exRNAdisease

Entry Detail

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General Information

Database ID: exR0000397 RNA Name: AHCTF1 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 246839098 End Site(bp): 246931967 External Links: ENSG00000153207

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 ADGRL2 chr1 81306160 81992436 + BBX chr3 107522936 107811339 + CTNND1 chr11 57753243 57819546 + DESI2 chr1 244653103 244709033 + DIP2A chr21 46458891 46570015 + DYM chr18 49041474 49461347 - FAF1 chr1 50437028 50960267 - FAM72D chr1 145095974 145112696 + FKBP8 chr19 18531751 18544077 - GANAB chr11 62624826 62646726 - GATA4 chr8 11676959 11760002 + KLHL42 chr12 27780048 27803040 + OAZ1 chr19 2269509 2273490 + OS9 chr12 57693955 57721557 + PML chr15 73994673 74047827 + PPP2R2A chr8 26291508 26372680 + PTMA chr2 231706895 231713541 + RPL18 chr19 48615328 48619184 - RPS8 chr1 44775251 44778779 + RRM2B chr8 102204502 102238961 - RTN3 chr11 63681446 63759891 + SDHC chr1 161314257 161375340 + SRSF9 chr12 120461672 120469748 - STK35 chr20 2101827 2177038 + UBE4B chr1 10032832 10181239 + ZSWIM8 chr10 73785582 73801797 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand FTX chrX 73940435 74293574 - XIST chrX 73820649 73852723 - 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.