exRNAdisease

Entry Detail

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General Information

Database ID: exR0000091 RNA Name: ABI1 RNA Type: mRNA Chromosome: chr10 Starnd: - Coordinate: Start Site(bp): 26746593 End Site(bp): 26861087 External Links: ENSG00000136754

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 B2M chr15 44711487 44718877 + RPS27L chr15 63125872 63158021 - MTRNR2L1 chr17 22523111 22524663 + PSMB1 chr6 170535120 170553307 - COPG1 chr3 129249606 129277773 + TTF1 chr9 132375548 132406851 - TCEA1 chr8 53966552 54022456 - AGK chr7 141551278 141655244 + WAC chr10 28532493 28623112 + ACLY chr17 41866917 41930542 - SUMO3 chr21 44805617 44818779 - LARP1 chr5 154712843 154817605 + IL10RB chr21 33266367 33310187 + RNF125 chr18 32018825 32073219 + AFF1 chr4 86935002 87141054 + PTMS chr12 6765516 6770952 + UBE3C chr7 157138916 157269370 + THOP1 chr19 2785503 2815807 + SLC30A5 chr5 69093949 69131069 + KIF23 chr15 69414246 69448427 + PAN3 chr13 28138506 28295335 + CCT4 chr2 61868085 61888671 - BUB1 chr2 110637528 110678063 - MTHFD2 chr2 74198610 74217565 + ARID1A chr1 26693236 26782104 + TAF10 chr11 6606294 6612539 - MYO19 chr17 36495633 36543435 - SRRM2 chr16 2752626 2772538 + SRPK1 chr6 35832966 35921342 - RPLP1 chr15 69452814 69456205 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC091564.7 chr11 6610883 6616594 - AL158066.1 chr13 52167709 52291557 - AL355075.4 chr14 20343048 20343685 - 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.