exRNAdisease

Entry Detail

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General Information

Database ID: exR0000127 RNA Name: ACBD4 RNA Type: mRNA Chromosome: chr17 Starnd: + Coordinate: Start Site(bp): 45132600 End Site(bp): 45144181 External Links: ENSG00000181513

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 ANP32A chr15 68778535 68820897 - BSG chr19 571277 583493 + CCDC6 chr10 59788747 59906556 - CDON chr11 125955796 126063335 - DYNLL2 chr17 58083419 58095542 + EIF3C chr16 28688558 28735730 + ENO1 chr1 8861000 8879190 - GAPDH chr12 6534512 6538374 + GATAD1 chr7 92447482 92460075 + HPN chr19 35040506 35066571 + KAT7 chr17 49788681 49835026 + LIN28A chr1 26410817 26429728 + LRP4 chr11 46856717 46918642 - MAD2L2 chr1 11674480 11691650 - PDE4D chr5 58969038 60522120 - PDHB chr3 58427630 58433857 - PPP6R1 chr19 55229779 55259017 - SCAND1 chr20 35953617 35959472 - TMA16 chr4 163494442 163520539 + TPM3 chr1 154155304 154194648 - TPRN chr9 137191617 137204193 - TSR1 chr17 2322396 2336657 - TUBA1B chr12 49127782 49131397 - USP39 chr2 85602856 85649283 + VPS26C chr21 37223420 37267919 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC027290.2 chr12 122865335 122867021 + 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.