exRNAdisease

Entry Detail

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General Information

Database ID: exR0000456 RNA Name: AKR1B1 RNA Type: mRNA Chromosome: chr7 Starnd: - Coordinate: Start Site(bp): 134442356 End Site(bp): 134459284 External Links: ENSG00000085662

Disease Information

Disease Name: Down Syndrome Disease Category: Congenital, Hereditary, and Neonatal Diseases and Abnormalities MeSH ID: D004314 Type: Diseases Category/Congenital, Hereditary, and Neonatal Diseases and Abnormalities Alias: Syndrome, Down//Mongolism//47,XY,+21//Trisomy G//47,XX,+21//Down's Syndrome//Downs Syndrome//Syndrome, Down's//Trisomy 21//Trisomy 21, Mitotic Nondisjunction//Down Syndrome, Partial Trisomy 21//Partial Trisomy 21 Down Syndrome//Trisomy 21, Meiotic Nondisjunction

Expression Detail

GEO ID: GSE16176 Description: Expression profiles of amniotic fluid from human fetuses with Down syndrome and euploid controls Experimental Design: Disease vs Control Case Disease Type: Down Syndrome Case Disease SubType: NA Case Sample: Down Syndrome Control Sample: Normal Number of Case: 7 Number of Control: 7 Number of Samples: 14

Regulatory Relationship

mRNA targets: Gene Symbol Chromosome Start Site(bp) End Site(bp) Strand TUBB chr6 30720352 30725426 + PKM chr15 72199029 72231822 - INPP5F chr10 119726042 119829147 + P4HB chr17 81843161 81860624 - RPL3 chr22 39312882 39320389 - CKB chr14 103519667 103522833 - SLC12A4 chr16 67943474 67969601 - CCNB1IP1 chr14 20311368 20333312 - RPL26 chr17 8377516 8383213 - ARHGDIB chr12 14942031 14961728 - EDARADD chr1 236348257 236502915 + KLHDC3 chr6 43014103 43021298 + STK4 chr20 44966479 45080021 + TRIR chr19 12730640 12734684 - PTGIS chr20 49503874 49568137 - C12orf49 chr12 116710171 116738070 - TOMM7 chr7 22812628 22822852 - FSCN3 chr7 127591409 127602144 + CFL1 chr11 65823022 65862026 - ATP5ME chr4 672436 674330 - YWHAH chr22 31944522 31957603 + ZNF516 chr18 76357682 76495242 - GDF1 chr19 18868545 18896158 - FLRT3 chr20 14322985 14337614 - AKR1A1 chr1 45550543 45570049 + ACTB chr7 5527148 5563784 - RPL36 chr19 5674947 5691875 + PTPA chr9 129110950 129148946 + HOXB1 chr17 48528526 48531011 - ZNF277 chr7 112206695 112343934 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC135178.2 chr17 8318088 8318712 - NORAD chr20 36045618 36051018 - POLR2J4 chr7 43940895 44019175 - SNHG12 chr1 28578538 28583132 - Display:

Experiment Detail

GEO ID: GSE16176 Sample Source: Amniotic Fluid Source Fraction: Supernatant Platform: GPL570 Method: Microarray Num of detected RNA Type: 1 Num of detected RNAs of this Type: 17063 Sample treatment protocol: NA RNA Extract protocol: RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer's protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA). RNA library preparation protocol: biotin Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

Reference

PMID: 19474297 Title: Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses Author: Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW Journal: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9425-9. Description: To characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we used Affymetrix microarrays to compare gene expression in uncultured amniotic fluid supernatant samples.