exRNAdisease

Entry Detail

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General Information

Database ID: exR0000017 RNA Name: AAR2 RNA Type: mRNA Chromosome: chr20 Starnd: + Coordinate: Start Site(bp): 36236459 End Site(bp): 36270918 External Links: ENSG00000131043

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 MCM3AP chr21 46235133 46286297 - PLCB2 chr15 40278176 40307935 - MANBAL chr20 37289638 37317260 + LDHA chr11 18394560 18408425 + DHX15 chr4 24517441 24584554 - YWHAH chr22 31944522 31957603 + M6PR chr12 8940361 8949761 - LSS chr21 46188141 46228824 - MTHFR chr1 11785723 11806455 - EGLN2 chr19 40798996 40808434 + COX6B1 chr19 35648323 35658782 + PKP2 chr12 32790745 32896840 - TEN1-CDK3 chr17 75979231 76005999 + TMEM47 chrX 34627075 34657285 - HMOX2 chr16 4474690 4510347 + BRF1 chr14 105209286 105315589 - CCDC77 chr12 389273 442642 + DDX17 chr22 38483438 38507660 - NELFE chr6 31952087 31959038 - PAGR1 chr16 29816152 29822489 + LMTK2 chr7 98106862 98209638 + RAB4B-EGLN2 chr19 40778242 40808418 + HNRNPH3 chr10 68331174 68343191 + ACTR1A chr10 102461881 102502712 - CANX chr5 179678628 179731641 + MCM7 chr7 100092728 100101940 - RPL3 chr22 39312882 39320389 - FLII chr17 18244815 18258738 - TUBA1A chr12 49184795 49189080 - PAICS chr4 56435741 56464579 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-103a-3p chr5 168560904 168560926 - hsa-miR-147a chr9 120244985 120245004 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand EBLN3P chr9 37079645 37090928 + 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.