|
| Status |
Public on Aug 20, 2022 |
| Title |
Gastric organoid 3D (A1) |
| Sample type |
SRA |
| |
|
| Source name |
gastric organoids
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: 3D gastric organoid
cell type: Epithelial gastric cells
treatment: untreated
disease state: Healthy
|
| Treatment protocol |
Infection: Organoid-derived monolayers were infected with Helicobacter pylori by adding the bacteria apically onto monolayers with a MOI of 1 for 6 h.
|
| Growth protocol |
Generation and culture of stomach gastric organoids was performed as described before (Bartfeld et al. 2015, Kayisoglu et al. 2020). Monolayers were allowed to grow using the culture media described above (ENRWFGTi_) and differentiate for 14 days to reach 90-100% confluency. Six days prior infection, primocin was exchange for H. pylori compatible antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ex vivo gastric units were isolated from gastric biopsies as described before (Bartfeld et al. 2015). Ex vivo gastric units, 3D organoids and 2D organoid-derived monolayers were made single cells by incubation with TripLE Express. Ex vivo units were stained for EpCam before sorting. Cells were then subjected to FACS sorting. Total RNA was isolated using 10x Chromium kit.
Cells were loaded in the 10X Genomics Chromium at a concentration of 200 cells/µl with the aim of recovering 3000 cells. Libraries were generated with the Chromium Single Cell 3’ Reagents Kit v2 Chemistry.
Chromium single cell 3'v2 (10X Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mRNA
|
| Data processing |
Data were analyzed using Cell Ranger™ pipelines which is available in 10x Genomics website.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix.
|
| |
|
| Submission date |
Feb 25, 2021 |
| Last update date |
Aug 21, 2022 |
| Contact name |
Antoine-Emmanuel Saliba |
| E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
|
| Phone |
+49-931-31-81341
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2 / D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE167561 |
Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis. |
|
| Relations |
| BioSample |
SAMN18059279 |
| SRA |
SRX10170788 |
