exRNAdisease

Entry Detail

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General Information

Database ID: exR0000428 RNA Name: AK3 RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 4709556 End Site(bp): 4742043 External Links: ENSG00000147853

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 CD74 chr5 150400041 150412929 - BAZ2A chr12 56595596 56636816 - ERCC3 chr2 127257290 127294166 - MT-ATP6 chrMT 8527 9207 + RPLP0 chr12 120196699 120201235 - DYNC1H1 chr14 101964573 102056443 + TPRN chr9 137191617 137204193 - ATP1A1 chr1 116372668 116410261 + FNDC5 chr1 32862268 32872482 - BX255925.3 chr9 137217452 137219361 + CD9 chr12 6199715 6238271 + THOC6 chr16 3024027 3027755 + RAB7A chr3 128726183 128814798 + RPS3 chr11 75399515 75422280 + APTX chr9 32886601 33025130 - EIF5 chr14 103333544 103345025 + GAPDH chr12 6534512 6538374 + ZNF280D chr15 56630181 56734086 - BRK1 chr3 10115675 10127190 + FZD3 chr8 28494205 28574267 + FBXO38 chr5 148383935 148442836 + MTFR1L chr1 25818640 25832942 + RPS17 chr15 82536750 82540459 - RPL17 chr18 49488453 49492523 - ZNF8 chr19 58278955 58302791 + CHD4 chr12 6570082 6614524 - WDR11 chr10 120851305 120909524 + SELENOO chr22 50200979 50217616 + RPL32 chr3 12834485 12841582 - ACTG1 chr17 81509971 81523847 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand HOTAIRM1 chr7 27095647 27100265 + NBR2 chr17 43125551 43153671 + OIP5-AS1 chr15 41283990 41309737 + 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.