exRNAdisease

Entry Detail

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General Information

Database ID: exR0004296 RNA Name: EDARADD RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 236348257 End Site(bp): 236502915 External Links: ENSG00000186197

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 AL136454.1 chr1 192716132 192716653 + AL020996.2 chr1 25811470 25823744 + AL035078.4 chr11 31812391 32104665 + ACTR2 chr2 65227753 65271253 + AKIRIN2 chr6 87674860 87702233 - ACO1 chr9 32384603 32454769 + AC245033.1 chr15 82536788 82573194 - ADGRE5 chr19 14380501 14408725 + AL138752.2 chr9 37588413 38068687 - AKAP11 chr13 42272152 42323261 + AC124312.1 chr15 24955034 25000276 + ACAD10 chr12 111686056 111757107 + ALDH2 chr12 111766887 111817532 + AC068946.1 chr2 219075329 219170827 - AKAP8 chr19 15353385 15379798 - AKR1A1 chr1 45550543 45570049 + ACTR8 chr3 53867066 53882152 - AC004832.3 chr22 30409255 30428990 + ACTG1 chr17 81509971 81523847 - ACLY chr17 41866917 41930542 - AC020909.1 chr19 50415799 50428409 + AK2 chr1 33007940 33080996 - ACAD9 chr3 128879596 128916067 + ABRAXAS2 chr10 124801819 124836667 + AKR1B1 chr7 134442356 134459284 - ADGRL2 chr1 81306160 81992436 + ADPRH chr3 119579268 119589945 + AL355315.1 chr10 97584374 97673910 + AC011462.1 chr19 41350853 41425001 + AC005832.4 chr12 4604944 4662643 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-21-5p chr17 59841273 59841294 + hsa-miR-4426 chr1 192716333 192716349 + hsa-miR-6728-3p chr1 8866502 8866522 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC007952.4 chr17 19112000 19112636 - AC010642.2 chr19 58309727 58327248 - AC012236.1 chr15 31221999 31230838 - AC016876.2 chr17 7581964 7584086 - AC026362.1 chr12 122975320 122982907 + AC125807.2 chr12 3041437 3044950 + AC245014.3 chr1 145281116 145281462 + AC245033.4 chr15 82533175 82540008 - AL022311.1 chr22 37876148 37895563 + AL096870.2 chr14 24209646 24215987 - 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.