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GSE123881

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DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis

Organism: Mus musculus
Platform: GPL21103
Samples: 8
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Dec 14 2018
Last Updated: Nov 13 2020
Status: Public on Aug 14 2020
Contact: Wendy,,Huang (University of California San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA510109 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP173481

Summary

Tumorigenesis in different segments of the intestinal tract involves tissue-specific oncogenic drivers. In the colon, complement component 3 (C3) activation is a major contributor to inflammation and malignancies. By contrast, tumorigenesis in the small intestine involves fatty acid–binding protein 1. However, little is known of the upstream mechanisms driving their expressions in different segments of the intestinal tract. Here, we report that the RNA-binding protein DDX5 binds to the mRNA transcripts of C3 and fatty acid–binding protein 1 to augment their expressions posttranscriptionally. Knocking out DDX5 in epithelial cells protected mice from intestinal tumorigenesis and dextran sodium sulfate–induced col- itis. Identification of DDX5 as a common upstream regulator of tissue-specific oncogenic molecules provides an excellent therapeutic target for intestinal diseases.

Overall Design

For steady state experiment, 8 week old littermates in wildtype or knockout genetic background were used for tissue harvest.

Analysis (3 steps)

View Data Processing
Processing steps for GSE123881
  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 (2)

GSE123881_healthy_Ileum.txt.gz Download
GSE123881_healthy_colon.txt.gz Download
GEO Samples (8)
GSM3515090 GSM3515091 GSM3515092 GSM3515093 GSM3515094 GSM3515095 GSM3515096 GSM3515097

Dataset Citations (1)

DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis.
PMID 32817263 · 2020 · Life science alliance
Nazia Abbasi, Tianyun Long, Yuxin Li, Brian A Yee, Benjamin S Cho, Juan E Hernandez, Evelyn Ma, Parth R Patel, Debashis Sahoo, Ibrahim M Sayed, Nissi Varki, Soumita Das, Pradipta Ghosh, Gene W Yeo, Wendy Jia Men Huang

SRA Experiments (8) and Runs (8)

Total: 22980 MB
SRX5133387 SRP173481 RNA-Seq PAIRED
GSM3515090: WT Ileum rep1; Mus musculus; RNA-Seq
Sample: SRS4146285
BioProject: PRJNA510109
BioSample: SAMN10595892
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Ileum
genotype: DDX5(+/+), Vil1Cre(+)
tissue: Small intestine_Ileum
sample type: EDTA fractionation
Original files (1)
Healthy Ileum
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320977 46461255 9292251000 3823.38 NA01_S1_L008_R1_001.fastq.gz, NA01_S1_L008_R2_001.fastq.gz, SRR832097… SRA
SRX5133388 SRP173481 RNA-Seq PAIRED
GSM3515091: WT Ileum rep2; Mus musculus; RNA-Seq
Sample: SRS4146286
BioProject: PRJNA510109
BioSample: SAMN10595891
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Ileum
genotype: DDX5(+/+), Vil1Cre(+)
tissue: Small intestine_Ileum
sample type: EDTA fractionation
Original files (1)
Healthy Ileum
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320978 29799020 5959804000 2413.47 NA03_S3_L008_R1_001.fastq.gz, NA03_S3_L008_R2_001.fastq.gz, SRR832097… SRA
SRX5133389 SRP173481 RNA-Seq PAIRED
GSM3515092: DDX5KO Ileum rep1; Mus musculus; RNA-Seq
Sample: SRS4146287
BioProject: PRJNA510109
BioSample: SAMN10595890
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Ileum
genotype: DDX5(fl/fl), Vil1Cre(+)
tissue: Small intestine_Ileum
sample type: EDTA fractionation
Original files (1)
Healthy Ileum
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320979 20877077 4175415400 1718.85 NA02_S2_L008_R1_001.fastq.gz, NA02_S2_L008_R2_001.fastq.gz, SRR832097… SRA
SRX5133390 SRP173481 RNA-Seq PAIRED
GSM3515093: DDX5KO Ileum rep2; Mus musculus; RNA-Seq
Sample: SRS4146288
BioProject: PRJNA510109
BioSample: SAMN10595889
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Ileum
genotype: DDX5(fl/fl), Vil1Cre(+)
tissue: Small intestine_Ileum
sample type: EDTA fractionation
Original files (1)
Healthy Ileum
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320980 34688172 6937634400 2845.5 NA04_S4_L008_R1_001.fastq.gz, NA04_S4_L008_R2_001.fastq.gz, SRR832098… SRA
SRX5133391 SRP173481 RNA-Seq PAIRED
GSM3515094: WT Colon rep1; Mus musculus; RNA-Seq
Sample: SRS4146289
BioProject: PRJNA510109
BioSample: SAMN10595888
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Colon
genotype: DDX5(+/+), Vil1Cre(+)
tissue: Large intestine-colon
sample type: EDTA fractionation
Original files (1)
Healthy Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320981 34622853 6924570600 2851.13 NA05_S5_L008_R1_001.fastq.gz, NA05_S5_L008_R2_001.fastq.gz, SRR832098… SRA
SRX5133392 SRP173481 RNA-Seq PAIRED
GSM3515095: WT Colon rep2; Mus musculus; RNA-Seq
Sample: SRS4146290
BioProject: PRJNA510109
BioSample: SAMN10595887
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Colon
genotype: DDX5(+/+), Vil1Cre(+)
tissue: Large intestine-colon
sample type: EDTA fractionation
Original files (1)
Healthy Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320982 39846955 7969391000 3321.86 NA07_S7_L008_R1_001.fastq.gz, NA07_S7_L008_R2_001.fastq.gz, SRR832098… SRA
SRX5133393 SRP173481 RNA-Seq PAIRED
GSM3515096: DDX5KO Colon rep1; Mus musculus; RNA-Seq
Sample: SRS4146291
BioProject: PRJNA510109
BioSample: SAMN10595886
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Colon
genotype: DDX5(fl/fl), Vil1Cre(+)
tissue: Large intestine-colon
sample type: EDTA fractionation
Original files (1)
Healthy Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320983 36294699 7258939800 3051.35 NA06_S6_L008_R1_001.fastq.gz, NA06_S6_L008_R2_001.fastq.gz, SRR832098… SRA
SRX5133394 SRP173481 RNA-Seq PAIRED
GSM3515097: DDX5KO Colon rep2; Mus musculus; RNA-Seq
Sample: SRS4146292
BioProject: PRJNA510109
BioSample: SAMN10595885
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Healthy Colon
genotype: DDX5(fl/fl), Vil1Cre(+)
tissue: Large intestine-colon
sample type: EDTA fractionation
Original files (1)
Healthy Colon
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8320984 35608496 7121699200 2954.42 NA08_S8_L008_R1_001.fastq.gz, NA08_S8_L008_R2_001.fastq.gz, SRR832098… SRA

Linked Publications (2)

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.
Gut · 2022
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis.
Life science alliance · 2020

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— NA01_S1_L008_R1_001.fastq.gz RNA-Seq 3.7 GB link
— NA02_S2_L008_R1_001.fastq.gz RNA-Seq 1.7 GB link
— NA03_S3_L008_R1_001.fastq.gz RNA-Seq 2.4 GB link
— NA04_S4_L008_R1_001.fastq.gz RNA-Seq 2.8 GB link
— NA05_S5_L008_R1_001.fastq.gz RNA-Seq 2.8 GB link
— NA06_S6_L008_R1_001.fastq.gz RNA-Seq 3.0 GB link
— NA07_S7_L008_R1_001.fastq.gz RNA-Seq 3.2 GB link
— NA08_S8_L008_R1_001.fastq.gz RNA-Seq 2.9 GB link