exRNAdisease

Entry Detail

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General Information

Database ID: exR0000013 RNA Name: AAK1 RNA Type: mRNA Chromosome: chr2 Starnd: - Coordinate: Start Site(bp): 69457997 End Site(bp): 69674349 External Links: ENSG00000115977

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 ACAP2 chr3 195274745 195443044 - ADD2 chr2 70607618 70768225 - BANP chr16 87949244 88077318 + CDC42 chr1 22025511 22101360 + CDK18 chr1 205504595 205532793 + CFLAR chr2 201116154 201176687 + CHPT1 chr12 101696947 101744140 + CNDP2 chr18 74495816 74523454 + CTNNA1 chr5 138610967 138935034 + GNL3 chr3 52681156 52694497 + HCN1 chr5 45254948 45696498 - HDLBP chr2 241227264 241317061 - HUWE1 chrX 53532096 53686728 - MT-ATP6 chrMT 8527 9207 + PAICS chr4 56435741 56464579 + PPP1CB chr2 28751640 28802940 + PRRC2B chr9 131373636 131500197 + PSMB2 chr1 35599541 35641526 - PTPRZ1 chr7 121873089 122062036 + SH2B3 chr12 111405923 111451623 + SLCO3A1 chr15 91853708 92172435 + SNRNP200 chr2 96274338 96321271 - SRP14 chr15 40035690 40039181 - SSH2 chr17 29625938 29930276 - TRIM65 chr17 75880335 75896951 - TRIO chr5 14143342 14532128 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC008764.6 chr19 16542746 16544814 + AC069544.1 chr10 14877688 14878686 - 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.