|
| Status |
Public on Jul 30, 2018 |
| Title |
Trachea epithelial single cell 170 |
| Sample type |
SRA |
| |
|
| Source name |
WT Mouse airway (trachea) epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: trachea epithelium
trachea region: distal
cell phenotype: Ionocyte
genotype: Wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Smart-seq2 method described by Picelli et al. (Nature Protocols 2014)
Nextera XT DNA Library Preperation Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
This sample represents a single cell processed with the SMART-Seq2 protocol.
Full-length RNAseq (SMART-Seq2). The expression levels for each gene (rows) in each single cell (column) in transcripts per million (TPM) as calculated using RSEM. Each column header provides the sequencing batch id, the cell identifier, the region of origin (proximal or distal trachea), and the cell type as identified by cluster analysis. Each ID is seperated by '_'
processed data file:
Trachea_fullLength_TPM.txt
|
| Data processing |
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
kNN-based graph clustering (R code)
genome build: mm10
processed data files format and content: Transcripts per million (TPM) expression values (derived from RSEM for each gene (rows) in each cell (columns)
|
| |
|
| Submission date |
Aug 31, 2017 |
| Last update date |
Jul 30, 2018 |
| 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) |
| GSE103354 |
A revised airway epithelial hierarchy includes CFTR-expressing ionocytes |
|
| Relations |
| BioSample |
SAMN07585607 |
| SRA |
SRX3151797 |
