exRNAdisease

Entry Detail

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General Information

Database ID: exR0009161 RNA Name: NACC1 RNA Type: mRNA Chromosome: chr19 Starnd: + Coordinate: Start Site(bp): 13116862 End Site(bp): 13141147 External Links: ENSG00000160877

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 AAGAB chr15 67200667 67255195 - ABCF1 chr6 30571393 30597179 + AC005726.1 chr17 28455752 28614185 - AC011511.1 chr19 10305427 10316009 - AC099811.2 chr17 42119674 42154916 - ACACA chr17 37084992 37406836 - AEBP2 chr12 19404045 19720801 + AGAP6 chr10 49982190 50010499 + AHSA1 chr14 77457870 77469472 + AL117348.2 chr1 225886696 225924278 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-103a-3p chr5 168560904 168560926 - hsa-miR-107 chr10 89592756 89592778 - hsa-miR-185-5p chr22 20033153 20033174 + hsa-miR-331-3p chr12 95308480 95308500 + hsa-miR-324-3p chr17 7223308 7223330 - hsa-miR-346 chr10 86264747 86264769 - hsa-miR-663a chr20 26208243 26208264 - hsa-miR-671-5p chr7 151238449 151238471 + hsa-miR-361-3p chrX 85903641 85903663 - hsa-miR-362-3p chrX 50009005 50009026 + hsa-miR-423-5p chr17 30117095 30117117 + hsa-miR-541-3p chr14 101064548 101064569 + hsa-miR-1294 chr5 154347153 154347174 + hsa-miR-1270 chr19 20399320 20399342 - hsa-miR-1307-3p chr10 103394301 103394322 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC002470.2 chr22 20979462 20998121 + AC018521.1 chr17 47945424 47981736 + AD000090.1 chr19 35557956 35581954 + 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.