exRNAdisease

Entry Detail

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General Information

Database ID: exR0000471 RNA Name: ALAD RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 113386312 End Site(bp): 113401290 External Links: ENSG00000148218

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 SUSD2 chr22 24181487 24189106 + EIF4G2 chr11 10797050 10808940 - RTL6 chr22 44492583 44498233 - FAM32A chr19 16185380 16192046 + PKM chr15 72199029 72231822 - MRPL12 chr17 81703367 81707517 + NEK1 chr4 169392857 169612629 - NAPB chr20 23374519 23421519 - TAF6L chr11 62771357 62787342 + GAPDH chr12 6534512 6538374 + UBR5 chr8 102252273 102412759 - CHD4 chr12 6570082 6614524 - TIPIN chr15 66336191 66386746 - ZCCHC8 chr12 122471599 122501073 - HNRNPK chr9 83968083 83980616 - AC139530.2 chr17 81703371 81720539 + ARHGDIA chr17 81867721 81871378 - RPL4 chr15 66498015 66524532 - PFN1 chr17 4945652 4949061 - HLA-DRA chr6 32439878 32445046 + POU5F1 chr6 31164337 31180731 - YBX3 chr12 10699089 10723323 - RAB13 chr1 153981617 153986358 - RPL41 chr12 56116590 56117967 + HSPBP1 chr19 55262223 55280381 - PLEC chr8 143915147 143976734 - HELLS chr10 94501434 94613905 + PRC1 chr15 90966040 90995629 - CRMP1 chr4 5748084 5893086 - C17orf100 chr17 6651762 6693202 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC068831.7 chr15 91022766 91023200 + 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.