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Sample GSM2358999 Query DataSets for GSM2358999
Status Public on Jan 03, 2017
Title Extracted RNA from bulk cells of organoids after 6 hours of Wnt, Notch and EGFR inhibition, replicate 3
Sample type SRA
 
Source name Small intestine
Organism Mus musculus
Characteristics strain: Bl/6
tissue: Small intestine
Extracted molecule total RNA
Extraction protocol Cells were sorted 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 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina NextSeq500 using 75bp paired end sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description EEC_diff_2_93_IDE_6h
Data processing Paired end reads were aligned to the transcriptome using bwa. 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 and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: *EEC_diff*.csv: Comma separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the GeneID and primer number of the sample. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
 
Submission date Oct 24, 2016
Last update date May 15, 2019
Contact name Kay Wiebrands
E-mail(s) [email protected]
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platform ID GPL19057
Series (1)
GSE80636 Producing enteroendocrine cells from Lgr5+ intestinal stem cells by manipulating quiescence
Relations
BioSample SAMN05936422
SRA SRX2265986

Supplementary file Size Download File type/resource
GSM2358999_EEC_diff_2_93_IDE_6h.csv.gz 85.2 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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