Genomics

Dataset Information

0

Defining Housekeeping Genes Suitable for RNA-seq Analysis of the Human Allograft Kidney Biopsy Tissue


ABSTRACT: This study has used nine different normalization methods to derive housekeeping genes from a RNA-seq data set of 47611 transcripts derived from 30 biopsies. Overall design: The biopsies were collected in a variety of clinical settings, with 5 replicates each of the following clinicla settings: 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 sets available in the Gene Expression Omnibus.

INSTRUMENT(S): Ion Torrent Proton (Homo sapiens)

ORGANISM(S): Homo sapiens  

SUBMITTER: Parmjeet Randhawa  

PROVIDER: GSE120495 | GEO | 2019-07-10

REPOSITORIES: GEO

Dataset's files

Source:
altmetric image

Publications

Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue.

Wang Zijie Z   Lyu Zili Z   Pan Ling L   Zeng Gang G   Randhawa Parmjeet P  

BMC medical genomics 20190617 1


<h4>Background</h4>RNA-seq is poised to play a major role in the management of kidney transplant patients. Rigorous definition of housekeeping genes (HKG) is essential for further progress in this field. Using single genes or a limited set HKG is inherently problematic since their expression might be altered by specific diseases in the patients being studied.<h4>Methods</h4>To generate a HKG set specific for kidney transplantation, we performed RNA-sequencing from renal allograft biopsies collec  ...[more]

Similar Datasets

2019-01-01 | S-EPMC6580566 | BioStudies
2020-01-01 | S-EPMC7486173 | BioStudies
2014-06-01 | E-GEOD-53605 | ArrayExpress
2011-02-02 | E-GEOD-26578 | ArrayExpress
2014-01-01 | S-EPMC4377109 | BioStudies
2016-01-01 | S-EPMC4986254 | BioStudies
2011-02-02 | GSE26578 | GEO
2013-01-01 | S-EPMC3537210 | BioStudies
2017-01-01 | S-EPMC5734859 | BioStudies
2009-01-01 | S-EPMC2697362 | BioStudies