exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000297 RNA Name: ADD3 RNA Type: mRNA Chromosome: chr10 Starnd: + Coordinate: Start Site(bp): 109996368 End Site(bp): 110135565 External Links: ENSG00000148700

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 ZNF90 chr19 20077994 20127076 + SLC2A3 chr12 7919230 7936187 - C16orf72 chr16 9091644 9121635 + SMARCB1 chr22 23786931 23838008 + MAGI1 chr3 65353525 66038834 - STK26 chrX 132023302 132075943 + GGH chr8 63015079 63038806 - AASS chr7 122073549 122144255 - AC011462.1 chr19 41350853 41425001 + COPS3 chr17 17246616 17281273 - HDGF chr1 156742109 156766925 - ATP6V1G1 chr9 114587769 114598879 + TIMELESS chr12 56416363 56449426 - CNTNAP2 chr7 146116002 148420998 + CNTN2 chr1 205042937 205078289 + TBCD chr17 82752065 82945914 + TM9SF4 chr20 32109714 32167258 + EXOSC8 chr13 36998816 37009614 + KHNYN chr14 24429286 24441843 + CLTA chr9 36190856 36304781 + MEST chr7 130486171 130506465 + MT-CO1 chrMT 5904 7445 + SELENOF chr1 86862445 86914424 - TOX4 chr14 21476597 21499175 + TMED5 chr1 93149742 93180516 - HILPDA chr7 128455849 128458418 + BCAS3 chr17 60677453 61392838 + RBMX chrX 136848004 136880764 - MRPS23 chr17 57834781 57850056 - TPT1 chr13 45333471 45341370 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC002470.2 chr22 20979462 20998121 + AC020928.1 chr19 36773112 36777078 + MALAT1 chr11 65497688 65506516 + 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.