exRNAdisease

Entry Detail

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General Information

Database ID: exR0006443 RNA Name: HNRNPK RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 83968083 End Site(bp): 83980616 External Links: ENSG00000165119

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 ABCA2 chr9 137007234 137028922 - ABCF2 chr7 151207837 151227166 - ABHD3 chr18 21650901 21704780 - ABHD4 chr14 22598237 22613215 + AC000093.1 chr22 19717220 19724772 + AC010422.3 chr19 12643831 12648397 - AC026464.4 chr16 69299682 69322700 + AC048338.1 chr12 122207779 122266423 - AC091167.2 chr15 90249556 90272208 + AC093525.2 chr16 2496032 2520218 + AC138811.2 chr16 18788063 18801519 - ACAP1 chr17 7336529 7351477 + ACO2 chr22 41469117 41528989 + ACTB chr7 5527148 5563784 - ACTN1 chr14 68874143 68979440 - ACTN4 chr19 38647649 38731589 + ACVRL1 chr12 51906908 51923361 + ADAM8 chr10 133262420 133276868 - ADAT3 chr19 1905399 1913447 + AFG3L2 chr18 12328944 12377227 - AGPAT1 chr6 32168212 32178096 - AGTPBP1 chr9 85546539 85742029 - AKT1 chr14 104769349 104795751 - AKT3 chr1 243488233 243851079 - AL358113.1 chr9 69035747 69255187 + ALAD chr9 113386312 113401290 - ALDOA chr16 30064164 30070457 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC016876.2 chr17 7581964 7584086 - AC020978.7 chr16 68224713 68227734 + AC023509.1 chr12 53441741 53467528 + AC106864.1 chr4 112693047 112706810 - AC242426.2 chr1 147172755 147295734 + AL022311.1 chr22 37876148 37895563 + AL121992.1 chr1 15586136 15603626 - 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.