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GSE124023

GSE GEO
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DDX5 targets tissue specific RNAs to promote intestine tumorigenesis

Organism: Mus musculus
Platform: GPL21103
Samples: 8
Experiment Types:
Other
Submitted: Dec 18 2018
Last Updated: Aug 23 2020
Status: Public on Aug 12 2020
Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA510585 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP173797

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 (FABP1). However, little is known of the upstream mechanisms driving their expressions in different segments of the intestinal tract. Here, we report that an RNA binding protein DDX5 augments C3 and FABP1 expressions post-transcriptionally to promote tumorigenesis in the colon and small intestine, respectively. Mice with epithelial-specific knockout of DDX5 are protected from intestine tumorigenesis. The identification of DDX5 as the common upstream regulator of tissue-specific oncogenic molecules provides a new therapeutic target for intestine cancers.

Overall Design

Primary small intestine epithelial cells and Th17 cells were harvested, crosslinked with UV, lysed and immunoprecipitated to enrich for RNA fragments bound to DDX5-containing protein complexes. Primary small intestine of 8wk adult female mice and colon epithelial cells from 120 days old Apcfl/+ CDX2Cre mice were harvested, crosslinked with UV, lysed and immunoprecipitated to enrich for RNA fragments bound to DDX5-containing protein complexes.

Analysis (22 steps)

View Data Processing
Processing steps for GSE124023
  1. Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1).
  2. Args: --length 10
  3. Reads were then trimmed with cutadapt (1.9.1).
  4. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
  5. Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events.
  6. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
  7. Trimmed reads were then mapped with STAR (2.4.0i) against a mouse-specific repeat element database (RepBase 18.05).
  8. Args: --runThreadN 16 \ --genomeDir mouse_repbase \ --readFilesIn path/to/read1 path/to/read2 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd
Showing first 8 steps.

Supplementary Files (3)

GSE124023_DDX5.IDR_reproducible_peaks.txt.gz Download
GSE124023_GT_G.IDR_reproducible_peaks.txt.gz Download
GSE124023_RAW.tar Download
GEO Samples (8)
GSM4491125 GSM4491126 GSM4491127 GSM4491128 GSM4491238 GSM4491239 GSM4491240 GSM4491241

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 (12)

Total: 10654 MB
SRX8157840 SRP173797 RIP-Seq PAIRED
GSM4491125: WT G, CLIP rep1; Mus musculus; RIP-Seq
Sample: SRS6519850
BioProject: PRJNA510585
BioSample: SAMN14671211
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Small intestine epithelium
rip antibody: DDX5 (Abcam, catalog# ab53216)
genotype: wild type
strain: C57BL/6
cell type: Small intestine
sample type: EDTA fractionation
Original files (1)
Small intestine epithelium
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11590535 38227477 4205022470 1497.63 IP_G1_S37_L003_R1_001.fastq, IP_G1_S37_L003_R2_001.fastq, SRR11590535… SRA
SRX8157841 SRP173797 RIP-Seq PAIRED
GSM4491126: WT G, Input rep1; Mus musculus; RIP-Seq
Sample: SRS6519851
BioProject: PRJNA510585
BioSample: SAMN14671210
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Small intestine epithelium
rip antibody: none
genotype: wild type
strain: C57BL/6
cell type: Small intestine
sample type: EDTA fractionation
Original files (1)
Small intestine epithelium
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11590536 39835089 4381859790 1563.64 INPUT_G1_S36_L003_R1_001.fastq, INPUT_G1_S36_L003_R2_001.fastq, SRR11… SRA
SRX8157842 SRP173797 RIP-Seq PAIRED
GSM4491127: WT G, CLIP rep2; Mus musculus; RIP-Seq
Sample: SRS6519855
BioProject: PRJNA510585
BioSample: SAMN14671209
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Small intestine epithelium
rip antibody: DDX5 (Abcam, catalog# ab53216)
genotype: wild type
strain: C57BL/6
cell type: Small intestine
sample type: EDTA fractionation
Original files (1)
Small intestine epithelium
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11590537 18779810 2065779100 736.25 IP_G2_S39_L003_R1_001.fastq, IP_G2_S39_L003_R2_001.fastq, SRR11590537… SRA
SRX8157843 SRP173797 RIP-Seq PAIRED
GSM4491128: WT G, Input rep2; Mus musculus; RIP-Seq
Sample: SRS6519852
BioProject: PRJNA510585
BioSample: SAMN14671208
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Small intestine epithelium
rip antibody: none
genotype: wild type
strain: C57BL/6
cell type: Small intestine
sample type: EDTA fractionation
Original files (1)
Small intestine epithelium
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11590538 52921117 5821322870 2070.89 INPUT_G2_S38_L003_R1_001.fastq, INPUT_G2_S38_L003_R2_001.fastq, SRR11… SRA
SRX8158035 SRP173797 RIP-Seq SINGLE
GSM4491238: mAb EP CLIP; Mus musculus; RIP-Seq
Sample: SRS6519998
BioProject: PRJNA510585
BioSample: SAMN14671400
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Colon epithelium
strain: C57BL/6
tissue: Colon
sample type: EDTA fractionation
genotype: wild type
rip antibody: DDX5 (Abcam, catalog# ab53216)
Original files (1)
Colon epithelium
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11591014 26890852 2043704752 746.67 mAb_IP_1_Ep_S36_L003_R1_001.fastq.gz, SRR11591014, SRR11591014.lite SRA
SRR11591015 19338248 1469706848 533.22 mAb_IP_2_Ep_S38_L003_R1_001.fastq.gz, SRR11591015, SRR11591015.lite SRA
SRX8158036 SRP173797 RIP-Seq SINGLE
GSM4491239: mAb EP size-matched input; Mus musculus; RIP-Seq
Sample: SRS6519999
BioProject: PRJNA510585
BioSample: SAMN14671399
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Colon epithelium
strain: C57BL/6
tissue: Colon
sample type: EDTA fractionation
genotype: wild type
rip antibody: none
Original files (1)
Colon epithelium
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11591016 19688460 1496322960 550.48 mAb_IN_1_Ep_S35_L003_R1_001.fastq.gz, SRR11591016, SRR11591016.lite SRA
SRR11591017 24900822 1892462472 695.15 mAb_IN_2_Ep_S37_L003_R1_001.fastq.gz, SRR11591017, SRR11591017.lite SRA
SRX8158037 SRP173797 RIP-Seq SINGLE
GSM4491240: rAb EP CLIP; Mus musculus; RIP-Seq
Sample: SRS6520000
BioProject: PRJNA510585
BioSample: SAMN14671398
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Colon epithelium
strain: C57BL/6
tissue: Colon
sample type: EDTA fractionation
genotype: wild type
rip antibody: DDX5 (Abcam, catalog# ab53216)
Original files (1)
Colon epithelium
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11591018 16319038 1240246888 457.51 rAb_IP_1_Ep_S40_L003_R1_001.fastq.gz, SRR11591018, SRR11591018.lite SRA
SRR11591019 19727727 1499307252 547.61 rAb_IP_2_Ep_S42_L003_R1_001.fastq.gz, SRR11591019, SRR11591019.lite SRA
SRX8158038 SRP173797 RIP-Seq SINGLE
GSM4491241: rAb EP size-matched input; Mus musculus; RIP-Seq
Sample: SRS6520001
BioProject: PRJNA510585
BioSample: SAMN14671397
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Colon epithelium
strain: C57BL/6
tissue: Colon
sample type: EDTA fractionation
genotype: wild type
rip antibody: none
Original files (1)
Colon epithelium
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11591020 22677218 1723468568 631.15 rAb_IN_1_Ep_S39_L003_R1_001.fastq.gz, SRR11591020, SRR11591020.lite SRA
SRR11591021 22464626 1707311576 623.39 rAb_IN_2_Ep_S41_L003_R1_001.fastq.gz, SRR11591021, SRR11591021.lite 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 (12)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— INPUT_G1_S36_L003_R1_001.fastq RIP-Seq 1.5 GB link
— INPUT_G2_S38_L003_R1_001.fastq RIP-Seq 2.0 GB link
— IP_G1_S37_L003_R1_001.fastq RIP-Seq 1.5 GB link
— IP_G2_S39_L003_R1_001.fastq RIP-Seq 736.2 MB link
— mAb_IN_1_Ep_S35_L003_R1_001.fastq.gz RIP-Seq 550.5 MB link
— mAb_IN_2_Ep_S37_L003_R1_001.fastq.gz RIP-Seq 695.1 MB link
— mAb_IP_1_Ep_S36_L003_R1_001.fastq.gz RIP-Seq 746.7 MB link
— mAb_IP_2_Ep_S38_L003_R1_001.fastq.gz RIP-Seq 533.2 MB link
— rAb_IN_1_Ep_S39_L003_R1_001.fastq.gz RIP-Seq 631.1 MB link
— rAb_IN_2_Ep_S41_L003_R1_001.fastq.gz RIP-Seq 623.4 MB link
— rAb_IP_1_Ep_S40_L003_R1_001.fastq.gz RIP-Seq 457.5 MB link
— rAb_IP_2_Ep_S42_L003_R1_001.fastq.gz RIP-Seq 547.6 MB link