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| Status |
Public on Dec 01, 2023 |
| Title |
T2DN_4 |
| Sample type |
SRA |
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| Source name |
whole FFPE renal biopsy sections (10 μm thickness)
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| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Type 2 diabetic nephropathy
age: 57
gender: Male
hypertension: yes
systolic bp: 160
diastolic bp: 85
diabetes: yes
egfr (ml/min/m2): 48.97
proteinuria (g/d): 21
arb/acei: Non
tissue: whole FFPE renal biopsy sections (10 μm thickness)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole FFPE renal biopsy sections (10 μm thickness) using the High Pure FFPE-tissue RNA Isolation kit (catalogue no. 06650775001; Roche Holding AG, Basel, Switzerland)
RNA inputs of 38 to 1324 ng total RNA per sample were used for library preparation using the TruSeq RNA Access Library Preparation Kit (Illumina, Inc., San Diego, CA, USA). RNA sequencing was performed on an Illumina NextSeq500 system (Illumina, Inc., San Diego, CA, USA) as 75-bp paired ends, at the Genomics Core Facility, Norwegian University of Science and Technology (NTNU, Trondheim, Norway).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Assembled reads were aligned to the Homo sapiens hg38 reference genome using Gencode (https://www.gencodegenes.org/)
In R LIMMA, genes with at least 3 cpm in at least four samples were used in consecutive analysis.
Differential expression was defined as absolute fold-change (FC) value >2, and adjusted p-value <0.05
Genome_build: hg38
Supplementary_files_format_and_content: txt, log2 transformed, normalized counts in cpm
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| Submission date |
Feb 05, 2021 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Philipp Strauss |
| E-mail(s) |
Philipp.Strauss@uib.no
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| Organization name |
University of Bergen
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| Street address |
Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst
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| City |
Bergen |
| ZIP/Postal code |
5020 |
| Country |
Norway |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE166239 |
Partial epithelial-to-mesenchymal transition (EMT) and T cell-mediated inflammation in hypertensive and diabetic nephropathy |
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| Relations |
| BioSample |
SAMN17808572 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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