|
| Status |
Public on Dec 21, 2019 |
| Title |
Colon mesenchyme 1A (C1A) |
| Sample type |
SRA |
| |
|
| Source name |
Colon mesenchyme
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon mesenchyme
strain: C57/BL6
age: 10 weeks
|
| Treatment protocol |
No treatment of mice. No treatement of cells.
|
| Growth protocol |
Standard mouse housing conditions, freshly isolated cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Epithelial depletion with EDTA and DTT. Mesenchymal cell isolation with Collagenase XI and Dispase
Drop-seq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Drop-seq preprocessing was performed using DropSeq tools (https://anaconda.org/bioconda/dropseq_tools).
The alignment was peformed using STAR (2.6)
Bead synthesis error was detected using DetectBeadSynthesisErrors in DropSeq tools.
Read counts per cell were generated using BAMTagHistogram in DropSeq tools.
Visualization was done using ggplot2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped text file which includes gene-by-cell count matrix
|
| |
|
| Submission date |
Dec 20, 2019 |
| Last update date |
Dec 22, 2019 |
| Contact name |
Richard Flavell |
| E-mail(s) |
richard.flavell@yale.edu
|
| Organization name |
Yale University
|
| Department |
Department of Immunobiology
|
| Street address |
300 Cedar Street, TAC S-569
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE142423 |
Single cell RNA sequencing analysis of the mouse colonic mesenchyme (Drop-seq) |
| GSE142431 |
Paracrine orchestration of intestinal tumorigenesis by a confined mesenchymal niche |
|
| Relations |
| BioSample |
SAMN13650896 |
| SRA |
SRX7421152 |
