exRNAdisease

Entry Detail

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General Information

Database ID: exR0005538 RNA Name: GAPDH RNA Type: mRNA Chromosome: chr12 Starnd: + Coordinate: Start Site(bp): 6534512 End Site(bp): 6538374 External Links: ENSG00000111640

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 A1BG chr19 58345178 58353492 - ACTN1 chr14 68874143 68979440 - AC011455.2 chr19 38915404 38949855 - ADD2 chr2 70607618 70768225 - AC007192.1 chr19 18153158 18178117 + AC010422.3 chr19 12643831 12648397 - ALDH18A1 chr10 95605941 95656711 - AL133352.1 chr10 100505628 100529881 - AC120057.2 chr17 7240427 7244635 - AKR1A1 chr1 45550543 45570049 + AC068946.1 chr2 219075329 219170827 - AL022238.4 chr22 40346529 40410054 + ACTR1A chr10 102461881 102502712 - AKT2 chr19 40230317 40285536 - AFG3L2 chr18 12328944 12377227 - AHCYL1 chr1 109984765 110023742 + AIMP2 chr7 6009255 6023834 + AASDH chr4 56338287 56387508 - AAAS chr12 53307456 53324864 - ABHD4 chr14 22598237 22613215 + AKT1S1 chr19 49869033 49878459 - AACS chr12 125065434 125143333 + AFAP1 chr4 7758714 7939926 - ADCY1 chr7 45574140 45723116 + ALAD chr9 113386312 113401290 - AL139011.2 chr1 160216800 160285130 - AL355916.3 chr14 61529128 61657964 + AASS chr7 122073549 122144255 - AC004922.1 chr7 99325879 99394653 + AC005258.1 chr19 2269525 2341172 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-183-5p chr7 129774967 129774988 - hsa-miR-302d-3p chr4 112648006 112648028 - hsa-miR-1224-5p chr3 184241405 184241423 + hsa-miR-622 chr13 90231242 90231262 + hsa-miR-3648 chr21 8987026 8987046 + hsa-miR-4426 chr1 192716333 192716349 + hsa-miR-4700-5p chr12 120723202 120723223 + hsa-miR-4700-3p chr12 120723233 120723258 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC108134.2 chr16 3156736 3157483 - AC007780.1 chr17 68413623 68524949 + AC012313.3 chr19 58346854 58362751 - AL117378.1 chr6 131901963 131920565 + AC007952.4 chr17 19112000 19112636 - AC079089.1 chr8 69834111 69854971 + AC068768.1 chr12 123262060 123262402 + AC005920.1 chr17 50934989 50944713 - AC113189.2 chr17 7420103 7444081 + AC020934.1 chr19 12825711 12832983 + AC079781.5 chr7 97851688 97972985 - AC008124.1 chr12 45718046 45727775 - AC018521.1 chr17 47945424 47981736 + AC104109.4 chr5 134205614 134371044 - AD000090.1 chr19 35557956 35581954 + AC002094.1 chr17 28357647 28381697 + AC006064.4 chr12 6537794 6538370 - AC016876.2 chr17 7581964 7584086 - AC113189.4 chr17 7439506 7445966 + AC010327.5 chr19 55216660 55221616 + AC023509.1 chr12 53441741 53467528 + AC021078.1 chr5 149494314 149504670 - AL031985.3 chr1 40464319 40466767 + AC133552.5 chr16 25106569 25107102 - AC074183.1 chr7 84939349 84940245 - AC097478.1 chr4 89743792 89744305 + AL021707.2 chr22 38667585 38681847 - AC009022.1 chr16 69976297 70065948 - AC022167.2 chr16 8848105 8860456 + AL022332.1 chr22 25279529 25282674 - 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.