|
| Status |
Public on Oct 19, 2018 |
| Title |
merged_D706_D502 |
| Sample type |
SRA |
| |
|
| Source name |
top_5cm_SI
|
| Organism |
Mus musculus |
| Characteristics |
strain: Neurod1-cre-eYFP
condition: S_wm
tissue: duodenum
cell type: enteroendocrine cells
|
| Treatment protocol |
VSG mice had ~70% of their stomach removed and sutured, sham were opened and had a suture around without pressure. A group of sham operated were weight matched for the VSG. All mice were fed on a standard chow except around the surgery for which they received liquid diet
|
| Growth protocol |
mice were grown on a 12h dark/light cycle with ad libitum access to water and standard chow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
epithelium was single-cell digested and FACS sorted for positive cells. RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer
2ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit
RNAseq SE-50 on an Illumina HiSEQ 40000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
V31_S1P
|
| Data processing |
data was demultiplexed using the Casava pipeline
data was mapped to the mouse genome GRCm38 using STAR v2.5.1 and raw counts generated simultaneously
Supplementary_files_format_and_content: Larraufie_VSG_EEC_mouse_rawcount.csv is a csv file of number of counts for ensembl gene ids of each biological sample
|
| |
|
| Submission date |
Oct 18, 2018 |
| Last update date |
Oct 19, 2018 |
| Contact name |
Pierre Larraufie |
| E-mail(s) |
pl418@medschl.cam.ac.uk
|
| Organization name |
Metabolic Research Laboratories and MRC Metabolic Diseases Unit
|
| Department |
WT-MRC Institute of Metabolic Science
|
| Lab |
Level 4
|
| Street address |
Box 289, Addenbrooke's Site
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE121489 |
Transcriptomics analysis of enteroendocrine cells after vertical sleeve gastrectomy |
| GSE121490 |
Transcriptomics analysis of enteroendocrine cells following vertical sleeve gastrectomy |
|
| Relations |
| BioSample |
SAMN10258302 |
| SRA |
SRX4904752 |
