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Sample GSM2367686 Query DataSets for GSM2367686
Status Public on Nov 01, 2017
Title micro-dissected cells [JC53]
Sample type SRA
 
Source name E15 fetal liver small structure dissection to single-cells
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Fetal liver
Extracted molecule total RNA
Extraction protocol Cells were directly placed into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5µg GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description E15 fetal liver small structure dissection to single-cells
Data processing Raw data files for single-cell samples contain data for 96 multiplexed cells. Raw data for bulk samples contain data for 2000 cells processed in bulk in a single library. The column number containing the data in the bulk sample processed data refers to the barcode ID. Cell-specific bar codes are available in the file cel-seq_barcodes.csv on the series record.
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
When indicated, reads were mapped to a modified RefSeq with inserted CAST/EiJ SNPs
Genome_build: mm10
Supplementary_files_format_and_content: *.gene.coutt.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by a space. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
 
Submission date Nov 01, 2016
Last update date May 15, 2019
Contact name Jean-Charles Boisset
E-mail(s) j.boisset@hubrecht.eu
Organization name Hubrecht Institute
Lab A. van Oudenaarden
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platform ID GPL19057
Series (2)
GSE89378 Single-cell and bulk RNA-seq of sorted and micro-dissected mouse bone marrow and fetal liver cells
GSE89379 Transcriptomics of single-cell and bulk sorted and micro-dissected mouse bone marrow, fetal liver and small intestine crypt cells
Relations
BioSample SAMN05960660
SRA SRX2313279

Supplementary file Size Download File type/resource
GSM2367686_JC53.coutt.csv.gz 343.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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