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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 28, 2024 |
| Title |
TH122, Control, Organoid, scRNA |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
age: 57
smoking status: Ex
pack years: 30
Sex: M
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The samples used in this study were obtained from patients with lung cancer at the Samsung Medical Center between 2019 and 2022. The collected tissue was immediately placed in advanced DMEM/F12 containing 1X glutamax, 10 mM HEPES, penicillin/streptomycin, and primocin (adDF + + +) and transferred to the laboratory for organoid culture. The samples were minced and then digested in 1 mL collagenase I (Stemcell-07902) at 37 °C for 1 h. The digested tissue suspension went through a sterile 70 μm filter, and adDF+++ with 10% FBS was added. After centrifuging at 1,300 rpm for 3 min, the pellet was resuspended in 40 μL ice-cold cultrex growth factor reduced BME type 2 (Trevigen-3533-010-02) and allowed to solidify on pre-warmed 24-well suspension culture plates (Greiner M9312) at 37 °C for 20 min. Then, 400 μL organoid culture medium were added to each well, and the plates were transferred to humidified 37 °C/5% CO2 incubators. Organoids were passaged every two weeks or at a diameter of 200 µm.
The library preparation was performed using the Chromium Next GEM Single cell 5’kit v2 (10x Genomics) with a cell recovery target of 5,000 per patient, following the manufacturer’s instruction. Following the manufacturer’s instructions, barcoded sequencing libraries were generated, and sequencing libraries were sequenced on an Illumina HiSeq 2500 system using 100 bp paired-end sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jun 24, 2024 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Jihwan Moon |
| E-mail(s) |
[email protected]
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| Phone |
+82 10-4199-7317
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| Organization name |
Sungkyunkwan University
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| Department |
Department of Digital Health
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| Street address |
gangnam-gu irwon-ro 81
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| City |
Seoul |
| ZIP/Postal code |
06351 |
| Country |
South Korea |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE270667 |
Single-cell sequencing highlights increased atypical AT2 interacting with M1 macrophage in COPD |
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| Relations |
| BioSample |
SAMN42019556 |
| SRA |
SRX25038161 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8349737_TH122N-Organoid_barcodes.tsv.gz |
25.1 Kb |
(ftp)(http) |
TSV |
| GSM8349737_TH122N-Organoid_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM8349737_TH122N-Organoid_matrix.mtx.gz |
48.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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