exRNAdisease

Entry Detail

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General Information

Database ID: exR0004994 RNA Name: FASN RNA Type: mRNA Chromosome: chr17 Starnd: - Coordinate: Start Site(bp): 82078338 End Site(bp): 82098294 External Links: ENSG00000169710

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 A3GALT2 chr1 33306766 33321098 - AASS chr7 122073549 122144255 - ABCA2 chr9 137007234 137028922 - ABHD8 chr19 17292131 17310236 - ABTB2 chr11 34150987 34358010 - AC011448.1 chr19 19516227 19536076 + AC023055.1 chr12 55757275 55827546 - AC026954.2 chr17 7312661 7319174 - AC068580.4 chr11 1734821 1763954 - AC107871.1 chr15 68184032 68229718 - ACAD9 chr3 128879596 128916067 + ADAMTS1 chr21 26835755 26845409 - ADCK1 chr14 77800109 77935014 + ADGRG2 chrX 18989307 19122637 - AFG3L2 chr18 12328944 12377227 - AGAP4 chr10 45825594 45853875 - AGBL5 chr2 27042364 27070622 + AGPAT4 chr6 161129967 161274061 - AGRN chr1 1020120 1056118 + AKAP12 chr6 151239967 151358559 + AKIRIN2 chr6 87674860 87702233 - AKT1 chr14 104769349 104795751 - AL021546.1 chr12 120438198 120460006 + AL133352.1 chr10 100505628 100529881 - AL139011.2 chr1 160216800 160285130 - ALDH16A1 chr19 49453225 49471050 + ALDH9A1 chr1 165662216 165698863 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-29a-3p chr7 130876748 130876769 - hsa-miR-29b-3p chr7 130877467 130877489 - hsa-miR-103a-3p chr5 168560904 168560926 - hsa-miR-107 chr10 89592756 89592778 - hsa-miR-29c-3p chr1 207801865 207801886 - hsa-miR-526b-5p chr19 53694406 53694428 + hsa-miR-652-3p chrX 110055389 110055409 + hsa-miR-663a chr20 26208243 26208264 - hsa-miR-541-3p chr14 101064548 101064569 + hsa-miR-147b-3p chr15 45433098 45433118 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC006538.1 chr19 2727743 2729327 - AC016876.2 chr17 7581964 7584086 - AC019205.1 chr6 73263212 73301789 + AC023509.1 chr12 53441741 53467528 + AC103702.2 chr17 48635923 48647023 - AC106864.1 chr4 112693047 112706810 - AC124068.2 chr15 89335053 89336161 + AD000090.1 chr19 35557956 35581954 + AL021707.3 chr22 38734730 38738990 + AL121992.1 chr1 15586136 15603626 - AL132780.1 chr14 22929607 22956374 + 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.