exRNAdisease

Entry Detail

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General Information

Database ID: exR0000135 RNA Name: ACER3 RNA Type: mRNA Chromosome: chr11 Starnd: + Coordinate: Start Site(bp): 76860867 End Site(bp): 77026797 External Links: ENSG00000078124

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 SLC39A13 chr11 47407132 47416496 + HLA-A chr6 29941260 29945884 + BANP chr16 87949244 88077318 + ARCN1 chr11 118572390 118603033 + PPIB chr15 64155812 64163205 - NDUFC2-KCTD14 chr11 78016971 78079865 - CCT2 chr12 69585426 69601570 + PTRH2 chr17 59674636 59707626 - TBC1D4 chr13 75283503 75482169 - NDUFC2 chr11 78068297 78079862 - KLHL7 chr7 23105758 23177914 + EIF3C chr16 28688558 28735730 + DNAJB6 chr7 157335381 157417439 + RPS10-NUDT3 chr6 34284887 34426071 - RPS10 chr6 34417454 34426069 - C22orf39 chr22 19351368 19448232 - MRFAP1L1 chr4 6707701 6709865 - SLC3A2 chr11 62856102 62888875 + TSKU chr11 76782251 76798153 + DPH1 chr17 2030110 2043430 + SYAP1 chrX 16719612 16765340 + HNRNPH1 chr5 179614178 179634784 - SHMT2 chr12 57229573 57234935 + RPL27A chr11 8682788 8714759 + FAM3C chr7 121348878 121396364 - PRDX3 chr10 119167720 119178812 - CNN2 chr19 1026586 1039068 + NOTCH2 chr1 119911553 120100779 - CDC42SE2 chr5 131245493 131398447 + AC010422.3 chr19 12643831 12648397 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-27a-3p chr19 13836447 13836467 - hsa-miR-129-5p chr7 128207876 128207896 + hsa-miR-27b-3p chr9 95085505 95085525 + 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.