|
| Status |
Public on Dec 07, 2022 |
| Title |
Airway 48h Mock_2 [bulk RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: Airway Organoids
genotype: WT
treatment: Mock
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen) or TRIzol.
RNAseq libraries were prepared using the TruSeq Stranded mRNA Library Preparation kit (Illumina) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
counts.AWO.48h.txt
rld.AWO.48h.txt
|
| Data processing |
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human GRCh37 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw reads counts were extracted using htseq-count v0.11.2.
Differential expression analysis was performed using DESeq2 v1.26.0
Assembly: hg19
Supplementary files format and content: txt file storing raw counts or normalized counts per gene per sample
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
Dec 07, 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) |
| GSE202963 |
A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [bulk RNA-seq] |
| GSE202967 |
A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection. |
|
| Relations |
| BioSample |
SAMN28235146 |
| SRA |
SRX15261151 |
