|
| Status |
Public on Nov 06, 2017 |
| Title |
Salmonella/H.poly Cell 17 |
| Sample type |
SRA |
| |
|
| Source name |
WT Mouse intestinal epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
stain: C57BL/6
genotype: Wild type
treatment: None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3' polyA RNA seq
10X Genomics Chromium Prep
Full length RNAseq (SMART-Seq2)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Full-length RNAseq (SMART-Seq2) reads
|
| Data processing |
3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
Genome_build: mm10
Supplementary_files_format_and_content: 3' polyA RNA-seq: UMI count expression values for each gene (rows) in each cell (columns)
Supplementary_files_format_and_content: Full-length RNAseq (SMART-Seq2): Transcripts per million (TPM) expression values (derived from RSEM for each gene (rows) in each cell (columns)
|
| |
|
| Submission date |
Dec 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Adam Haber |
| E-mail(s) |
ahaber@hsph.harvard.edu
|
| Organization name |
Harvard T. H. Chan School of Public Health
|
| Street address |
665 Huntington Ave, HSPH Building 1, Room 305
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE92332 |
A single-cell survey of the small intestinal epithelium |
|
| Relations |
| BioSample |
SAMN06139923 |
| SRA |
SRX2418128 |
