exRNAdisease

Entry Detail

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General Information

Database ID: exR0000084 RNA Name: ABHD17C RNA Type: mRNA Chromosome: chr15 Starnd: + Coordinate: Start Site(bp): 80679684 End Site(bp): 80755621 External Links: ENSG00000136379

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 NUB1 chr7 151341699 151378449 + PLEKHG3 chr14 64704102 64750249 + KIAA1671 chr22 24952730 25197448 + TCFL5 chr20 62841005 62861822 - AGPAT1 chr6 32168212 32178096 - EEF2 chr19 3976056 3985463 - MEX3A chr1 156072013 156082465 - MKKS chr20 10401009 10434222 - ANXA2 chr15 60347134 60402883 - BTBD7 chr14 93237550 93333092 - CLTA chr9 36190856 36304781 + CDC37 chr19 10391133 10420121 - FMR1 chrX 147911951 147951125 + ZFHX3 chr16 72782885 73891871 - GJA1 chr6 121435595 121449727 + CLEC2D chr12 9664969 9699553 + NISCH chr3 52455118 52493068 + PRTG chr15 55611544 55743152 - SUZ12 chr17 31937007 32001038 + GNAS chr20 58839718 58911192 + MLLT1 chr19 6210381 6279975 - TRAPPC12 chr2 3379675 3485094 + NARS2 chr11 78435968 78574874 - PAIP1 chr5 43526267 43557758 - NUP93 chr16 56730118 56850286 + AK1 chr9 127866486 127877675 - HM13 chr20 31514410 31577923 + CBX3 chr7 26201162 26213607 + MRPS16 chr10 73248843 73252693 - RBM4B chr11 66664998 66677887 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC079949.1 chr12 127142029 127146532 - AL157935.2 chr9 127934503 127940952 + 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.