|
Status |
Public on Feb 29, 2024 |
Title |
LungProgenitor_1 [airway] |
Sample type |
SRA |
|
|
Source name |
B2-3
|
Organism |
Homo sapiens |
Characteristics |
cell line: B2-3 cell type: iPSC-derived CPM+ time point: Day0
|
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 100 or 200 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at cell density 3x10^5 cells/well. The LPs were differentiated into airway epithelial cells in the medium as the following steps: “PAL(-)” medium made of PneumaCult-ALI medium (Veritas, ST-05001) containing 500nM hydrocortisone, 10 μM heparin, and 10 μM Y27632 for initial two days and thereafter PAL(+) medium made of PAL(-) medium supplemented with 10 mM DAPT. Each medium was changed every two days.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA of Hoechst-high or Hoechst-low cells isolated by FACS was extracted using RNeasy micro (Qiagen). 1 ng of the total RNA was reverse transcribed and amplified for 11 cycles using SMART-Seq HT (Clontech Laboratories, Z4456N). The amplified cDNA was used for preparation of sequencing libraries using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Carboxypeptidase M (CPM) was used as a surface-antigen protein of the lung progenitor cells.
|
Data processing |
Sequenced reads of the Hoechst-high (Edge) or Hoechst-low (Center) cells were trimmed using fastp (S. Chen et al. 2018), and the trimmed reads were aligned to GRCh38 using STAR 2.7.1a (Dobin et al. 2013). Transcripts per million (TPM) values were calculated using RSEM (B. Li and Dewey 2011). Assembly: hg38 Supplementary files format and content: patterning_PAL+_Center_Edge.txt: Tab-delimited text file includes count values and TPM for each sample.
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|
|
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 |
GPL24676 |
Series (2) |
GSE236840 |
Micro-patterned culture of iPSC-derived airway epithelial cells [airway] |
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 |
SAMN36360387 |
SRA |
SRX20942214 |