exRNAdisease

Entry Detail

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General Information

Database ID: exR0012395 RNA Name: RPS18 RNA Type: mRNA Chromosome: chr6 Starnd: + Coordinate: Start Site(bp): 33272075 End Site(bp): 33276511 External Links: ENSG00000231500

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 AHCY chr20 34280268 34311802 - AKIRIN1 chr1 38991276 39006059 + AC015802.6 chr17 76563710 76570544 - AC024592.3 chr19 5866171 5903787 - ABRACL chr6 139028745 139043302 + ABTB2 chr11 34150987 34358010 - ADGRL2 chr1 81306160 81992436 + AIFM1 chrX 130129362 130165887 - ALDOA chr16 30064164 30070457 + AKR1A1 chr1 45550543 45570049 + AC005258.1 chr19 2269525 2341172 + AFG3L2 chr18 12328944 12377227 - ABCB7 chrX 75051048 75156732 - AGO2 chr8 140520156 140635633 - AASDH chr4 56338287 56387508 - AKT1S1 chr19 49869033 49878459 - AC011462.1 chr19 41350853 41425001 + ACTB chr7 5527148 5563784 - AEBP2 chr12 19404045 19720801 + ACTR3 chr2 113890063 113962596 + AAR2 chr20 36236459 36270918 + AC008982.1 chr19 38817471 38840178 - ACAA2 chr18 49782164 49813953 - AC007040.2 chr2 70939318 70995336 - ADRA2A chr10 111077029 111080907 + AC011005.1 chr7 129126518 129130793 + AC023055.1 chr12 55757275 55827546 - ACTR2 chr2 65227753 65271253 + AC010422.3 chr19 12643831 12648397 - AC073508.2 chr17 40627356 40665141 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC004080.6 chr7 27128969 27152561 - AC004687.1 chr17 58330884 58332508 - AC021078.1 chr5 149494314 149504670 - AC040162.3 chr16 67882461 67886367 + AC091564.7 chr11 6610883 6616594 - AC105339.2 chr15 82752884 82757208 + AC138089.1 chr1 248484245 248485484 - 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.