|
| Status |
Public on Dec 21, 2019 |
| Title |
Ptger4 flox-1 (F1A) |
| Sample type |
SRA |
| |
|
| Source name |
Ptger4 flox crypt cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Ptger4 flox crypt cells
strain: C57BL6
age: 10 weeks
tissue: Small intestine, freshly isolated crypts
|
| 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 |
Crypt isolation from the small intestine with EDTA and dissociation with trypsin
Drop-seq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
F1A
|
| 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) |
| GSE142418 |
Single cell RNA sequencing of cells isolated from the intestinal crypts of mice bearing epithelial cell-specific Ptger4 ablation (Drop-seq) |
| GSE142431 |
Paracrine orchestration of intestinal tumorigenesis by a confined mesenchymal niche |
|
| Relations |
| BioSample |
SAMN13649582 |
| SRA |
SRX7421136 |
