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| Status |
Public on Aug 05, 2021 |
| Title |
Extracted RNA from EGFP+ and EGFP- cells of skin epidermis of adult Troy-EGFP-IRES-CreERT2 mice, replicate 1 |
| Sample type |
SRA |
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| Source name |
Murine skin epidermis
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| Organism |
Mus musculus |
| Characteristics |
genotype: Troy-EGFP-IRES-CreERT2
tissue: Skin epidermis
strain: C57BL/6
age: Adult
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| Extracted molecule |
total RNA |
| Extraction protocol |
Live single cells were sorted in 384- well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an 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 |
TroyM01
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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: coutt files contain UMI barcode normalised abundance counts
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| Submission date |
Jun 25, 2021 |
| Last update date |
Aug 05, 2021 |
| Contact name |
Kai Kretzschmar |
| E-mail(s) |
[email protected]
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| Organization name |
University Hospital Würzburg
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| Street address |
Josef-Schneider-Str. 2
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| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE165379 |
Troy/Tnfrsf19 marks epidermal cells that govern interfollicular epidermal renewal and cornification |
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| Relations |
| BioSample |
SAMN19873729 |
| SRA |
SRX11230317 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5401057_TroyM01.coutt.csv.gz |
285.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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