exRNAdisease

Entry Detail

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General Information

Database ID: exR0000075 RNA Name: ABHD13 RNA Type: mRNA Chromosome: chr13 Starnd: + Coordinate: Start Site(bp): 108218392 End Site(bp): 108234243 External Links: ENSG00000139826

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 ANKRD46 chr8 100509752 100559784 - ARMT1 chr6 151452258 151470101 + CCR7 chr17 40553769 40565472 - CHIC1 chrX 73563200 73687102 + CUL4A chr13 113208193 113267108 + HDAC2 chr6 113933028 114011308 - HSPA4 chr5 133052013 133106449 + IDH1 chr2 208236227 208266074 - LIN28A chr1 26410817 26429728 + MRI1 chr19 13764522 13774282 + MT-ND4 chrMT 10760 12137 + PPM1G chr2 27381195 27409591 - RAB18 chr10 27504174 27542237 + RAB7A chr3 128726183 128814798 + RCN2 chr15 76931738 76954393 + RHEB chr7 151466012 151520120 - RHOT1 chr17 32142454 32253374 + RNF138 chr18 32091874 32131561 + SCAMP3 chr1 155255979 155262430 - SSRP1 chr11 57325986 57335892 - STIM2 chr4 26857601 27025381 + SV2A chr1 149903318 149917844 - TRIP6 chr7 100867387 100873454 + U2AF1 chr21 43092956 43107587 - U2AF1L5 chr21 6484623 6499261 - UBR4 chr1 19074510 19210266 - 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.