|
| Status |
Public on Dec 05, 2014 |
| Title |
Extracted RNA from Control Stomach organoids Control_Sto_2 |
| 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 |
| 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) |
| GSE62784 |
Cell-autonomous transformation of Lgr5-positive intestinal stem cells into gastric stem cells upon loss of transcription factor Cdx2 |
|
| Relations |
| BioSample |
SAMN03145613 |
| SRA |
SRX878149 |
