exRNAdisease

Entry Detail

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General Information

Database ID: exR0000206 RNA Name: ACTR3B RNA Type: mRNA Chromosome: chr7 Starnd: + Coordinate: Start Site(bp): 152759749 End Site(bp): 152855378 External Links: ENSG00000133627

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 ASH1L chr1 155335268 155562807 - RPL27A chr11 8682788 8714759 + AC010422.3 chr19 12643831 12648397 - CNIH4 chr1 224356858 224379459 + GAB2 chr11 78215293 78418348 - POU5F1 chr6 31164337 31180731 - SPOUT1 chr9 128819651 128829794 - RNF40 chr16 30761745 30776307 + TRIM14 chr9 98069275 98119222 - EEF2 chr19 3976056 3985463 - IPO7 chr11 9384652 9448127 + RPS12 chr6 132814569 132817564 + TRIM26 chr6 30184455 30213427 - SLC25A37 chr8 23528956 23575463 + HSP90AB1 chr6 44246166 44253888 + DAXX chr6 33318558 33323016 - PLS3 chrX 115561174 115650861 + MTFR2 chr6 136231024 136250335 - GSTK1 chr7 143244093 143270854 + SLC39A1 chr1 153959099 153968184 - EIF5A chr17 7306999 7312463 + SRSF4 chr1 29147743 29181900 - EIF5B chr2 99337371 99401326 + UBR5 chr8 102252273 102412759 - ZNF638 chr2 71276561 71435069 + STX7 chr6 132445867 132513198 - ALG10B chr12 38316762 38329721 + INCENP chr11 62123998 62153169 + EIF3L chr22 37848868 37889407 + RBBP7 chrX 16839283 16870414 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL022311.1 chr22 37876148 37895563 + LINC00963 chr9 129476946 129513687 + LINC01315 chr22 42364390 42369284 - 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.