|
| Status |
Public on Mar 27, 2024 |
| Title |
Gabbr1_WT |
| Sample type |
SRA |
| |
|
| Source name |
small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: small intestine
cell line: mouse primary cells
cell type: CD127+ immune cells and EpCAM+ epithelial cells
genotype: Gabbr1 wild-type
strain: C57BL/6J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were then loaded onto microfluidic devices.
ScRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies) . Individual libraries were diluted to 4nM and pooled for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10XGenomics
|
| Data processing |
Pools were sequenced on Illumina NovaSeq 6000 with 150 bp paired end reads. Raw reads were processed with fastQC and fastp to remove low quality reads. Poly-A tails and adaptor sequences were removed by cutadapt.
After quality control, reads were mapped to the reference genome mm10 using STAR. Gene counts and UMI counts were acquired by featureCounts software. Expression matrix files for subsequent analyses were generated based on gene counts and UMI counts.
ScRNA-seq data were further analyzed using R version 4.2.2, Seurat package version 4.3.0. CD45+CD127+ immune cells and CD45-EpCAM+ epithelial cells were discriminated by expression of marker genes (including Ptprc, Il7r and Epcam).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files
|
| |
|
| Submission date |
Dec 18, 2023 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Nian Liu |
| E-mail(s) |
liunian181@mails.ucas.ac.cn
|
| Phone |
+8618100502042
|
| Organization name |
Institute of Biophysics, Chinese Academy of Sciences
|
| Street address |
Institute of Biophysics,#15 Datun Road
|
| City |
Chaoyang Distric |
| State/province |
Beijing |
| ZIP/Postal code |
100010 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE250452 |
A single cell survey of CD127+ immune cells and EpCAM+ epithelial cells from wild type mice and Gabbr1-deficient mice |
|
| Relations |
| BioSample |
SAMN38909106 |
| SRA |
SRX22934630 |
