exRNAdisease

Entry Detail

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General Information

Database ID: exR0000042 RNA Name: ABCB6 RNA Type: mRNA Chromosome: chr2 Starnd: - Coordinate: Start Site(bp): 219209772 End Site(bp): 219218994 External Links: ENSG00000115657

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 CLCN5 chrX 49922596 50099235 + CHMP1A chr16 89644435 89657721 - COA1 chr7 43608456 43729717 - PA2G4 chr12 56104537 56113910 + PYCR2 chr1 225919877 225924340 - HLA-E chr6 30489509 30494194 + SNRPD2 chr19 45687454 45692569 - GADD45GIP1 chr19 12953119 12957223 - VCL chr10 73995193 74121363 + SNRPD3 chr22 24555958 24582052 + FARSA chr19 12922479 12934037 - SMDT1 chr22 42079691 42084284 + EEF2 chr19 3976056 3985463 - POU3F3 chr2 104853287 104858574 + GRK2 chr11 67266473 67286556 + GAPDH chr12 6534512 6538374 + WSB1 chr17 27294076 27315926 + MYCBP2 chr13 77044657 77327094 - SAC3D1 chr11 65040901 65044828 + PPP4C chr16 30075978 30085376 + KRT7 chr12 52232520 52252186 + AC068946.2 chr2 219209772 219222738 - PTPRS chr19 5158495 5340803 - SETD1B chr12 121804180 121832584 + ARID1B chr6 156776020 157210779 + CAMK2G chr10 73812501 73874591 - POU6F1 chr12 51186936 51217708 - PFN1 chr17 4945652 4949061 - LAMP1 chr13 113297239 113323672 + RAD51D chr17 35092208 35121522 - 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.