|
| Status |
Public on Nov 05, 2018 |
| Title |
WT_DT_M3 |
| Sample type |
SRA |
| |
|
| Source name |
Wild type control mouse rep. 3 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [WT_DT_M3]
|
| Organism |
Mus musculus |
| Characteristics |
cell type: WT mouse intestinal epithelial cells
strain: C57BL/6
treatment: DT injection
time point: Day 7
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3' polyA RNA seq
Full length RNAseq (SMART-Seq2)
10X Genomics Chromium Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
3' polyA RNA-seq
CellRanger 1.3.1
PCA (prcomp in R)
kNN-based graph clustering (R code)
Supplementary_files_format_and_content: 10X genomics CellRanger output
Genome_build: mm10
Supplementary_files_format_and_content: UMI count expression values for each gene (rows) in each cell (columns)
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM for each gene (rows) in each cell (columns)
|
| |
|
| Submission date |
Nov 05, 2018 |
| Last update date |
Nov 06, 2018 |
| Contact name |
Adam Haber |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE106510 |
T helper cells modulate intestinal stem cell renewal and differentiation |
|
| Relations |
| BioSample |
SAMN10379123 |
| SRA |
SRX4978805 |
