exRNAdisease

Entry Detail

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General Information

Database ID: exR0000170 RNA Name: ACSF3 RNA Type: mRNA Chromosome: chr16 Starnd: + Coordinate: Start Site(bp): 89088375 End Site(bp): 89164121 External Links: ENSG00000176715

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 REXO1 chr19 1815248 1848483 - PBX1 chr1 164555584 164899296 + RBFOX2 chr22 35738736 36028824 - FAM193B chr5 177519789 177554563 - SLC47A1 chr17 19495385 19579034 + ATG2A chr11 64894546 64917211 - TP63 chr3 189631389 189897276 + ARID1A chr1 26693236 26782104 + SBNO2 chr19 1107637 1174268 - AKT2 chr19 40230317 40285536 - LRRC14 chr8 144517992 144525172 + DGKD chr2 233354507 233472104 + SATB1 chr3 18345377 18445588 - DCTD chr4 182890060 182917936 - NHSL1 chr6 138422043 138692571 - SOX4 chr6 21593751 21598619 + ZNF227 chr19 44207547 44237268 + FAM189B chr1 155247205 155255483 - PAK4 chr19 39125770 39182816 + SNRPB chr20 2461634 2470853 - RPL18A chr19 17859910 17864153 + NDUFV2 chr18 9102630 9134345 + ABR chr17 1003518 1229738 - TANGO2 chr22 20017014 20067164 + BPTF chr17 67825503 67984378 + UBA52 chr19 18571730 18577550 + SYAP1 chrX 16719612 16765340 + ADAR chr1 154582057 154628013 - TXNL1 chr18 56597209 56651600 - NUP153 chr6 17615035 17706834 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AP005263.1 chr18 9102736 9254346 + 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.