exRNAdisease

Entry Detail

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General Information

Database ID: exR0000419 RNA Name: AIMP1 RNA Type: mRNA Chromosome: chr4 Starnd: + Coordinate: Start Site(bp): 106315544 End Site(bp): 106349456 External Links: ENSG00000164022

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 TBCK chr4 106041599 106316683 - MED19 chr11 57703714 57712323 - CD2AP chr6 47477789 47627263 + DENND1C chr19 6467207 6482557 - RCOR1 chr14 102592649 102730561 + PPTC7 chr12 110533245 110583318 - ANXA5 chr4 121667946 121696995 - TRAP1 chr16 3651639 3717553 - PTOV1 chr19 49850735 49860744 + TRAPPC6B chr14 39147811 39170532 - FBXO7 chr22 32474676 32498829 + CD79A chr19 41877279 41881372 + PRRC2C chr1 171485551 171593511 + UBE3C chr7 157138916 157269370 + LRPPRC chr2 43886224 43995989 - EPCAM chr2 47345158 47387601 + RPL26 chr17 8377516 8383213 - EEF1B2 chr2 206159585 206162928 + BBS5 chr2 169479480 169506655 + RCC1 chr1 28505943 28539300 + ARID4B chr1 235131634 235328219 - PPIE chr1 39692182 39763914 + ARHGAP9 chr12 57472264 57488814 - PDPR chr16 70113626 70162537 + HLA-C chr6 31268749 31272130 - EIF4B chr12 53006158 53042209 + RPL27A chr11 8682788 8714759 + B4GALT7 chr5 177600132 177610330 + CHEK2 chr22 28687743 28742422 - RPL4 chr15 66498015 66524532 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand SNHG16 chr17 76557764 76565348 + SNHG3 chr1 28505980 28510892 + 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.