|
| Status |
Public on Oct 19, 2018 |
| Title |
Post_D707rna_D502rna |
| Sample type |
SRA |
| |
|
| Source name |
jejunum enteorendocrine cells
|
| Organism |
Homo sapiens |
| Characteristics |
stain: CHGA+SCG2
time: post-surgery
tissue: jejunum
cell type: enteroendocrine cells
|
| Growth protocol |
some jejunal part removed from patients undergoing gasterctomy Roux-en-Y reconstruction was collected or from jejunal biopsies 6 months after surgery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
epithelium was single-cell digested, PFA fixed and stained with CHGA and SCG2 antibodies and FACS sorted for positive cells . RNA was extracted using a Ambion Recoverall Total nucleic acid isolation kit for FFPE
5ng of RNA was used for library construction using Clontech SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian v1 (Takara Bio, USA) without fragmentation step
RNAseq SE-50 on an Illumina HiSEQ 40000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
data was demultiplexed using the Casava pipeline
data was mapped to the mouse genome GRCh38 using STAR v2.5.1 and raw counts generated simultaneously
Supplementary_files_format_and_content: Larraufie_VSG_EEC_human_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 |
GPL20301 |
| Series (2) |
| GSE121486 |
Transcriptomics analysis of human jejunal enteroendocrine cells after vertical sleeve gastrectomy |
| GSE121490 |
Transcriptomics analysis of enteroendocrine cells following vertical sleeve gastrectomy |
|
| Relations |
| BioSample |
SAMN10257960 |
| SRA |
SRX4903830 |
