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Sample GSM2174263 Query DataSets for GSM2174263
Status Public on Sep 28, 2017
Title 22yr_male_cell2382
Sample type SRA
 
Source name Pancreatic islet
Organism Homo sapiens
Characteristics donor_age: 22
gender: male
inferred_cell_type: beta
Extracted molecule total RNA
Extraction protocol Single-cells were collected in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturer’s instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Single cell from human pancreas
Data processing Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample
 
Submission date May 20, 2016
Last update date May 15, 2019
Contact name Martin Enge
E-mail(s) martin.enge@gmail.com
Organization name Stanford University
Department Bioengineering
Lab Stephen Quake
Street address James H. Clark Center, 318 Campus Drive,
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL18573
Series (1)
GSE81547 Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
Relations
BioSample SAMN05161553
SRA SRX1790203

Supplementary file Size Download File type/resource
GSM2174263_1000102803.E4.csv.gz 66.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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