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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 (2)

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

Data Files (6)

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