|
| Status |
Public on Apr 29, 2024 |
| Title |
Neisseria-treated gastric organoids [Ns-3] |
| Sample type |
SRA |
| |
|
| Source name |
gastric organoids
|
| Organism |
Mus musculus |
| Characteristics |
cell type: gastric organoid
treatment: Neisseria subflava
|
| Treatment protocol |
Gastric organoids were incubated with bacteria for 4 hours
|
| Growth protocol |
Gastric organoids were cultured in matrigel with standard culture medium, and at the first passage they were put on matrigel with growth factor-free, antibiotic-free medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted by Rneasy Mini kit
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are ready for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Gastric organoids treated with Neisseria
|
| Data processing |
Crude readings were subjected to quality control checks, after which the clean readings were aligned to the mouse genome reference sequences (GRCm38). The aligned reads were mapped and quantified using CLC Genomics Workbench software v7.5
Supplementary files format and content: Excel file that has total read counts, TPM, CPM, and RPKM of all genes in all cells
|
| |
|
| Submission date |
May 09, 2022 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Yoku Hayakawa |
| E-mail(s) |
hayakawayoku@gmail.com, yhayakawa-tky@umin.ac.jp
|
| Phone |
81-3-38155411
|
| Organization name |
University of Tokyo
|
| Street address |
7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425
|
| City |
Tokyo |
| State/province |
TOKYO |
| ZIP/Postal code |
1138655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE202509 |
RNA sequencing of gastric organoids treated with bacteria |
|
| Relations |
| BioSample |
SAMN28159718 |
| SRA |
SRX15209079 |
