|
| Status |
Public on Nov 03, 2021 |
| Title |
Sample_135687_c |
| Sample type |
SRA |
| |
|
| Source name |
CD45neg CD31neg cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: Gli1_Cre_ERT2/WT; Rosa_mTmG/WT mouse
tissue: lung
age: 8 weeks
|
| Treatment protocol |
Lungs from Gli1CreERT2/WT;Rosa26mTmG/WT B6D2F1/J mice were harvested, sorted for CD45neg CD31neg cells
|
| Growth protocol |
Tamoxifen-dosed Gli1CreERT2/WT;Rosa26mTmG/WT B6D2F1/J mice of age ~8 weeks were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single Cell 3' v3
RNA libraries were prepared for sequencing using single cell gene expression (3/ GEX); Cell Ranger Version 3.0.0
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
10x Genomics Cell Ranger 3.0.0
The single cell RNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 3′ Kit v3.1 (part number 1000268) following the manufacturer’s protocol.
The libraries were run on an Agilent TapeStation 4200 (part number G2991BA) for library quality control before sequencing.
Libraries were sequenced on a NovaSeq6000 with the following run configuration: Read 1 - 150 cycles; i7 index read - 8 cycles; Read 2 - 150 cycles. The total number of cells recovered was 11,118.
Genome_build: mm10
Supplementary_files_format_and_content: differential_expression.csv: table indicating which features are differentially expressed in each cluster relative to all other clusters
Supplementary_files_format_and_content: metrics_summary.csv: summary of Number of Cells,Mean Reads per Cell, etc
Supplementary_files_format_and_content: html file containing summary of the processed data
Supplementary_files_format_and_content: Cell Ranger output for cell level counts
|
| |
|
| Submission date |
Jun 28, 2021 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Vibha N. Lama |
| E-mail(s) |
[email protected]
|
| Phone |
734-615-7818
|
| Organization name |
University of Michigan
|
| Department |
Internal Medicine
|
| Lab |
6200 MSRB3
|
| Street address |
1150 W. Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE179034 |
Single-cell RNA sequencing of enriched cells from Gli1_Cre_ERT2/WT; Rosa_mTmG/WT mouse |
|
| Relations |
| BioSample |
SAMN19919147 |
| SRA |
SRX11243113 |
