|
Status |
Public on Oct 19, 2018 |
Title |
Pre_D701rna_D502rna |
Sample type |
SRA |
|
|
Source name |
jejunum enteorendocrine cells
|
Organism |
Homo sapiens |
Characteristics |
stain: CHGA+SCG2 time: pre-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 |
SAMN10257964 |
SRA |
SRX4903827 |