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Sample GSM6266906 Query DataSets for GSM6266906
Status Public on Sep 22, 2023
Title KC_bulkRNAseq_1
Sample type SRA
 
Source name PKC19
Organism Homo sapiens
Characteristics cell line: PKC19
cell type: Epidermal keratinocytes
genotype: WT
Growth protocol primary KCs  were cultured in Keratinocyte Basal Medium supplemented with 100 U/mL Penicillin/Streptomycin, 0.1 mM ethanolamine, 0.1 mM O-phosphoethanolamine, 0.4% bovine pituitary extract, 0.5 μg/mL hydrocortisone, 5 μg/mL insulin and 10 ng/mL epidermal growth factor. Medium was refreshed every other day until the cells were 90% confluent.  LSC were cultured in KSFM supplemented with 25 μg/ml Bovine Pituitary Extract, 0.2 ng/ml Epidermal Growth Factor, 0.4 mM CaCl2, 2 mM Glutamine and 100 U/ml Penicillin/Streptomicin. Medium was refreshed every other day untill the cells were 90% confluent.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Quick–RNA MicroPrep kit, according to the manufacturer’s protocol. RNA concentrations were measured using the the DeNovix DS-11FX spectrometer.
500 ng of RNA was was prepared for sequencing using the KAPA RNA HyperPrep Kit with. Libraries were sequenced on the Illumina NextSeq 500, generating an average of 15–20 million reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description KC_bulkRNAseq_1
Data processing Preprocessing of reads was done automatically with workflow tool seq2science v0.7.1
Paired-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.11.1. The effective genome size was estimated per sample by khmer v2.0 by calculating the number of unique kmers with k being the average read length per sample. Reads of RNAseq samples were aligned with STAR v2.7.6a with default options. Afterwards, duplicate reads were marked with Picard MarkDuplicates v2.23.8. General alignment statistics were collected by samtools stats v1.14. Mapped reads were removed if they did not have a minimum mapping quality of 30, were a (secondary) multimapper or aligned inside the ENCODE blacklist. RNAseq sample counting and summarizing to gene-level was performed on filtered bam using HTSeq-count v0.12. Sample sequencing strandedness was inferred using RSeQC v4.0.0 order to improve quantification accuracy.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene count values for each Sample
 
Submission date Jun 24, 2022
Last update date Sep 22, 2023
Contact name Jo Huiqing Zhou
E-mail(s) jo.zhou@radboudumc.nl
Organization name Radboud University
Street address Geert Grooteplein 26/28
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
 
Platform ID GPL18573
Series (2)
GSE206922 Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease [RNA-seq]
GSE206924 Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease
Relations
BioSample SAMN29336054
SRA SRX15891797

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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