exRNAdisease

Entry Detail

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General Information

Database ID: exR0000019 RNA Name: AARSD1 RNA Type: mRNA Chromosome: chr17 Starnd: - Coordinate: Start Site(bp): 42950526 End Site(bp): 42964498 External Links: ENSG00000266967

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 PTMS chr12 6765516 6770952 + KBTBD7 chr13 41189834 41194569 - PPDPF chr20 63520765 63522206 + PPP1CC chr12 110719680 110742939 - BLOC1S5-TXNDC5 chr6 7881522 8064364 - ZNF777 chr7 149431363 149461062 - CALM3 chr19 46601074 46610782 + HIGD2A chr5 176388751 176389761 + RPL35A chr3 197950190 197956610 + HNRNPF chr10 43385617 43409166 - CCNT2 chr2 134918235 134959342 + ERI2 chr16 20780193 20900349 - RPUSD3 chr3 9837849 9844602 - TPT1 chr13 45333471 45341370 - RNPS1 chr16 2253116 2268397 - CALR chr19 12938578 12944489 + PTGES3L-AARSD1 chr17 42950526 42980528 - RNF213 chr17 80260866 80398786 + SASH3 chrX 129779949 129795201 + EDARADD chr1 236348257 236502915 + CST3 chr20 23626706 23638473 - SKI chr1 2228319 2310213 + MRPL13 chr8 120380761 120445402 - TMEM258 chr11 61768501 61792802 - ASB8 chr12 48147789 48181213 - RPL27 chr17 42998273 43002959 + GSPT2 chrX 51743442 51746232 + TXNDC5 chr6 7881517 7910788 - DYNLL1 chr12 120469850 120498493 + TRMU chr22 46330875 46357340 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand Z95114.1 chr22 36071000 36085573 + 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.