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Sample GSM1533371 Query DataSets for GSM1533371
Status Public on Dec 05, 2014
Title Extracted RNA from Control Stomach organoids Control_Sto_4
Sample type SRA
Source name Extracted RNA from Control Stomach organoids
Organism Mus musculus
Characteristics genotype: Control
tissue: Stomach organoids
Growth protocol Cdx2null, Control SI and Control Sto clonal organoids were generated and expanded in Matrigel from FACS sorted Lgr5-EGFPhi single cells in stomach specific culture medium (ENRWfg). Cdx2+ Stomach (Sto) organoids were generated by infection of the wild type stomach organoids with lentiviral stock expressing Cdx2 and were cultured in stomach medium (ENRWfg). Medium was refreshed every 2 days. Organoids were passaged about once per week by mechanical disruption in split ratios of 1:4.
Extracted molecule total RNA
Extraction protocol Organoids were freed from Matrigel and resuspended in RTL buffer (Qiagen). RNA was extracted from Cdx2null SI, Control SI, Control Sto and Cdx2+ Sto organoids using the RNeasy Mini RNA Extraction Kit (Qiagen).
10ng of total RNA per sample was processed using the previously described CEL-seq technique. 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 were aligned to the transcriptome using bwaPaired 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 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: data_counts_ORG.txt: Processed data for Organoid1. Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the sample type, SI for intestine and Sto for stomach, Cdx2null for Cdx2 knock out and Cdx2+ for Cdx2 overexpression. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Submission date Oct 28, 2014
Last update date May 15, 2019
Contact name Lennart Kester
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
Platform ID GPL19057
Series (1)
GSE62784 Cell-autonomous transformation of Lgr5-positive intestinal stem cells into gastric stem cells upon loss of transcription factor Cdx2
BioSample SAMN03145611
SRA SRX878151

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

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