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Sample GSM2804248 Query DataSets for GSM2804248
Status Public on Jul 02, 2018
Title ORG_noNR_HFmedium_DF_2
Sample type SRA
Source name RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, without Noggin and R-Spondin-1, differentiation medium, replicate 2
Organism Canis lupus familiaris
Characteristics cell type: bulk cells of organoids, from hair follicles
protocol: mid-term in culture, 7 days after culture, without Noggin and R-Spondin-1, differentiation medium
passages: 3-6
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description cells from cultured organoids
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.
Submission date Oct 05, 2017
Last update date May 15, 2019
Contact name Onur BASAK
Organization name Hubrecht Institute
Lab Clevers
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
Platform ID GPL21400
Series (1)
GSE104622 Establishment of adult epidermal organoid cultures from canine hair follicles and interfollicular epidermis
BioSample SAMN07740604
SRA SRX3244847

Supplementary file Size Download File type/resource
GSM2804248_ORG_noNR_HFmedium_DF_2.csv.gz 71.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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