 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 30, 2020 |
| Title |
IPF2_Lin |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
disease diagnosis: Idiopathic pulmonary fibrosis (IPF)
sorted cell type: Lineage-
individual identifier: IPF2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung tissues were minced into 1 x 1 x 1 mm pieces and digested with protease solution (Collagenase A, Dispase II, DNase I in RPMI with 10 mM HEPES) at 37°C for 60 min with trituration every 20 min. Cells were stained with antibodies. For murine samples, Col-GFP+ or Col-GFP- cells were sorted. For human samples, lineage (CD31, CD45, CD235a, EPCAM)- cells, or all cells (CD235a-) were sorted. Approximately 10,000 sorted cells were loaded onto 10x Genomics Chromium controller.
Single cell libraries were generated using Chromium Single Cell 3' v2 Reagent Kit (10x Genomics) according to the manufacturer's protocol. The libraries were sequenced on Illumina HiSeq 4000 for murine samples or NovaSeq 6000 for human samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing data were demultiplexed, aligned to the mouse genome mm10 or human genome GRCh38, and UMI-collapsed with the Cell Ranger toolkit (version 2.0 or 3.0, 10X Genomics).
Genome_build: mm10 (mouse), GRCh38 (human)
Supplementary_files_format_and_content: barcodes.tsv: barcodes
Supplementary_files_format_and_content: genes.tsv: genes
Supplementary_files_format_and_content: matrix.mtx: gene-barcode matrix
|
| |
|
| Submission date |
Jun 14, 2019 |
| Last update date |
Jan 30, 2020 |
| Contact name |
Tatsuya Tsukui |
| E-mail(s) |
tatsuya.tsukui@ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Medicine
|
| Street address |
555 Mission Bay Blvd South, 282
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE132771 |
Single cell RNA-sequencing of normal and fibrotic lungs in mouse and human |
|
| Relations |
| BioSample |
SAMN12060027 |
| SRA |
SRX6073195 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3891628_IPF2_Lin_barcodes.tsv.gz |
23.7 Kb |
(ftp)(http) |
TSV |
| GSM3891628_IPF2_Lin_genes.tsv.gz |
258.6 Kb |
(ftp)(http) |
TSV |
| GSM3891628_IPF2_Lin_matrix.mtx.gz |
21.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
