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GSE146014

GSE GEO
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DDX5 in colonic tumors

Organism: Mus musculus
Platform: GPL21103
Samples: 6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Feb 26 2020
Last Updated: Dec 03 2021
Status: Public on Dec 03 2021
Contact: Wendy,,Huang (University of California San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA608978 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP251151

Summary

The Asp-Glu-Ala-Asp (DEAD)-box RNA binding protein, DDX5, is ubiquitously expressed in many cell types, yet its role in RNA metabolism and its downstream function in vivo has not been fully elucidated. In the intestine, DDX5 is highly expressed in the intestinal epithelial cell (IECs) and contributes to tumorigenesis. Here, we used a conditional mouse lines where DDX5 is knocked out in IECs upon Tamoxifen administration to uncover mechanisms underlying DDX5 functions in colon tumors.

Overall Design

For tumor collection, 8 week old littermates were treated with Tamoxifen on day 1, 2, 3 and tumor tissues were harvested betwee day 30-37 post first Tamoxifen (TAM) administration.

Analysis (3 steps)

View Data Processing
Processing steps for GSE146014
  1. Sequenced reads were mapped to mm10 using STAR v2.6.1a with parameters "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
  2. Uniquely mapped reads overlapping with the exons were counted using featureCounts for each gene in GENCODE.vM19 annotation.
  3. Differential expression analysis were performed by DESeq2(v1.18.1) package

Supplementary Files (1)

GSE146014_tumor_colon.txt.gz Download
GEO Samples (6)
GSM3515098 GSM3515099 GSM3515100 GSM3515101 GSM3515102 GSM3515103

Dataset Citations (1)

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.
PMID 34853057 · 2022 · Gut
Tianyun Long, Nazia Abbasi, Juan E Hernandez, Yuxin Li, Ibrahim M Sayed, Shengyun Ma, Attilio Iemolo, Brian A Yee, Gene W Yeo, Francesca Telese, Pradipta Ghosh, Soumita Das, Wendy Jia Men Huang

SRA Experiments (6) and Runs (6)

Total: 11515 MB
SRX7824597 SRP251151 RNA-Seq PAIRED
GSM3515102: DDX5KO Tumor rep2; Mus musculus; RNA-Seq
Sample: SRS4146297
BioProject: PRJNA608978
BioSample: SAMN10595879
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Tumor Colon
genotype: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/fl)
tissue: Large intestine-colon
sample type: Tumor excision_day 33 post TAM
Original files (1)
Tumor Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11211658 25773413 5154682600 1951.61 1995_Tumor_S8_L004_R1_001.fastq, 1995_Tumor_S8_L004_R2_001.fastq, SRR… SRA
SRX7824598 SRP251151 RNA-Seq PAIRED
GSM3515103: DDX5KO Tumor rep3; Mus musculus; RNA-Seq
Sample: SRS4146298
BioProject: PRJNA608978
BioSample: SAMN10595878
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Tumor Colon
genotype: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/fl)
tissue: Large intestine-colon
sample type: Tumor excision_day 30 post TAM
Original files (1)
Tumor Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11211659 21893597 4378719400 1673.75 2072_Tumor_S10_L004_R1_001.fastq, 2072_Tumor_S10_L004_R2_001.fastq, S… SRA
SRX7824599 SRP251151 RNA-Seq PAIRED
GSM3515098: WT Tumor rep1; Mus musculus; RNA-Seq
Sample: SRS4146293
BioProject: PRJNA608978
BioSample: SAMN10595883
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Tumor Colon
genotype: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/+)
tissue: Large intestine-colon
sample type: Tumor excision_day 37 post TAM
Original files (1)
Tumor Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11211654 28403702 5680740400 2184.74 1555_Tumor_S5_L004_R1_001.fastq, 1555_Tumor_S5_L004_R2_001.fastq, SRR… SRA
SRX7824600 SRP251151 RNA-Seq PAIRED
GSM3515099: WT Tumor rep2; Mus musculus; RNA-Seq
Sample: SRS4146294
BioProject: PRJNA608978
BioSample: SAMN10595882
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Tumor Colon
genotype: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/+)
tissue: Large intestine-colon
sample type: Tumor excision_day 33 post TAM
Original files (1)
Tumor Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11211655 22384214 4476842800 1637.12 1998_Tumor_S7_L004_R1_001.fastq, 1998_Tumor_S7_L004_R2_001.fastq, SRR… SRA
SRX7824601 SRP251151 RNA-Seq PAIRED
GSM3515100: WT Tumor rep3; Mus musculus; RNA-Seq
Sample: SRS4146295
BioProject: PRJNA608978
BioSample: SAMN10595881
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Tumor Colon
genotype: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/+)
tissue: Large intestine-colon
sample type: Tumor excision_day 30 post TAM
Original files (1)
Tumor Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11211656 25893615 5178723000 2040.84 2070_Tumor_S9_L004_R1_001.fastq, 2070_Tumor_S9_L004_R2_001.fastq, SRR… SRA
SRX7824602 SRP251151 RNA-Seq PAIRED
GSM3515101: DDX5KO Tumor rep1; Mus musculus; RNA-Seq
Sample: SRS4146296
BioProject: PRJNA608978
BioSample: SAMN10595880
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Tumor Colon
genotype: APC(fl/fl), Cdx2Cre-ERT2(+), DDX5(fl/fl)
tissue: Large intestine-colon
sample type: Tumor excision_day 37 post TAM
Original files (1)
Tumor Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11211657 26854506 5370901200 2026.92 1553_Tumor_S6_L004_R1_001.fastq, 1553_Tumor_S6_L004_R2_001.fastq, SRR… SRA

Linked Publications (1)

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.
Gut · 2022

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 1553_Tumor_S6_L004_R1_001.fastq RNA-Seq 2.0 GB link
— 1555_Tumor_S5_L004_R1_001.fastq RNA-Seq 2.1 GB link
— 1995_Tumor_S8_L004_R1_001.fastq RNA-Seq 1.9 GB link
— 1998_Tumor_S7_L004_R1_001.fastq RNA-Seq 1.6 GB link
— 2070_Tumor_S9_L004_R1_001.fastq RNA-Seq 2.0 GB link
— 2072_Tumor_S10_L004_R1_001.fastq RNA-Seq 1.6 GB link
— SRR11211654.lite RNA-Seq 2.1 GB link
— SRR11211656.lite RNA-Seq 2.0 GB link