exRNAdisease

Entry Detail

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General Information

Database ID: exR0000455 RNA Name: AKR1A1 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 45550543 End Site(bp): 45570049 External Links: ENSG00000117448

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 COG8 chr16 69320140 69339667 - ATXN7L3 chr17 44191805 44200113 - HNRNPUL1 chr19 41262496 41307787 + SNRPB chr20 2461634 2470853 - ZMAT2 chr5 140698680 140706686 + MRPL10 chr17 47823272 47831541 - EPS15 chr1 51354263 51519266 - FBLN1 chr22 45502238 45601135 + EEF1G chr11 62559596 62574086 - SLC2A4RG chr20 63739776 63744050 + POU3F2 chr6 98834574 98839458 + UBAP2L chr1 154220179 154271510 + PDK1 chr2 172555373 172608669 + RNF126 chr19 647526 663233 - MTRNR2L6 chr7 142666272 142667718 + DR1 chr1 93345907 93369493 + ZNF292 chr6 87152833 87265943 + TKT chr3 53224712 53256052 - CLUH chr17 2689386 2712663 - FP565260.6 chr21 5155499 5165472 - WDR74 chr11 62832342 62841809 - SEC13 chr3 10293131 10321112 - CDKN1A chr6 36676460 36687339 + MRPL33 chr2 27771717 27988087 + RNF114 chr20 49936336 49953885 + C1orf43 chr1 154206696 154220637 - HDGF chr1 156742109 156766925 - NAA60 chr16 3443649 3486953 + CBS chr21 43053191 43076943 - RPL3 chr22 39312882 39320389 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AD000090.1 chr19 35557956 35581954 + AC069287.1 chr11 112967 125927 - AL031005.1 chr1 21266082 21267251 + AL359924.1 chr1 237862175 237928321 + LINC01641 chr1 227393554 227431035 + MALAT1 chr11 65497688 65506516 + POLR2J4 chr7 43940895 44019175 - SLX1A-SULT1A3 chr16 30193892 30204310 + SNHG1 chr11 62851984 62855953 - SNHG3 chr1 28505980 28510892 + ZNF528-AS1 chr19 52388842 52397783 - 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.