exRNAdisease

Entry Detail

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General Information

Database ID: exR0000154 RNA Name: ACOT8 RNA Type: mRNA Chromosome: chr20 Starnd: - Coordinate: Start Site(bp): 45841721 End Site(bp): 45857405 External Links: ENSG00000101473

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 BAHD1 chr15 40439721 40468236 + RPS14 chr5 150442635 150449739 - C19orf53 chr19 13774456 13778773 + B2M chr15 44711487 44718877 + CHST15 chr10 124007668 124093598 - HAUS7 chrX 153447666 153495516 - CANX chr5 179678628 179731641 + SRPK2 chr7 105110704 105399308 - SZRD1 chr1 16352575 16398145 + CCL3 chr17 36088256 36090169 - HVCN1 chr12 110627841 110704950 - MAP7D1 chr1 36155579 36180849 + VMP1 chr17 59707192 59842255 + NCF4 chr22 36860988 36878017 + WBP1 chr2 74458400 74460891 + SBK1 chr16 28259246 28323849 + SLC16A1 chr1 112911847 112957013 - ARPC4 chr3 9792495 9807726 + CIC chr19 42268537 42295797 + PPP2R5C chr14 101761798 101927989 + CDK2 chr12 55966781 55972789 + GCSAM chr3 112120839 112133270 - EP400 chr12 131949942 132080460 + ABCD4 chr14 74285269 74303055 - RPL27A chr11 8682788 8714759 + PYURF chr4 88520998 88523776 - SAP18 chr13 21140514 21149084 + H6PD chr1 9234775 9271337 + NOP53 chr19 47745546 47757058 + TRIM45 chr1 117111060 117122587 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand BX890604.2 chrX 3817528 3937855 - 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.