exRNAdisease

Entry Detail

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General Information

Database ID: exR0000111 RNA Name: ACAD10 RNA Type: mRNA Chromosome: chr12 Starnd: + Coordinate: Start Site(bp): 111686056 End Site(bp): 111757107 External Links: ENSG00000111271

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 NDUFA10 chr2 239892450 240025345 - GPCPD1 chr20 5544439 5611006 - IPP chr1 45694324 45750653 - MRM2 chr7 2234195 2242205 - SLAMF6 chr1 160485030 160523262 - MYH9 chr22 36281277 36388067 - SLC52A2 chr8 144354135 144361272 + CPT1C chr19 49690898 49713731 + PSMD11 chr17 32444379 32483319 + HMGB2 chr4 173331376 173334432 - SP110 chr2 230167293 230225729 - CBX3 chr7 26201162 26213607 + DNAJC25 chr9 111631334 111654351 + PTP4A3 chr8 141391995 141432454 + CMTR1 chr6 37433219 37482827 + PLXNA1 chr3 126988594 127037392 + ZBED4 chr22 49853844 49890080 + ST8SIA1 chr12 22063773 22437041 - ACTN1 chr14 68874143 68979440 - UBE2Z chr17 48908407 48929056 + GRK2 chr11 67266473 67286556 + DCTN2 chr12 57530102 57547331 - FOXM1 chr12 2857681 2877155 - MT-ND1 chrMT 3307 4262 + VIPAS39 chr14 77426675 77457952 - EPM2AIP1 chr3 36985043 36993131 - ST6GAL1 chr3 186930502 187078553 + TPGS2 chr18 36777647 36829216 - AL132780.3 chr14 22946270 22982258 - FSCN3 chr7 127591409 127602144 + miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.