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| Status |
Public on May 31, 2024 |
| Title |
LP03009 |
| Sample type |
SRA |
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| Source name |
gingiva
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| Organism |
Homo sapiens |
| Characteristics |
tissue: gingiva
cell line: primary cells
cell type: gingival fibroblasts
genotype: wildtype
treatment: untreated
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| Treatment protocol |
Gingival fibroblasts were exposed to 30% PRF lysate and 10% PRF serum for 6 hours under standard conditions at 37 °C, 5% CO2, and 95% humidity.
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| Growth protocol |
Gingival fibroblasts were grown in Minimum Essential Medium Eagle (Sigma–Aldrich, St. Louis, MO, USA) supplemented with 10% fetal calf serum (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics (Sigma). The cells were seeded at 30,000 cells/cm2 onto culture dishes one day before being stimulated.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated utilizing the ExtractMe total RNA kit manufactured by Blirt S.A., Gdańsk, Poland.
Sequencing libraries were prepared at the Core Facility Genomics, Medical University of Vienna, using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocols (New England Biolabs, Ipswich, MA) with unique dual indices (UDI). Libraries were QCchecked on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA H.S. Assay (Invitrogen, Waltham, MA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
none
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| Data processing |
Illumina bcl2fastq command line tool (v2.19.1.403)
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403), incl. trimming of the sequencing adapters.
Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Raw reads per gene were counted by STAR. Batch correction was performed using ComBat from sva version 3.35.2.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: ProcessedDataMatrix.txt.gz contains a matrix with raw gene counts, gene symbols and gene types for each sample
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| Submission date |
May 23, 2024 |
| Last update date |
May 31, 2024 |
| Contact name |
Reinhard Gruber |
| E-mail(s) |
reinhard.gruber@meduniwien.ac.at
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| Organization name |
Medical University Vienna
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| Department |
University Dental Clinic
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| Lab |
Competence Center Oral Biology
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| Street address |
Sensengasse 2a,
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| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE268248 |
RNAseq of gingival fibroblasts exposed to PRF membranes and PRF serum. |
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| Relations |
| BioSample |
SAMN41513438 |
| SRA |
SRX24672008 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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