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| Status |
Public on Oct 01, 2023 |
| Title |
hPSC_AO_Mock_1 |
| Sample type |
SRA |
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| Source name |
hPSC_AO_Mock
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hPSC-derived airway organoids
treatment: Mock
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| Treatment protocol |
hPSC-AOs or hPSC-COs were fragmented into small cell clusters and plated on 10% matrigel-coated plates. The infection was performed in the culture media at the indicated MOIs at 37°C. For pre-infection treatment experiments, hPSC-AOs or hPSC-COs were pretreated with DMSO (control), 10 µM GW6471, 10 µM Xanthohumol or 1 µM Chemotin for 4 hours prior to infection.
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| Growth protocol |
Airway organoid differentiation hPSC-AOs were derived using a protocol slightly modified from previous studies (15, 18). For definitive endoderm (DE) differentiation, cells were passaged with Accutase (Innovative Cell Technology) at 1:2-1:3 for the first day. When achieving 80-90% confluency, hESCs were treated with 3 μM CHIR99021 (CHIR, Sigma) and 100 ng/ml Activin A (R&D systems) in basal medium RPMI1640 (Cellgro) supplemented with 1X Pen-Strep (Gibco) for 1 day, and changed to the basal medium containing 100 ng/ml Activin A and 2% FBS for the next 48 hours. To induce anterior foregut endoderm, the endoderm cells were cultured in completed serum free differentiation (cSFD) medium supplemented with 1.5 μM dorsomorphin dihydrochloride (R&D Systems) and 10 μM SB431542 (R&D Systems) for 24 hours, and then switched to 10 μM SB431542 and 1 μM IWP2 (R&D Systems) treatment for 24 hours. For induction of early stage lung progenitor cells (day 15), the anterior foregut endoderm was treated with 3 μM CHIR99021, 10 ng/ml human BMP4 (peprotech) and 50 nM all-trans retinoic acid (ATRA) in cSFD medium. At day 15, the lung progenitor cells detached from 2D culture by trypsinization, mixed with matrigel, and replated to form 70 μL domes on 24-well plate. The 3D culture was maintained in cSFD containing 100 ng/ml human FGF10, 250 ng/ml human FGF2, 50 nM dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich) and 0.1 mM IBMX (Sigma Aldrich).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. cDNA libraries were sequenced with pair-end 51 bps using an Illumina NovaSeq6000 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
airway_m_1
processed data file:
raw_counts.hPSC_AO.txt
raw_counts.hPSC_AO.downsample.txt
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| 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 hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw read counts were quantified using HTSeq-count v0.11.2.
Genome_build: hg19
Supplementary_files_format_and_content: txt files storing raw read counts per gene per sample
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| Submission date |
Oct 27, 2020 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Shuibing Chen |
| E-mail(s) |
shuibing.chen@gmail.com
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| Phone |
2127465431
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| Organization name |
Weill Cornell Medical College
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| Department |
Surgery
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| Street address |
A 827B, 1300 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE160230 |
hPSC-derived Airway Organoids-based Screen Reveals the Role of HIF1/Glycolysis Axis in SARS-CoV-2 Infection [bulk RNA-seq] |
| GSE160232 |
hPSC-derived Airway Organoids-based Screen Reveals the Role of HIF1/Glycolysis Axis in SARS-CoV-2 Infection. |
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| Relations |
| BioSample |
SAMN16574218 |
| SRA |
SRX9379223 |
| 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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