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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 03, 2017 |
| Title |
Extracted RNA from bulk cells of organoids after 96 hours of Wnt, Notch and Mek inhibition, replicate 1 |
| Sample type |
SRA |
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| Source name |
Small intestine
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| Organism |
Mus musculus |
| Characteristics |
strain: Bl/6
tissue: Small intestine
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
EEC_diff_4_94_IDM_96h
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| 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.
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| Submission date |
Oct 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kay Wiebrands |
| E-mail(s) |
[email protected]
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| Organization name |
Hubrecht Institute
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE80636 |
Producing enteroendocrine cells from Lgr5+ intestinal stem cells by manipulating quiescence |
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| Relations |
| BioSample |
SAMN05936404 |
| SRA |
SRX2266005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2359018_EEC_diff_4_94_IDM_96h.csv.gz |
83.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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