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Sample GSM5066713 Query DataSets for GSM5066713
Status Public on Dec 01, 2023
Title T2DN_3
Sample type SRA
 
Source name whole FFPE renal biopsy sections (10 μm thickness)
Organism Homo sapiens
Characteristics diagnosis: Type 2 diabetic nephropathy
age: 81
gender: Female
hypertension: yes
systolic bp: 210
diastolic bp: 80
diabetes: yes
egfr (ml/min/m2): 47.2
proteinuria (g/d): 10.6
arb/acei: ACEI, ARB
tissue: whole FFPE renal biopsy sections (10 μm thickness)
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
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
 
Submission date Feb 05, 2021
Last update date Dec 01, 2023
Contact name Philipp Strauss
E-mail(s) Philipp.Strauss@uib.no
Organization name University of Bergen
Street address Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst
City Bergen
ZIP/Postal code 5020
Country Norway
 
Platform ID GPL18573
Series (1)
GSE166239 Partial epithelial-to-mesenchymal transition (EMT) and T cell-mediated inflammation in hypertensive and diabetic nephropathy
Relations
BioSample SAMN17808573

Supplementary data files not provided
Processed data are available on Series record
Raw data not provided for this record

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