exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000034 RNA Name: ABCA7 RNA Type: mRNA Chromosome: chr19 Starnd: + Coordinate: Start Site(bp): 1039997 End Site(bp): 1065572 External Links: ENSG00000064687

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 AC008982.1 chr19 38817471 38840178 - AGPAT2 chr9 136673143 136687457 - ANP32E chr1 150218417 150236156 - ATP2B4 chr1 203626561 203744081 + CCNE1 chr19 29811991 29824312 + CD99 chrX 2691187 2741309 + EIF4G3 chr1 20806292 21176888 - FAM50A chrX 154444141 154450654 + GNB1 chr1 1785285 1891117 - HMGXB3 chr5 150000046 150053142 + HNRNPL chr19 38836388 38852347 - ILF3 chr19 10654261 10692417 + LRRK1 chr15 100919327 101078257 + MDH2 chr7 76048051 76067508 + METTL24 chr6 110245928 110358272 - MPG chr16 77007 85853 + MT-CO1 chrMT 5904 7445 + MTRNR2L8 chr11 10507894 10509186 - PARP6 chr15 72241181 72272999 - SLC29A2 chr11 66362521 66372214 - SNX17 chr2 27370496 27377535 + SRSF1 chr17 58000919 58007346 - TMCO3 chr13 113491021 113554590 + TMEM201 chr1 9588911 9614877 + TMEM69 chr1 45688181 45694436 + TNKS chr8 9555912 9782346 + TSPAN3 chr15 77041404 77083984 - TUBA1A chr12 49184795 49189080 - ZNF200 chr16 3222325 3236221 - ZNF800 chr7 127346790 127431924 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand LINC01783 chr1 16533886 16536172 - SNHG17 chr20 38419638 38435409 - 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.