exRNAdisease

Entry Detail

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General Information

Database ID: exR0000114 RNA Name: ACAD9 RNA Type: mRNA Chromosome: chr3 Starnd: + Coordinate: Start Site(bp): 128879596 End Site(bp): 128916067 External Links: ENSG00000177646

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 ATP5F1E chr20 59025475 59032345 - AC138811.2 chr16 18788063 18801519 - GNA12 chr7 2728105 2844308 - MAVS chr20 3846799 3876123 + TGS1 chr8 55773446 55826445 + RPS4X chrX 72255679 72277248 - CABIN1 chr22 24011192 24178628 + SLC30A9 chr4 41990502 42090461 + SRSF7 chr2 38743599 38751494 - RPS13 chr11 17074388 17077715 - MIB2 chr1 1615415 1630610 + EDARADD chr1 236348257 236502915 + ARFIP1 chr4 152779937 152918463 + EI24 chr11 125569280 125584684 + RPS25 chr11 119015712 119018691 - GTF3C2 chr2 27325849 27357034 - ATP6V1F chr7 128862856 128865847 + SLC36A1 chr5 151437046 151492379 + RBMX chrX 136848004 136880764 - MT-ND2 chrMT 4470 5511 + B2M chr15 44711487 44718877 + TOB1 chr17 50862223 50867978 - ZNF551 chr19 57681969 57717301 + PEBP1 chr12 118136124 118145584 + ATP5MC2 chr12 53632726 53677408 - EEF2 chr19 3976056 3985463 - VIPAS39 chr14 77426675 77457952 - SLC18A2 chr10 117241093 117279430 + MID1IP1 chrX 38801432 38806537 + SNRNP200 chr2 96274338 96321271 - miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.