exRNAdisease

Entry Detail

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General Information

Database ID: exR0000083 RNA Name: ABHD17B RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 71862452 End Site(bp): 71910931 External Links: ENSG00000107362

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 FBN2 chr5 128257909 128659185 - EIF4G2 chr11 10797050 10808940 - TXNDC12 chr1 52020131 52055191 - CSTF3 chr11 33077188 33162371 - GDI2 chr10 5765223 5842132 - VAT1 chr17 43014607 43025123 - PNRC2 chr1 23956839 23963462 + MDK chr11 46380756 46383837 + IBTK chr6 82169986 82247754 - TMPO chr12 98515512 98550379 + SRP9 chr1 225777813 225790468 + FBXL20 chr17 39252663 39402523 - TPX2 chr20 31739271 31801805 + SLC2A3 chr12 7919230 7936187 - DDX42 chr17 63773603 63819317 + SKA3 chr13 21153595 21176552 - PA2G4 chr12 56104537 56113910 + GOT2 chr16 58707131 58734342 - CENPV chr17 16342534 16353656 - TOMM7 chr7 22812628 22822852 - WBP4 chr13 41061509 41084006 + RPS9 chr19 54200809 54249003 + RPL37A chr2 216498825 216579180 + MT-CO2 chrMT 7586 8269 + MRPL43 chr10 100969458 100987515 - LAMA5 chr20 62307955 62367312 - VPS51 chr11 65089324 65111862 + GNAL chr18 11689264 11885685 + EEF1G chr11 62559596 62574086 - KLHDC2 chr14 49768130 49786385 + 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.