exRNAdisease

Entry Detail

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General Information

Database ID: exR0000112 RNA Name: ACAD11 RNA Type: mRNA Chromosome: chr3 Starnd: - Coordinate: Start Site(bp): 132558138 End Site(bp): 132660082 External Links: ENSG00000240303

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 NPHP3-ACAD11 chr3 132558142 132722459 - BET1L chr11 167784 207428 - P4HB chr17 81843161 81860624 - STIM1 chr11 3854527 4093210 + HLA-DQA1 chr6 32628179 32647062 + FAR1 chr11 13668668 13732346 + PUM2 chr2 20248691 20352234 - TCIRG1 chr11 68039025 68050895 + PIK3C2A chr11 17077730 17207983 - PRPF8 chr17 1650629 1684867 - RPS8 chr1 44775251 44778779 + HADH chr4 107989714 108035175 + ZNF311 chr6 28994785 29005316 - MDN1 chr6 89642498 89819794 - PPOX chr1 161166056 161178013 + CD52 chr1 26317958 26320523 + RPL12 chr9 127447674 127451406 - PMF1 chr1 156212993 156240042 + HSPA9 chr5 138553756 138575416 - SH3PXD2B chr5 172325000 172454525 - CACNA2D3 chr3 54122547 55074557 + TK1 chr17 78174091 78187233 - DNAJB1 chr19 14514769 14529770 - ATP5IF1 chr1 28236109 28246906 + NBDY chrX 56729241 56819179 + RABGAP1L chr1 174159410 174995308 + ZNF146 chr19 36214602 36238774 + EHMT2 chr6 31879759 31897687 - SGTB chr5 65665928 65723035 - MTHFD2 chr2 74198610 74217565 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AD000090.1 chr19 35557956 35581954 + 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.