|
| Status |
Public on Jun 04, 2020 |
| Title |
GF1_EEC |
| Sample type |
SRA |
| |
|
| Source name |
intestine
|
| Organism |
Danio rerio |
| Characteristics |
group: Germ-free
cell type: Enteroendocrine cells
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Gnotobiotic zebrafish
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit (Beckman) following the manufacturer’s instructions. RNA amplification prior to library preparation had to be performed. The Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara) was used to generate full-length cDNA. mRNA transcripts were converted into cDNA through Clontech’s oligo(dT)-priming method.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapters were trimmed using Trim Galore!(Galaxy Version 0.4.2) by automatic detection
Trimmed reads were mapped to the danRer10 genome using HISAT2(Galaxy Version 2.0.5.1) using default settings
Gene counts were generated using ht-seq count (Galaxy Version 0.6.1galaxy3) and Ensembl gene annotations (GRCz10.82) using default settings and a minimum quality of 10.
Gene count tables were used as input for Deseq2 (Galaxy Version 2.11.39) using default settings
Genome_build: danRer10
Supplementary_files_format_and_content: Matrix table with gene counts for everygene and every sample
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Lihua Ye |
| E-mail(s) |
lihua.ye@duke.edu
|
| Phone |
9196600894
|
| Organization name |
Duke University
|
| Department |
MGM Department
|
| Lab |
Rawls lab
|
| Street address |
213 Research Drive, 327 CARL building
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL21741 |
| Series (1) |
| GSE151711 |
Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways |
|
| Relations |
| BioSample |
SAMN15092617 |
| SRA |
SRX8463982 |
