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Chromatin accessibility maps and RNA-seq of human kidney cortex and medulla

ABSTRACT: Chromatin accessibility maps and RNA-seq of human kidney cortex and medulla

PROVIDER: PRJNA638925 | ENA |

REPOSITORIES: ENA

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Chromatin accessibility maps in human kidney cortex and medulla

Project description:We report chromatin accessibility (ATAC-seq) maps from macro-dissected human kidney cortex and medulla from 3 individuals

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Chromatin accessibility maps in human kidney cortex and medulla

Project description:We report chromatin accessibility (ATAC-seq) maps from macro-dissected human kidney cortex and medulla from 3 individuals. The samples were from patients undergoing kidney removal for tumors, but the tissues used in the study itself were normal tissue/cultured cells not involved by tumor.

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Project description:We report gene expression (RNA-seq) from macro-dissected human kidney cortex and medulla from 3 individuals. The samples were from patients undergoing kidney removal for tumors, but the tissues used in the study itself were normal tissue/cultured cells not involved by tumor.

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The effect of cortex/medulla proportions on molecular diagnoses in kidney transplant biopsies: rejection and injury can be assessed in medulla

Project description:Histologic assessment of kidney transplant biopsies relies on cortex rather than medulla, but for microarray studies, the proportion cortex in a biopsy is typically unknown and could affect the molecular readings. The present study aimed to develop a molecular estimate of proportion cortex in biopsies and examine its effect on molecular diagnoses. Microarrays from 26 kidney transplant biopsies divided into cortex and medulla components and processed separately showed that many of the most significant differences were in glomerular genes e.g. NPHS2, NPHS1, CLIC5, PTPRO, PLA2R1, PLCE1, PODXL and REN. Using NPHS2 (podocin) to estimate proportion cortex, we examined whether proportion cortex influenced molecular assessment in the Molecular Microscope Diagnostic System. In 1190 unselected kidney transplant indication biopsies (Clinicaltrials.govNCT01299168), only 11% had <50% cortex. Molecular scores for ABMR, TCMR, and injury were independent of proportion cortex. Rejection was diagnosed in many biopsies that were mostly or all medulla. Agreement in molecular diagnoses in paired cortex/medulla samples (23/26) was similar to biological replicates (32/37). We conclude that NPHS2 expression can estimate proportion cortex; that proportion cortex has little influence on molecular diagnosis of rejection, and that, although histology cannot assess medulla, rejection does occur in medulla as well as cortex.

2017-04-27 | GSE95611 | GEO

The effect of cortex/medulla proportions on molecular diagnoses in kidney transplant biopsies: rejection and injury can be assessed in medulla

2017-04-27 | E-GEOD-95611 | biostudies-arrayexpress

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