exRNAdisease

Entry Detail

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General Information

Database ID: exR0000043 RNA Name: ABCB7 RNA Type: mRNA Chromosome: chrX Starnd: - Coordinate: Start Site(bp): 75051048 End Site(bp): 75156732 External Links: ENSG00000131269

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 YWHAZ chr8 100916523 100953388 - DDX5 chr17 64498254 64508199 - MAPKAPK2 chr1 206684944 206734283 + YWHAQ chr2 9583967 9630997 - MT-CO1 chrMT 5904 7445 + CSNK2B chr6 31665236 31670343 + MAGED1 chrX 51803007 51902357 + PBX2 chr6 32184733 32190202 - CCNI chr4 77047155 77075989 - CFL1 chr11 65823022 65862026 - TM7SF3 chr12 26971579 27014434 - ADD1 chr4 2843857 2930076 + AP002990.1 chr11 62559603 62591531 - RARA chr17 40309180 40357643 + RPAIN chr17 5419641 5432876 + RPS12 chr6 132814569 132817564 + IPO5 chr13 97953658 98024296 + NOMO3 chr16 16232528 16294811 + JMJD1C chr10 63167221 63521850 - MEN1 chr11 64803510 64811294 - RAB11A chr15 65726054 65891989 + P4HB chr17 81843161 81860624 - EEF1G chr11 62559596 62574086 - TMSB4X chrX 12975110 12977227 + CAPN15 chr16 527712 554636 + RABEP1 chr17 5282265 5386340 + LPCAT1 chr5 1456480 1523962 - INSIG1 chr7 155297776 155310235 + ANP32B chr9 97983341 98015943 + TMED5 chr1 93149742 93180516 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand EBLN3P chr9 37079645 37090928 + LINC00205 chr21 45288050 45297806 + 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.