|
| Status |
Public on Feb 29, 2024 |
| Title |
Airway_BA.1_1 [SARS-CoV-2] |
| Sample type |
SRA |
| |
|
| Source name |
B2-3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: B2-3
cell type: Micro-patterned airway epithelial cells
treatment: SARS-CoV-2 BA.1 variant
|
| Treatment protocol |
The iPSC-derived pulmonary epithelial cells were infected with SARS-CoV-2 (0.1 MOI) in the micro-pattern culture plate.
|
| Growth protocol |
The MACS-isolated iPSC-derived lung progenitor cells (LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round-shaped cell-attachment areas in 100 diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities ranging from 1 or 3 x10^5 cells/well. The LPs were differentiated into alveolar epithelial cells in DCIK+3i medium or airway epithelial cells in PAL medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each total RNA sample was isolated from human iPSC-derived airway and alveolar cells in the micro-patterned culture plates using ISOGENE (NIPPON GENE).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Illumina RTA version 3.9.25 and bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v4.1. The trimmed reads were mapped to the human reference genome sequences (hg38) and SARS-CoV-2/Hu/DP/Kng/19-027 RNA complete genome (LC528233.1) with the GENCODE (Release 32 (GRCh38.p13)) gtf file using STAR v2.7.10a.
The raw counts for the genes was calculated using htseq-count v2.0.2 with the GENCODE gtf file and annotation data based on LC528233.1.
Assembly: hg38, LC528233.1
Supplementary files format and content: RawCounts_for_GEO_upload.txt: Matrix table with raw counts for every gene and every sample.
|
| |
|
| Submission date |
Jul 07, 2023 |
| Last update date |
Feb 29, 2024 |
| Contact name |
Shimpei Gotoh |
| Organization name |
Kyoto University
|
| Department |
Center for iPS cell Research and Application
|
| Lab |
Gotoh Lab
|
| Street address |
53 Kawaharacho, Shogoin, Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE236841 |
Human iPSC-derived pulmonary epithelial cells infected with SARS-CoV-2 variants in the micro-patterned culture plates [SARS-CoV-2] |
| GSE236842 |
Transcriptomes of human iPSC-derived alveolar and airway cells in the micro-patterned culture plates and their responses to SARS-CoV-2 variant infection |
|
| Relations |
| BioSample |
SAMN36366964 |
| SRA |
SRX20943555 |
