exRNAdisease

Entry Detail

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General Information

Database ID: exR0000383 RNA Name: AGPAT4 RNA Type: mRNA Chromosome: chr6 Starnd: - Coordinate: Start Site(bp): 161129967 End Site(bp): 161274061 External Links: ENSG00000026652

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 CLIC1 chr6 31730581 31739763 - TMEM237 chr2 201620184 201643570 - EIF4G2 chr11 10797050 10808940 - METAP1 chr4 98995659 99062809 + TNFRSF13B chr17 16929816 16972118 - ILF2 chr1 153661788 153671028 - SPAG16 chr2 213284379 214410501 + FASN chr17 82078338 82098294 - DCK chr4 70992538 71030914 + RPL13 chr16 89560657 89566828 + HEXIM1 chr17 45148502 45152101 + DDB1 chr11 61299451 61342596 - PRR14 chr16 30650717 30656440 + RPS27A chr2 55231903 55235853 + SYMPK chr19 45815410 45863194 - SNRPD2 chr19 45687454 45692569 - RALY chr20 33993646 34108308 + BSG chr19 571277 583493 + RFT1 chr3 53088483 53130453 - LRRN1 chr3 3799431 3849834 + HP1BP3 chr1 20740266 20787323 - RTF1 chr15 41408408 41483563 + PHLDA1 chr12 76025447 76033932 - CLIP1 chr12 122271432 122422632 - GART chr21 33503931 33543491 - TOMM22 chr22 38681957 38685421 + CCDC102A chr16 57512181 57536571 - TXLNA chr1 32179675 32198285 + TMED9 chr5 177592203 177597242 + YIF1B chr19 38303558 38317273 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC005394.2 chr19 28435388 28727680 - AL353719.1 chr10 99621055 99621918 + JAKMIP2-AS1 chr5 147559994 147662009 + 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.