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Data from: Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue
Internal Dataset

UID: 80

Author(s): Wang, Zijie, Randhawa, Parmjeet*+ * Corresponding Author + University of Pittsburgh Author
Description
This study used nine different normalization methods to derive housekeeping genes from a RNA-seq data set of 47,611 transcripts derived from 30 biopsies. The biopsies were collected in a variety of clinical settings, with 5 replicates each: normal function, acute tubular injury, acute rejection, interstitial nephritis, interstitial fibrosis/tubular atrophy, and polyomavirus nephropathy. Transcripts with coefficient of variation below the 2nd percentile were designated as housekeeping genes, and validated by showing their virtual absence in diseased allograft derived transcriptomic data.
Timeframe
2018
Geographic Coverage
Pittsburgh, Pennsylvania
Subject of Study
Humans
Population Age
Adult
Subject Sex
Male
Female
Keywords
Allografts
Biopsy
Housekeeping Genes
Kidney
Sequence Analysis, RNA
Transplantation, Kidney
Access via GEO

Expression profiling by high throughput sequencing.
Accession #: GSE120495

Access via SRA

Raw data for 30 samples.
Accession #: SRP162632

Access via BioProject

Overall project information and data.
Accession #: PRJNA493201

Access Restrictions
Free to all
Access Instructions
The NCBI Gene Expression Omnibus, Sequence Read Archive, and BioProject databases provide open access to these files.
Associated Publications
Wang Z, Lyu Z, Pan L, Zeng G, Randhawa P. Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue. BMC Med Genomics. 2019 Jun 17;12(1):86. doi: 10.1186/s12920-019-0538-z. PMID: 31208411; PMCID: PMC6580566.
Data Type
Genetic/Genomic
Equipment Used
Ion Torrent Proton

High throughput sequencer

Software Used
Ingenuity Pathway Analysis

For modeling, analyzing, and understanding complex 'omics data

Dataset Format(s)
SOFT (.soft), MINiML (.miniml, .xml), XLS (.xls, .xlsx, .xlm, .xlsm), TXT (.txt)
Resource Type(s)
Dataset
Data Catalog Record Updated
2021-12-06

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