|
| Status |
Public on Aug 15, 2020 |
| Title |
Map3k2-regulated intestinal stromal cells define a distinct intestine stem cell niche for tissue repair |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
intestinal mesenchymal stromal cell subset specific accessible elements were analyzed using ATAC-seq
Bulk RNA-seq Purpose: The goals of this study are to compare WT and Map3k2 deficient mice colon tissue transcriptome upon Naive and DSS treatment for 1 day
Bulk RNA-seq Methods: Colon Tissue mRNA profiles of Naive or 2% DSS treated 16-week-old wild-type (WT) and MEKK2 knockout (Map3k2-/-) mice were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the gene level with : Bowtie2 followed by HTSeq-Count and Normalized by DESeq2
Bulk RNA-seq Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm10) and identified 13,284 transcripts in the colon tissues of WT and Map3k2-/- mice.
Single-cell RNA-seq Purpose: The goals of this study are to characterize murine colon mesenchymal stromal cell heterogeneity upon DSS treatment for 3 days
Single-cell RNA-seq Methods: Mesenchymal Stromal Cell Single Cell Suspension Dissociated from 2% DSS treated 12-week-old wild-type (WT) mice has undergone 10x genomics single cell RNA sequencing using Illumina NextSeq 500.
Single-cell RNA-seq Results: Using CellRanger and Seurat we identified 11,284 cells after quality control and filtering
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| |
|
| Overall design |
Examination of accessible chromatin in sorted intestinal mesenchymal stromal cell populations.
Colon Tissue mRNA profiles of 16 Week old wild type (WT) and Map3k2-/- mice upon H2O and 2% DSS Treatment
Single Cell Profiles of 12 Week old DSS treated wild type (WT) mice upon 2% DSS Treatment
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| |
|
| Contributor(s) |
Sun H, Gao C, Wu N, Su B |
| Citation(s) |
33658717 |
| BioProject |
PRJNA595166 |
| |
| Submission date |
Aug 14, 2020 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Hongxiang Sun |
| E-mail(s) |
sun758426@sjtu.edu.cn
|
| Organization name |
Shanghai Jiaotong University
|
| Department |
Shanghai Institute of Immunology
|
| Lab |
Bing Su
|
| Street address |
280 South Chongqing Rd.
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21273 |
HiSeq X Ten (Mus musculus) |
|
| Samples (21)
|
|
| Relations |
| SRA |
SRP237295 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156245_CD138_Specific_Peaks.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSE156245_CD138_Total_Peaks.bed.gz |
3.2 Mb |
(ftp)(http) |
BED |
| GSE156245_CD34_Specific_Peaks.bed.gz |
765.8 Kb |
(ftp)(http) |
BED |
| GSE156245_CD34_Total_Peaks.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
| GSE156245_MEKK2_KO_RNASeq.xlsx |
1.8 Mb |
(ftp)(http) |
XLSX |
| GSE156245_MRISC_Specific_Peaks.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE156245_MRISC_Total_Peaks.bed.gz |
2.7 Mb |
(ftp)(http) |
BED |
| GSE156245_Myofibroblast_Specific_Peaks.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
| GSE156245_Myofibroblast_Total_Peaks.bed.gz |
2.7 Mb |
(ftp)(http) |
BED |
| GSE156245_RAW.tar |
2.2 Gb |
(http)(custom) |
TAR (of BW, MTX, RDS, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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