exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000403 RNA Name: AHNAK RNA Type: mRNA Chromosome: chr11 Starnd: - Coordinate: Start Site(bp): 62433542 End Site(bp): 62556235 External Links: ENSG00000124942

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 SRRM2 chr16 2752626 2772538 + C15orf39 chr15 75195643 75212169 + DGKI chr7 137381037 137847092 - LRRC8A chr9 128882112 128918039 + PPP1R8 chr1 27830782 27851676 + COMT chr22 19941733 19969975 + SLC16A1 chr1 112911847 112957013 - RBM33 chr7 155644451 155781485 + PSMD8 chr19 38374536 38383824 + PSMB1 chr6 170535120 170553307 - DNMT3A chr2 25227855 25342590 - PABPC3 chr13 25095868 25099254 + TOR1AIP2 chr1 179839967 179877803 - APP chr21 25880550 26171128 - MPZL1 chr1 167721192 167791919 + DCAF8 chr1 160215715 160262549 - FBXO31 chr16 87326987 87392142 - SORL1 chr11 121452314 121633763 + RABEP1 chr17 5282265 5386340 + ARL2BP chr16 57245259 57253635 + HUWE1 chrX 53532096 53686728 - RACK1 chr5 181236897 181248096 - KDM6A chrX 44873177 45112602 + CCNG2 chr4 77157207 77433388 + TMEM132A chr11 60924463 60937159 + PPP6R1 chr19 55229779 55259017 - R3HCC1 chr8 23270120 23296279 + TTC38 chr22 46267961 46294008 + MFN2 chr1 11980181 12013514 + MORF4L2 chrX 103675496 103688158 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC002470.2 chr22 20979462 20998121 + AC010327.5 chr19 55216660 55221616 + AD000090.1 chr19 35557956 35581954 + AL139385.1 chr13 110613082 110616353 - LINC00174 chr7 66376044 66493566 - RMRP chr9 35657751 35658018 - 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.