exRNAdisease

Entry Detail

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General Information

Database ID: exR0000804 RNA Name: APP RNA Type: mRNA Chromosome: chr21 Starnd: - Coordinate: Start Site(bp): 25880550 End Site(bp): 26171128 External Links: ENSG00000142192

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 ABCF2 chr7 151207837 151227166 - ABRACL chr6 139028745 139043302 + AC008695.1 chr5 131425891 131796983 - AC012254.2 chr18 47108188 47176345 - AC093525.2 chr16 2496032 2520218 + AC138811.2 chr16 18788063 18801519 - AC245033.1 chr15 82536788 82573194 - ACAA2 chr18 49782164 49813953 - ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ACTR10 chr14 58200080 58235636 + ADAR chr1 154582057 154628013 - ADI1 chr2 3497366 3519531 - ADK chr10 74151202 74709963 + AGL chr1 99850361 99924023 + AGPAT1 chr6 32168212 32178096 - AHNAK chr11 62433542 62556235 - AIF1L chr9 131096476 131123152 + AKIRIN1 chr1 38991276 39006059 + AL133352.1 chr10 100505628 100529881 - AL136454.1 chr1 192716132 192716653 + AL139011.2 chr1 160216800 160285130 - AL355916.3 chr14 61529128 61657964 + AL589666.1 chr6 85557978 85615234 - ALAS1 chr3 52198086 52214327 + ALDOA chr16 30064164 30070457 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-17-5p chr13 91350618 91350640 + hsa-miR-20a-5p chr13 91351072 91351094 + hsa-miR-21-5p chr17 59841273 59841294 + hsa-miR-29a-3p chr7 130876748 130876769 - hsa-miR-29b-3p chr7 130877467 130877489 - hsa-miR-106a-5p chrX 134170244 134170266 - hsa-miR-214-3p chr1 172138816 172138837 - hsa-miR-106b-5p chr7 100094043 100094063 - hsa-miR-29c-3p chr1 207801865 207801886 - hsa-miR-302a-3p chr4 112648186 112648208 - hsa-miR-302c-3p chr4 112648366 112648388 - hsa-miR-373-3p chr19 53788748 53788770 + hsa-miR-20b-5p chrX 134169850 134169872 - hsa-miR-520e-3p chr19 53675764 53675784 + hsa-miR-520a-3p chr19 53690933 53690954 + hsa-miR-520b-3p chr19 53701267 53701287 + hsa-miR-520c-3p chr19 53707506 53707527 + hsa-miR-520d-3p chr19 53720149 53720170 + hsa-miR-4426 chr1 192716333 192716349 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC016876.2 chr17 7581964 7584086 - AC021078.1 chr5 149494314 149504670 - AC023509.1 chr12 53441741 53467528 + AC024940.6 chr12 31280422 31280895 - 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.