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| Status |
Public on Jun 23, 2016 |
| Title |
Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 1 |
| Sample type |
SRA |
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| Source name |
Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 1
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| Organism |
Mus musculus |
| Characteristics |
tissue: Small intestine
strain: Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice
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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 |
8WKYA1
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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: *.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 an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: expdata.txt: Tab-separated data file for final processed dataset without ERCC spike-ins, listing all genes (rows) and the number of sequenced transcripts. Column name indicate the experiment and cell number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: cel-seq_barcodes.txt: Tab-separated data file containing all cell-specific barcodes. First column contains barcode number and second column contains barcode sequence.
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| Submission date |
Dec 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kay Wiebrands |
| E-mail(s) |
k.wiebrands@hubrecht.eu
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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) |
| GSE76408 |
Single-cell RNA-seq reveals distinct maturation stages of the Paneth cell lineage |
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| Relations |
| BioSample |
SAMN04376668 |
| SRA |
SRX1507766 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1987578_8WKYA1.gene.coutt.csv.gz |
562.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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