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| Status |
Public on Jul 02, 2018 |
| Title |
ORG_EFA83_HFearly_3 |
| Sample type |
SRA |
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| Source name |
RNA from bulk cells of organoids, from hair follicles, early in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 3
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| Organism |
Canis lupus familiaris |
| Characteristics |
cell type: bulk cells of organoids, from hair follicles
protocol: early in culture, 7 days after culture, with Tgf-beta inhibitor
passages: 0-1
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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-seq2 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 |
cells from cultured organoids
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| Data processing |
Paired end reads were aligned to the transcribed regions on the canis lupus (dog) genome using bwa. Since no reliable fully annotated transcriptome of dog was available, ncbi gff annotation (version 103) was used to build the transcriptome file using the CanFam3.1 genome build as a reference. Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. 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. Reads mapping to multiple loci were also included and distributed to the matching target loci. 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 total number of reads for every transcript.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: *.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.
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| Submission date |
Oct 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Onur BASAK |
| E-mail(s) |
onurbasak@yahoo.com
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| Organization name |
Hubrecht Institute
|
| Lab |
Clevers
|
| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platform ID |
GPL21400 |
| Series (1) |
| GSE104622 |
Establishment of adult epidermal organoid cultures from canine hair follicles and interfollicular epidermis |
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| Relations |
| BioSample |
SAMN07740617 |
| SRA |
SRX3244840 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2804241_ORG_EFA83_HFearly_3.csv.gz |
92.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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