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Sample GSM2772973 Query DataSets for GSM2772973
Status Public on Apr 16, 2018
Title sorted single cells, GK5a-M2-4
Sample type SRA
Source name Small intestinal crypts
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Small intestinal crypts
Extracted molecule total RNA
Extraction protocol Cells were mouth pipetted or sorted directly into 384-well plates containing 0.02 μL of 1:50,000 ERCC Spike-in RNA (Ambion), 0.015 µL of 1% IGEPAL (Sigma), 0.035 µL of RNAse inhibitor (Clonetech), and 0.020 µL of 10 mM dNTPs and water to a total volume of 100 nL, covered with 5µL of mineral oil
RNA was processed using the previously described CEL-seq2 technique (with modifications as described in Muraro et al., Cell Systems, 2016). 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
Data processing 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).
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 Sep 05, 2017
Last update date May 15, 2019
Contact name Jean-Charles Boisset
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)
GSE89379 Transcriptomics of single-cell and bulk sorted and micro-dissected mouse bone marrow, fetal liver and small intestine crypt cells
GSE103516 Single-cell RNA-seq of murine small intestine crypts
BioSample SAMN07606104
SRA SRX3161818

Supplementary file Size Download File type/resource
GSM2772973_GK5a-M2-4_AHHMMVBGX2_S6.coutt.csv.gz 1.1 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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