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Sample GSM3151855 Query DataSets for GSM3151855
Status Public on Dec 31, 2018
Title Jej_4_L
Sample type SRA
 
Source name Jejunum
Organism Homo sapiens
Characteristics facs population: GLP1+/CHGA+/SCG2+
participant: 4
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 Jejunum GLP1+/CHGA+/SCG2+ from participant 4
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 SAMN09245809
SRA SRX4119633

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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