|
| Status |
Public on Dec 31, 2018 |
| Title |
Ileum_2_L |
| Sample type |
SRA |
| |
|
| Source name |
Ileum
|
| Organism |
Homo sapiens |
| Characteristics |
facs population: GLP1+/CHGA+/SCG2+
participant: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human jejunal mucosal samples were dissociated to single cells, fixed in paraformaldehyde (4%), permeabilised with Saponin, Antibody labelled against GLP-1, CHGA and SCG2 and FACS sorted into 3x populations (GLP1-/CHGA+/SCG2+ [Single positive]; GLP1+/CHGA+/SCG2+ [Double positive]; triple negative [Neg]). RNA was extracted using the Ambion Recoverall total Nucelic Acid isolation kit following the MARIS protocol and concentrated using a Qiagen RNeasy Minelute cleanup kit.
The library was constructed with 4ng of input RNA using the Clontech Smarter Stranded total RNA-seq - Pico Input mammalian kit v1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Human Ileum GLP1+/CHGA+/SCG2+ from participant 2
|
| Data processing |
Sequenced reads were trimmed for adapter sequence and mapped to the human genome (GRCh37) using Tophat and raw counts generated with Htseq-count
Differential gene expression modelling and normalised counts per million were generated using DESEQ2.
Genome_build: GRCh37
Supplementary_files_format_and_content: all_raw_counts.txt is tab delimited file of number of counts for ensembl gene ids for each biological sample
|
| |
|
| Submission date |
May 24, 2018 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Brian Yee Hong Lam |
| E-mail(s) |
yhbl2@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Metabolic Research Laboratories
|
| Street address |
Box 289 Addenbookes Hospital, Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE114853 |
Human enteroendocrine cell transcriptomic profiling |
|
| Relations |
| BioSample |
SAMN09245810 |
| SRA |
SRX4119632 |
