exRNAdisease

Entry Detail

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General Information

Database ID: exR0000137 RNA Name: ACIN1 RNA Type: mRNA Chromosome: chr14 Starnd: - Coordinate: Start Site(bp): 23058564 End Site(bp): 23095614 External Links: ENSG00000100813

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 HNRNPA2B1 chr7 26173057 26201529 - CD74 chr5 150400041 150412929 - EEF1G chr11 62559596 62574086 - MANEAL chr1 37793802 37801137 + CGN chr1 151510510 151538692 + LRRC58 chr3 120324509 120349354 - RGPD5 chr2 109792758 109857705 + IVNS1ABP chr1 185296388 185317273 - TTLL3 chr3 9808086 9855138 + SDHAF3 chr7 97117698 97181763 + JAGN1 chr3 9890574 9894349 + RPL39 chrX 119786504 119791630 - CFAP20 chr16 58113592 58129381 - PCDHGA3 chr5 141343829 141512979 + PCDHGA1 chr5 141330571 141512981 + ALDH7A1 chr5 126531200 126595362 - EEF1A1 chr6 73515750 73523797 - PMF1 chr1 156212993 156240042 + WWC3 chrX 10015562 10144478 + RACK1 chr5 181236897 181248096 - SFXN1 chr5 175477062 175529742 + TPT1 chr13 45333471 45341370 - MRPS7 chr17 75261674 75266376 + RNASEK chr17 7012417 7014532 + TRAF7 chr16 2155698 2178129 + CERK chr22 46684410 46738252 - TSC2 chr16 2047967 2089491 + CNP chr17 41966763 41977740 + RPL11 chr1 23691742 23696835 + PCDHGA10 chr5 141412987 141512979 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC027682.2 chr16 67542123 67542963 - AC124068.2 chr15 89335053 89336161 + AL132780.1 chr14 22929607 22956374 + AL355075.4 chr14 20343048 20343685 - AP001496.2 chr18 5232876 5238526 - AP005263.1 chr18 9102736 9254346 + BISPR chr19 17405686 17419324 + NEAT1 chr11 65422774 65445540 + XIST chrX 73820649 73852723 - Z83843.1 chrX 74209976 74213660 - 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.