAW.tar Download
GEO Samples (6)
GSM3596797 GSM3596798 GSM3596799 GSM3596800 GSM3596801 GSM3596802

Dataset Citations (1)

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.
PMID 36473869 · 2022 · Nature communications
Michelle M Kameda-Smith, Helen Zhu, En-Ching Luo, Yujin Suk, Agata Xella, Brian Yee, Chirayu Chokshi, Sansi Xing, Frederick Tan, Raymond G Fox, Ashley A Adile, David Bakhshinyan, Kevin Brown, William D Gwynne, Minomi Subapanditha, Petar Miletic, Daniel Picard, Ian Burns, Jason Moffat, Kamil Paruch, Adam Fleming, Kristin Hope, John P Provias, Marc Remke, Yu Lu, Tannishtha Reya, Chitra Venugopal, Jüri Reimand, Robert J Wechsler-Reya, Gene W Yeo, Sheila K Singh

SRA Experiments (6) and Runs (6)

Total: 2335 MB
SRX5356954 SRP185353 RNA-Seq PAIRED
GSM3596797: Control replicate 1; Homo sapiens; RNA-Seq
Sample: SRS4347799
BioProject: PRJNA521634
BioSample: SAMN10907722
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SU_MB002 shControl
cell line: SU_MB002
cell line source: 3 year old male
cell type: Group 3 medulloblastoma
genotype/variation: shControl
Original files (1)
SU_MB002 shControl
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8555180 7717593 1173074136 541.25 MB002-03-5-1_S16_R1_001.fastq.gz, MB002-03-5-1_S16_R2_001.fastq.gz, S… SRA
SRX5356955 SRP185353 RNA-Seq PAIRED
GSM3596798: Control replicate 2; Homo sapiens; RNA-Seq
Sample: SRS4347800
BioProject: PRJNA521634
BioSample: SAMN10907721
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SU_MB002 shControl
cell line: SU_MB002
cell line source: 3 year old male
cell type: Group 3 medulloblastoma
genotype/variation: shControl
Original files (1)
SU_MB002 shControl
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8555181 6499606 987940112 459.54 MB002-03-5-2_S17_R1_001.fastq.gz, MB002-03-5-2_S17_R2_001.fastq.gz, S… SRA
SRX5356956 SRP185353 RNA-Seq PAIRED
GSM3596799: Control replicate 3; Homo sapiens; RNA-Seq
Sample: SRS4347801
BioProject: PRJNA521634
BioSample: SAMN10907720
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SU_MB002 shControl
cell line: SU_MB002
cell line source: 3 year old male
cell type: Group 3 medulloblastoma
genotype/variation: shControl
Original files (1)
SU_MB002 shControl
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8555182 4078033 619861016 285.9 MB002-03-5-3_S18_R1_001.fastq.gz, MB002-03-5-3_S18_R2_001.fastq.gz, S… SRA
SRX5356957 SRP185353 RNA-Seq PAIRED
GSM3596800: MSI1 shRNA replicate 1; Homo sapiens; RNA-Seq
Sample: SRS4347802
BioProject: PRJNA521634
BioSample: SAMN10907719
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SU_MB002 shMsi1
cell line: SU_MB002
cell line source: 3 year old male
cell type: Group 3 medulloblastoma
genotype/variation: MSI1 shRNA
Original files (1)
SU_MB002 shMsi1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8555183 5253682 798559664 384.68 MB002-shGFP-1_S19_R1_001.fastq.gz, MB002-shGFP-1_S19_R2_001.fastq.gz,… SRA
SRX5356958 SRP185353 RNA-Seq PAIRED
GSM3596801: MSI1 shRNA replicate 2; Homo sapiens; RNA-Seq
Sample: SRS4347803
BioProject: PRJNA521634
BioSample: SAMN10907718
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SU_MB002 shMsi1
cell line: SU_MB002
cell line source: 3 year old male
cell type: Group 3 medulloblastoma
genotype/variation: MSI1 shRNA
Original files (1)
SU_MB002 shMsi1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8555184 4779371 726464392 342.49 MB002-shGFP-2_S20_R1_001.fastq.gz, MB002-shGFP-2_S20_R2_001.fastq.gz,… SRA
SRX5356959 SRP185353 RNA-Seq PAIRED
GSM3596802: MSI1 shRNA replicate 3; Homo sapiens; RNA-Seq
Sample: SRS4347804
BioProject: PRJNA521634
BioSample: SAMN10907717
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: SU_MB002 shMsi1
cell line: SU_MB002
cell line source: 3 year old male
cell type: Group 3 medulloblastoma
genotype/variation: MSI1 shRNA
Original files (1)
SU_MB002 shMsi1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8555185 4511860 685802720 321.32 MB002-shGFP-3_S21_R1_001.fastq.gz, MB002-shGFP-3_S21_R2_001.fastq.gz,… SRA

Linked Publications (1)

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.
Nature communications · 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.

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.
Nature communications · 2022

Data Files (12)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— MB002-03-5-1_S16_R1_001.fastq.gz RNA-Seq 541.2 MB link
— MB002-03-5-2_S17_R1_001.fastq.gz RNA-Seq 459.5 MB link
— MB002-03-5-3_S18_R1_001.fastq.gz RNA-Seq 285.9 MB link
— MB002-shGFP-1_S19_R1_001.fastq.gz RNA-Seq 384.7 MB link
— MB002-shGFP-2_S20_R1_001.fastq.gz RNA-Seq 342.5 MB link
— MB002-shGFP-3_S21_R1_001.fastq.gz RNA-Seq 321.3 MB link
— SRR8555180_GSM3596797 RNA-Seq 541.0 MB link
— SRR8555181_GSM3596798 RNA-Seq 459.0 MB link
— SRR8555182_GSM3596799 RNA-Seq 285.0 MB link
— SRR8555183_GSM3596800 RNA-Seq 384.0 MB link
— SRR8555184_GSM3596801 RNA-Seq 342.0 MB link
— SRR8555185_GSM3596802 RNA-Seq 321.0 MB link