|
| Status |
Public on Aug 05, 2023 |
| Title |
Lung.V.1 |
| Sample type |
SRA |
| |
|
| Source name |
hALO.Virus
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
treatment: SARS-CoV-2 infection
sars-cov-2 strain: EPI_ISL_402124
|
| Treatment protocol |
Infected with SARS-CoV-2 strain EPI_ISL_402124 [https://www.nature.com/articles/s41586-020-2012-7]
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA in the cells was extracted using Trizol (Invitrogen) according to the manufacturer’s protocol, and 1ug RNA was used to reverse transcribed into cDNA using Oligo (dT). Fragmented RNA (average length approximately 200 bp) was subjected to first strand and second strand cDNA synthesis followed by adaptor ligation and enrichment with a low-cycle according to the instructions of NEBNext" UltraTM RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit"2.0(Life Technologies, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode human transcriptome using RSEM
The gene expression level was calculated by using RSEM
Reads were aligned to the mouse reference genome hg38 with bowtie2, and RSEM was used to quantify the reads mapped to each gene. Gene expression was normalized by EDASEQ. Differentially expressed genes were obtained using DESeq2 (version 1.10.1), a cutoff of Q-value < 0.05 and log2 (fold-change) > 1 was used for identify differentially expressed genes. All differentially expressed mRNAs were selected for GO analyses clusterProfiler. Other analysis was performed using glbase
Genome_build: hg38
|
| |
|
| Submission date |
Aug 05, 2020 |
| Last update date |
Aug 05, 2023 |
| Contact name |
Jiangping He |
| E-mail(s) |
he_jiangping@grmh-gdl.cn
|
| Organization name |
Guangzhou Institutes of Biomedicine and Health (GIBH), CAS
|
| Street address |
Kai yuan avenue 190
|
| City |
GuangZhou |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE155717 |
SARS-CoV-2 infection of human embryonic stem cell-derived lung organoids |
|
| Relations |
| BioSample |
SAMN15734401 |
| SRA |
SRX8889714 |
