|
| Status |
Public on Apr 12, 2018 |
| Title |
Sca1neg |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal crypt epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6J
tissue: Intestinal crypt epithelium
cell type: non-granuloma
infection status: 6d H Polygyrus infection
cell markers: CD45-EpCam+CD44+Sca1-
|
| Treatment protocol |
Sca-1+ or Sca-1– crypt cells were sorted from one mouse infected with H. polygyrus for 6 days.
|
| Growth protocol |
Primary cell isolates from in vivo intestial epithelium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell suspensions of live Sca1+ and Sca1- sorted cells were submitted for molecular barcoding onto the Chromium Controller apparatus (10X Genomics)
Single cell cDNA libraries were prepared using the Single Cell 3' v2 Library Kit (10X Genomics, PN-120236/37/62) following the manufacturer's recommendations. The resulting single-indexed RNA-seq libraries were loaded at 300 pM on an Illumina HiSeq 4000, and paired-end sequenced using 10X Genomics specific run parameters: 26 bp Read, 8 bp I7 Index, and 98 bp Read2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Sca-1- crypt cells (Non-Granuloma)
Single Cell RNAseq
26 bp Read, 8 bp I7 Index, and 98 bp Read2.
|
| Data processing |
Downstream analysis of the results was performed using the Seurat package (v2.0)44,45. Samples were merged after read depth correction, with cells expressing less than 200 genes and genes detected in less than 10 cells filtered out. Variable gene expression was then assessed in the filtered dataset after correction for mitochondrial gene expression, and unsupervised tSNE clustering was performed. Cluster identity was then determined using the DoHeatmap function of the Seurat package and published lists28,31 of markers for various intestinal crypt cell types
Genome_build: mm10
Supplementary_files_format_and_content: Matrix file of reads per cell, and individual clusters
|
| |
|
| Submission date |
Dec 18, 2017 |
| Last update date |
Apr 12, 2018 |
| Contact name |
Ysbrand Nusse |
| E-mail(s) |
Ysbrand.Nusse@ucsf.edu
|
| Organization name |
UCSF
|
| Street address |
513 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94122 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE108233 |
Single cell analysis of Granuloma crypt epithelium |
|
| Relations |
| BioSample |
SAMN08200109 |
| SRA |
SRX3480830 |
