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| Status |
Public on Jun 18, 2020 |
| Title |
IPF patient 15 |
| Sample type |
SRA |
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| Source name |
cultured epithelial cells
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| Organism |
Homo sapiens |
| Characteristics |
condition: idiopathic pulmonary fibrosis (IPF)
cell type: Epithelial cells differentiated from mesenchymal stems cell-like cells
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| Treatment protocol |
Epithelial cell-specific growth medium Cnt-17 (CELLnTEC Advanced Cell Systems AG, Bern, Switzerland)
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| Growth protocol |
DMEM supplemented with fetal bovine serum (10%), penicillin (20 U/l), streptomycin (20 μg/ml), amphotericin B (2.5 μg/ml) (37°C, 21% O2, 5% CO2)
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| Extracted molecule |
total RNA |
| Extraction protocol |
MicroElute Total RNA Kit (Omega Bio-Tek, Norcross, GA)
TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina, San Diego, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
BSSE_QGF_105593
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| Data processing |
Primary analysis of sequencing data was conducted using RTA version 2.4.11 and bcl2fastq v2.20.0.422 (both from Illumina)
All analyses were done using the R statistical software, including packages from the Bioconductor such edgeR (v. 3.24.3)
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the human hg38 genome assembly with STAR with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax =10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Gene expression was quantified by the qCount function of the Bioconductor package QuasR as the number of reads that started within any annotated exon of a gene from the UCSC knownGenes annotation (downloaded on 2017-04-03). Read and alignment quality was evaluated using the qQCReport function of QuasR.
Genome_build: hg38
Supplementary_files_format_and_content: dataset2_hg38AnalysisSet_knownGene_geneLevel_counts.rds, dataset2_hg38AnalysisSet_knownGene_geneLevel_counts.csv
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| Submission date |
Jun 02, 2020 |
| Last update date |
Jun 18, 2020 |
| Contact name |
Florent Baty |
| E-mail(s) |
[email protected]
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| Phone |
0041 71 494 2809
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| Organization name |
Cantonal Hospital St. Gallen
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| Department |
Lung Center
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| Street address |
Rorschacherstrasse 95
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| City |
St. Gallen |
| ZIP/Postal code |
9007 |
| Country |
Switzerland |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE151673 |
Transcriptomic Profiling of Fibrosis-Specific Epithelial Cells in Idiopathic Pulmonary Fibrosis |
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| Relations |
| BioSample |
SAMN15086229 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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