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Sample GSM6420003 Query DataSets for GSM6420003
Status Public on May 01, 2024
Title NP36
Sample type SRA
 
Source name renal tissue, FFPE
Organism Homo sapiens
Characteristics tissue: renal tissue, FFPE
gender: Male
age: 33
analysis group: nonprog
igan: yes
Treatment protocol The diagnostic kidney biopsy specimens were processed and stored as formalin-fixed and paraffin-embedded (FFPE) tissue, as routinely done at our institution. Laser capture microdissection for isolation of 10µm thick glomerular cross-sections was carried out using Leica LMD7 (Wetzlar, Germany). We collected on average 62 glomerular cross sections from each biopsy.
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using the miRNeasy FFPE kit (cat. no. 217504; Qiagen, Venlo, The Netherlands), as described previously (13). Following RNA extraction, the samples were stored at -80oC until further use.
RNA library preparation and sequencing were carried out at Functional Genomics Centre Zurich (University of Zurich, Switzerland). The quantity and quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Tapestation (Agilent, Waldbronn, Germany). Median DV200 values of the included patients were 36.4% (IQR 29.4-42.7%). The SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clontech Laboratories, Inc., A Takara Bio Company, California, USA) was used in the succeeding steps. Quality and quantity of the enriched libraries was validated using Qubit® (1.0) Fluorometer and Tapestation (Agilent, Waldbronn, Germany). The NovaSeq 6000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocol. For a detailed description, see Supplementary Methods.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Trimmed sequence reads were mapped to Genome Reference Consortium Human Build 38 (GRCh38)
Counts per millions were log transformed and Trimmed mean of M values normalization was applied to adjust for variation in library size.
Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) and Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) were used for assembly of reads and alignment of the contigs to the human genome assembly
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample
 
Submission date Jul 29, 2022
Last update date May 01, 2024
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 GPL24676
Series (1)
GSE210098 Glomerular transcriptomics predicts outcome and identifies therapeutic strategies for patients with assumed benign IgA nephropathy

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

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