|
| Status |
Public on Dec 07, 2022 |
| Title |
WT_SARS-CoV-2 [scRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: Airway Organoids
genotype: WT
treatment: SARS-CoV-2 Infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 24 hpi, hPSC-AWOs were dissociated into a single cell suspension using Accutase cell detachment solution (Innovative Cell Technologies) and incubated at 37 oC for ~5 min followed by gentle pipetting to break apart groups of cells. Cells were then washed twice in 1x PBS and filtered using a 40 μm Flowmi cell strainer (Bel-Art Scienceware). Cell count and cell viability were then determined using trypan blue staining and a Countess II automated cell counter (ThermoFisher Scientific).
Target cell inputs of 10,000 cells for each condition were then loaded into a Chromium Controller using Chromium Next GEM (Gel Bead-In Emulsion) single Cell 5’ Library & Gel Bead Kit v1.1 (10× Genomics) according to manufacturer’s instructions. After generation of GEMs, cDNA synthesis and library preparation of all samples was completed using the Chromium Single Cell 5’ Library Kit v1.1 (10× Genomics) according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v5.0.0)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus SARS-CoV-2 viral genome (NC_045512.2) and to extract gene expression UMI counts matrix.
Assembly: hg19
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Shuibing Chen |
| E-mail(s) |
shuibing.chen@gmail.com
|
| Phone |
2127465431
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Surgery
|
| Street address |
A 827B, 1300 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE202964 |
A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [scRNA-seq] |
| GSE202967 |
A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection. |
|
| Relations |
| BioSample |
SAMN28233770 |
| SRA |
SRX15263318 |
