exRNAdisease

Entry Detail

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General Information

Database ID: exR0000059 RNA Name: ABCD3 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 94418389 End Site(bp): 94518666 External Links: ENSG00000117528

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 SLC25A6 chrX 1386152 1392113 - RPL13 chr16 89560657 89566828 + ACYP2 chr2 53970838 54305300 + RPL15 chr3 23916545 23924374 + C18orf25 chr18 46173553 46266992 + GFM1 chr3 158644278 158692575 + SH3KBP1 chrX 19533977 19887600 - EGLN2 chr19 40798996 40808434 + MIF chr22 23894383 23895227 + LTA4H chr12 96000753 96043520 - RIC1 chr9 5629025 5776557 + EIF3L chr22 37848868 37889407 + SMIM13 chr6 11093834 11138733 + ZKSCAN8 chr6 28141883 28159460 + NACA chr12 56712427 56731628 - CBX4 chr17 79833156 79839440 - RPS6 chr9 19375715 19380236 - HNRNPR chr1 23303771 23344336 - RPL28 chr19 55385345 55403250 + MYCN chr2 15940550 15947007 + PELP1 chr17 4669774 4704337 - HSP90AA1 chr14 102080738 102139699 - GMPS chr3 155870650 155944020 + COPA chr1 160288594 160343273 - PLEKHO2 chr15 64841883 64868002 + MAP2K4 chr17 12020829 12143830 + LAPTM4B chr8 97775057 97853013 + RBX1 chr22 40951347 40973309 + C11orf24 chr11 68261338 68272001 - CRYL1 chr13 20403666 20525873 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL022311.1 chr22 37876148 37895563 + XIST chrX 73820649 73852723 - 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.