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Sample GSM5909504 Query DataSets for GSM5909504
Status Public on Jan 19, 2023
Title RNA-seq primary fibroblast WT2
Sample type SRA
 
Source name primary cutaneous fibroblasts
Organism Homo sapiens
Characteristics proband: WT2
Treatment protocol No treatment
Growth protocol Primary patient-derived Fibroblast cells were cultured at 5% CO2 and 37°C in high glucose DMEM (HyClone) supplemented with 10% fetal bovine serum (FBS) (HyClone), 1X penicillin/streptomycin (Thermo Fisher Scientific) and 2 mM L-glutamine (Biological Industries)
Extracted molecule polyA RNA
Extraction protocol RNA from primary dermal fibroblasts was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing according to standard manufacturer's protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Mapping: Reads are aligned using the STAR aligner (v2.5.3a) (Dobin et al., 2013) with the default parameters to the human GRCh38.p12 reference genome. The alignment was performed with the GENCODE annotation v28.
Quantification: Transcript abundance of the annotated genes from GENCODE v2852 using HTSeq v0.11.453 in 'union' mode.
Genome_build: Human (hg38/GRCh38)
Supplementary_files_format_and_content: bigWig files: transcript coverage of uniquely mapped reads.
 
Submission date Feb 21, 2022
Last update date Jan 19, 2023
Contact name Dr. Andreas Mayer
Organization name Max-Plack-Institute for molecular genetics
Street address Ihnestraße 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
 
Platform ID GPL24676
Series (2)
GSE197118 A Progeroid Syndrome with Severe Osteogenesis Imperfecta segregates with an Intronic TAPT1 homozygous Variant that Creates a knockout allele [RNA-seq]
GSE197120 A Progeroid Syndrome with Severe Osteogenesis Imperfecta segregates with an Intronic TAPT1 homozygous Variant that Creates a knockout allele
Relations
BioSample SAMN26137515
SRA SRX14241587

Supplementary file Size Download File type/resource
GSM5909504_RHK134.neg.bw 68.3 Mb (ftp)(http) BW
GSM5909504_RHK134.pos.bw 69.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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