exRNAdisease

Entry Detail

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General Information

Database ID: exR0002821 RNA Name: CKB RNA Type: mRNA Chromosome: chr14 Starnd: - Coordinate: Start Site(bp): 103519667 End Site(bp): 103522833 External Links: ENSG00000166165

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 AHNAK chr11 62433542 62556235 - AL513165.2 chr9 37512547 37592469 - AC093525.2 chr16 2496032 2520218 + AC068580.4 chr11 1734821 1763954 - AL669918.1 chr6 32813767 32838822 - AC116366.3 chr5 132410832 132646079 + ACADVL chr17 7217125 7225266 + AHCY chr20 34280268 34311802 - AL136295.1 chr14 24189157 24213473 - AHSA1 chr14 77457870 77469472 + AATF chr17 36948954 37056871 + AC069503.2 chr12 121888809 121921470 + ADD1 chr4 2843857 2930076 + ALDH9A1 chr1 165662216 165698863 - AKAP8L chr19 15380050 15419141 - AFF1 chr4 86935002 87141054 + AL121845.3 chr20 63708864 63739103 + ACACA chr17 37084992 37406836 - AGO2 chr8 140520156 140635633 - ALDOA chr16 30064164 30070457 + ACOT7 chr1 6264269 6394391 - AC010132.3 chr7 42909273 42932174 - AC011448.1 chr19 19516227 19536076 + AIF1L chr9 131096476 131123152 + AKR1B1 chr7 134442356 134459284 - AGAP1 chr2 235494043 236131800 + AL360181.3 chr10 133380017 133420271 + ACTB chr7 5527148 5563784 - AC010323.1 chr19 8308283 8321379 - ACTG1 chr17 81509971 81523847 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC010729.1 chr2 5726253 5730355 + AC016876.2 chr17 7581964 7584086 - AC023509.1 chr12 53441741 53467528 + AC026471.1 chr16 31456711 31459736 - AC093827.4 chr4 86924630 86936202 - AC108134.2 chr16 3156736 3157483 - AL049795.2 chr1 32170733 32176568 + AL133367.1 chr14 103525010 103529072 - 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.