exRNAdisease

Entry Detail

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General Information

Database ID: exR0000327 RNA Name: ADPRHL2 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 36088892 End Site(bp): 36093932 External Links: ENSG00000116863

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 RPS6KL1 chr14 74903951 74923302 - VDAC2 chr10 75210154 75231448 + MT-ND3 chrMT 10059 10404 + ANAPC1 chr2 111611639 111884690 - TESC chr12 117038923 117099479 - HCFC2 chr12 104064531 104106524 + ATP5F1B chr12 56638175 56645984 - SRRT chr7 100875103 100888664 + CDK4 chr12 57747727 57756013 - RAB14 chr9 121178133 121223014 - OXSM chr3 25782917 25794534 + OAZ2 chr15 64687573 64703281 - CA12 chr15 63321378 63381846 - TTC28 chr22 27978014 28679865 - MIGA1 chr1 77779624 77879539 + CPZ chr4 8592660 8619759 + MCM5 chr22 35400134 35425431 + BRWD1 chr21 39184176 39321559 - IDI1 chr10 1039152 1049170 - STX16 chr20 58651253 58679526 + HLA-DQB1 chr6 32659467 32668383 - TNFRSF1A chr12 6328757 6342114 - STRAP chr12 15882387 15903478 + HLA-B chr6 31269491 31357188 - SPCS1 chr3 52704955 52711148 + TAGLN2 chr1 159918107 159925732 - RNASEK chr17 7012417 7014532 + EID2 chr19 39538707 39540161 - C1orf21 chr1 184387029 184629019 + SLC7A5 chr16 87830023 87869507 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC144548.1 chr12 110387463 110445548 - AL035458.2 chr20 34234840 34281173 - LINC01641 chr1 227393554 227431035 + 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.