GSE125970
GSE GEOSingle-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine
Organism:
Homo sapiens
Platform:
GPL20795
Samples:
6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Jan 31 2019
Last Updated:
Feb 24 2021
Status:
Public on Oct 21 2019
Contact:
Ye-guang,,Chen (Tsinghua University)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA518129
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP183081
Summary
14537 epithelial cells from adult human ileum, colon and rectum are performed single-cell transcriptome analysis, cell types and signature genes are presented, so as new representative genes. Bases on the gene expression pattern, difference of cell types, signaling changes, absorption funciton, inmmunity and hormone activity are analyzed. In addition, species diversity is briefly performed by analysis of human and mouse ileum single-cell database.
Overall Design
identify cell consititution and function difference of ileum, colon and rectum at single-cell level.
Analysis (4 steps)
View Data Processing
Processing steps for GSE125970
- Quality control and preprocessing of high throughput sequencing data were using SOAPnuke with parameters -n 0.1 -l 10 -A 0.25 -Q 2 -G --seqType 1
- 16 bp 10xTM Barcodes and 10bp UMIs were encoded at the start of Read 1 (R1).
- Reads alignment, filtering, barcode counting, and UMI counting were performed using cellranger 2.1 with default parameters
- Sample normalization and scaled gene expression data were calculated by Seurat2.3.2
Supplementary Files (3)
GEO Samples (6)
Dataset Citations (1)
SRA Experiments (6) and Runs (6)
Total: 345968 MBGSM3587008: Ileum-1; Homo sapiens; RNA-Seq
Sample: SRS4313817
BioProject: PRJNA518129
BioSample: SAMN10853961
Platform: ILLUMINA
Instrument: HiSeq X Ten
Organism: Homo sapiens
Sample attributes
source_name: adult human ileum epithelial cells
cell type: Epithelia cell
tissue: small intestine
age of human: 61
Original files (1)
adult human ileum epithelial cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8513794 | 414982680 | 124494804000 | 54866.0 | SRR8513794, SRR8513794.sralite | SRA |
GSM3587009: Ileum-2; Homo sapiens; RNA-Seq
Sample: SRS4313818
BioProject: PRJNA518129
BioSample: SAMN10853960
Platform: ILLUMINA
Instrument: HiSeq X Ten
Organism: Homo sapiens
Sample attributes
source_name: adult human ileum epithelial cells
cell type: Epithelia cell
tissue: small intestine
age of human: 67
Original files (1)
adult human ileum epithelial cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8513795 | 432775872 | 129832761600 | 58729.84 | SRR8513795, SRR8513795.sralite | SRA |
GSM3587010: Colon-1; Homo sapiens; RNA-Seq
Sample: SRS4313819
BioProject: PRJNA518129
BioSample: SAMN10853959
Platform: ILLUMINA
Instrument: HiSeq X Ten
Organism: Homo sapiens
Sample attributes
source_name: adult human colon epithelial cells
cell type: Epithelia cell
tissue: large intestine
age of human: 55
Original files (1)
adult human colon epithelial cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8513796 | 439803104 | 131940931200 | 58382.21 | SRR8513796, SRR8513796.sralite | SRA |
GSM3587011: Colon-2; Homo sapiens; RNA-Seq
Sample: SRS4313820
BioProject: PRJNA518129
BioSample: SAMN10853958
Platform: ILLUMINA
Instrument: HiSeq X Ten
Organism: Homo sapiens
Sample attributes
source_name: adult human colon epithelial cells
cell type: Epithelia cell
tissue: large intestine
age of human: 67
Original files (1)
adult human colon epithelial cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8513797 | 412164297 | 123649289100 | 58390.43 | SRR8513797, SRR8513797.sralite | SRA |
GSM3587012: Rectum-1; Homo sapiens; RNA-Seq
Sample: SRS4313821
BioProject: PRJNA518129
BioSample: SAMN10853957
Platform: ILLUMINA
Instrument: HiSeq X Ten
Organism: Homo sapiens
Sample attributes
source_name: adult human rectum epithelial cells
cell type: Epithelia cell
tissue: large intestine
age of human: 67
Original files (1)
adult human rectum epithelial cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8513798 | 407453499 | 122236049700 | 56760.29 | SRR8513798, SRR8513798.sralite | SRA |
GSM3587013: Rectum-2; Homo sapiens; RNA-Seq
Sample: SRS4313822
BioProject: PRJNA518129
BioSample: SAMN10853956
Platform: ILLUMINA
Instrument: HiSeq X Ten
Organism: Homo sapiens
Sample attributes
source_name: adult human rectum epithelial cells
cell type: Epithelia cell
tissue: large intestine
age of human: 49
Original files (1)
adult human rectum epithelial cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8513799 | 431484970 | 129445491000 | 58839.67 | SRR8513799, SRR8513799.lite | SRA |
Linked Publications (2)
Stratification of enterochromaffin cells by single-cell expression analysis.
bioRxiv : the preprint server for biology · 2025
Data Files (12)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | SRR8513794 | RNA-Seq | 53.6 GB | link | |||
| — | SRR8513794 | RNA-Seq | 53.6 GB | link | |||
| — | SRR8513795 | RNA-Seq | 57.4 GB | link | |||
| — | SRR8513795 | RNA-Seq | 57.4 GB | link | |||
| — | SRR8513796 | RNA-Seq | 57.0 GB | link | |||
| — | SRR8513796 | RNA-Seq | 57.0 GB | link | |||
| — | SRR8513797 | RNA-Seq | 57.0 GB | link | |||
| — | SRR8513797 | RNA-Seq | 57.0 GB | link | |||
| — | SRR8513798 | RNA-Seq | 55.4 GB | link | |||
| — | SRR8513798 | RNA-Seq | 55.4 GB | link | |||
| — | SRR8513799 | RNA-Seq | 57.5 GB | link | |||
| — | SRR8513799 | RNA-Seq | 57.5 GB | link |