exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000347 RNA Name: AFF1 RNA Type: mRNA Chromosome: chr4 Starnd: + Coordinate: Start Site(bp): 86935002 End Site(bp): 87141054 External Links: ENSG00000172493

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 AP1G1 chr16 71729000 71809201 - TMBIM6 chr12 49707725 49764934 + UBALD2 chr17 76265348 76271298 + KIF1C chr17 4997950 5028401 + ERAL1 chr17 28855010 28861061 + HNRNPM chr19 8444767 8489114 + DUSP5 chr10 110497907 110511533 + VPS13A chr9 77177445 77421537 + RAB5C chr17 42124976 42155044 - RAVER2 chr1 64745095 64833232 + RSU1 chr10 16590611 16817463 - DNAJC5 chr20 63895126 63936031 + RHEB chr7 151466012 151520120 - TSR1 chr17 2322396 2336657 - CHD8 chr14 21385194 21456126 - UNC13D chr17 75827225 75844717 - MCM2 chr3 127598410 127622436 + RANBP2 chr2 108719482 108785809 + ACTG1 chr17 81509971 81523847 - PRDX6 chr1 173477330 173488815 + BAZ1B chr7 73440406 73522293 - ABI1 chr10 26746593 26861087 - KRAS chr12 25205246 25250936 - STRBP chr9 123109500 123268586 - CC2D1A chr19 13906201 13930879 + COPS8 chr2 237085882 237100474 + DEDD chr1 161120974 161132688 - SSRP1 chr11 57325986 57335892 - CASP8 chr2 201233443 201287711 + TMEM237 chr2 201620184 201643570 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC025181.2 chr5 32174471 32175272 + MAPKAPK5-AS1 chr12 111839764 111842902 - 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.