|
| Status |
Public on Mar 10, 2023 |
| Title |
NGT133F-gCDH1 |
| Sample type |
SRA |
| |
|
| Source name |
Fundic gland
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Stomach - human Gastric Organoids
genotype: CDH1 KO
|
| Growth protocol |
hGOs were routinely generated from fragmented and digested normal gastric glands and were cultured in Matrigel with specific supplements. To manufacture genetic KO of CDH1, hGOs were transfected lentiviral vectors encoding Cas9 protein and the guideRNA sequence that was complematary to CDH1 gene. WT hGOs were transfected lentiviral vectors encoding Cas9 protein and guideRNA sequence that was not complemntary to any genes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from hGO cells using ISOGEN (Nippon Gene, Tokyo, Japan). NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the reference genome by HISAT2.
The resulting BAMs were input to featureCounts to generate the count table.
Genome_build: hg19
Supplementary_files_format_and_content: The tab-delimited text file contains read counts per genes.
|
| |
|
| Submission date |
Mar 10, 2020 |
| Last update date |
Mar 10, 2023 |
| Contact name |
Yuichiro Semba |
| E-mail(s) |
semba.yuichiro.208@m.kyushu-u.ac.jp
|
| Organization name |
Kyushu University
|
| Street address |
3-1-1 Maidashi
|
| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE146716 |
Transcriptome analysis of wild-type (WT) and CDH1 knockout (KO) human Gastric Organoids (hGOs) |
|
| Relations |
| BioSample |
SAMN14343796 |
| SRA |
SRX7886958 |
