exRNAdisease

Entry Detail

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General Information

Database ID: exR0000278 RNA Name: ADAT2 RNA Type: mRNA Chromosome: chr6 Starnd: - Coordinate: Start Site(bp): 143422832 End Site(bp): 143450695 External Links: ENSG00000189007

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 AC011511.4 chr19 10315471 10320678 - AC118549.1 chr1 77562416 77683419 - AP002990.1 chr11 62559603 62591531 - ATP5F1B chr12 56638175 56645984 - B4GALT6 chr18 31622247 31685836 - DDI2 chr1 15617458 15669044 + DUSP1 chr5 172768096 172771195 - EEF1A1 chr6 73515750 73523797 - EEF1G chr11 62559596 62574086 - FBXO31 chr16 87326987 87392142 - FBXO41 chr2 73254682 73284431 - FNDC3B chr3 172039578 172401669 + GLO1 chr6 38675925 38703145 - KNTC1 chr12 122527246 122626396 + LEPROT chr1 65420587 65436007 + PSME1 chr14 24136163 24138967 + RAVER1 chr19 10316212 10333638 - RPS6KB2 chr11 67428460 67435401 + RSC1A1 chr1 15659869 15661722 + SRSF10 chr1 23964347 23980927 - YWHAQ chr2 9583967 9630997 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-18a-5p chr13 91350756 91350778 + hsa-miR-18b-5p chrX 134170084 134170106 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand 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.