exRNAdisease

Entry Detail

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General Information

Database ID: exR0000334 RNA Name: ADRA2C RNA Type: mRNA Chromosome: chr4 Starnd: + Coordinate: Start Site(bp): 3766348 End Site(bp): 3768526 External Links: ENSG00000184160

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 AC010422.3 chr19 12643831 12648397 - AC093525.1 chr16 2513965 2527955 + AGPS chr2 177392757 177559299 + ATP6V0C chr16 2513952 2520218 + BRCA1 chr17 43044295 43170245 - EEF2 chr19 3976056 3985463 - EIF1 chr17 41688885 41692668 + EMID1 chr22 29205896 29259597 + MAGED1 chrX 51803007 51902357 + MARK2 chr11 63838928 63911019 + MFGE8 chr15 88898683 88913381 - NAP1L1 chr12 76036585 76084958 - PCBP1 chr2 70087477 70089203 + PKM chr15 72199029 72231822 - POLR3D chr8 22245133 22254601 + PRKD1 chr14 29576479 30191898 - PSIP1 chr9 15464066 15510995 - PTMA chr2 231706895 231713541 + RACK1 chr5 181236897 181248096 - RPL8 chr8 144789765 144792587 - SAMD11 chr1 923928 944581 + SH3BP4 chr2 234952017 235055714 + SNRPB chr20 2461634 2470853 - USO1 chr4 75724593 75814286 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC060780.1 chr17 43148368 43171037 - FOXD3-AS1 chr1 63320884 63324441 - 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.