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| Status |
Public on Feb 29, 2024 |
| Title |
Alveolar_Day14_HoechstHigh_1 [alveolar] |
| Sample type |
SRA |
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| Source name |
B2-3
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| Organism |
Homo sapiens |
| Characteristics |
cell line: B2-3
cell type: Alveolar epithelial cells
cell population: HoechstHigh cell population in micro-patterned culture
time point: Day14
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| 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 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities 1x10^5 cells/well. The LPs were differentiated into alveolar epithelial cells in DCIK+3i medium: Ham's F12 (Fujifilm Wako, 087-08335) containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA (Thermo Fisher Scientific, 15260-037), 15 mM HEPES (Thermo Fisher Scientific, 17557-94), 0.8 mM CaCl2, 0.1% ITS premix (Corning), and 50 U/mL Penicillin/Streptomycin.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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_DCIK+3i_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
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| Department |
Center for iPS cell Research and Application
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| Lab |
Gotoh Lab
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| Street address |
53 Kawaharacho, Shogoin, Sakyo-ku
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| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE236839 |
Micro-patterned culture of iPSC-derived alveolar epithelial cells [alveolar] |
| 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 |
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| Relations |
| BioSample |
SAMN36360351 |
| SRA |
SRX20942211 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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