exRNAdisease

Entry Detail

---



General Information

Database ID: exR0004321 RNA Name: EEF2 RNA Type: mRNA Chromosome: chr19 Starnd: - Coordinate: Start Site(bp): 3976056 End Site(bp): 3985463 External Links: ENSG00000167658

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 AAMP chr2 218264123 218270257 - AHNAK chr11 62433542 62556235 - ACIN1 chr14 23058564 23095614 - ALAS1 chr3 52198086 52214327 + ABHD12 chr20 25294742 25390835 - AL365205.1 chr6 41780349 41790141 + AC073612.1 chr12 71674204 71698968 + AKT2 chr19 40230317 40285536 - AC010422.3 chr19 12643831 12648397 - AC008763.2 chr19 7629796 7643048 + AC092073.1 chr19 34396315 34409364 + AASS chr7 122073549 122144255 - AKAP8L chr19 15380050 15419141 - AL021546.1 chr12 120438198 120460006 + AC093525.2 chr16 2496032 2520218 + ACO1 chr9 32384603 32454769 + ACSS1 chr20 25006230 25058980 - ACAP3 chr1 1292390 1309609 - AC011448.1 chr19 19516227 19536076 + ADAR chr1 154582057 154628013 - ABCF1 chr6 30571393 30597179 + AC034102.2 chr12 56101331 56109289 + ABCF2 chr7 151207837 151227166 - AC008695.1 chr5 131425891 131796983 - AKAP17A chrX 1591604 1602520 + ALDOA chr16 30064164 30070457 + ACTA2 chr10 88935074 88991339 - ADRA2A chr10 111077029 111080907 + ACAP1 chr17 7336529 7351477 + AL136454.1 chr1 192716132 192716653 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-20b-5p chrX 134169850 134169872 - hsa-miR-1291 chr12 48654494 48654517 - hsa-miR-4426 chr1 192716333 192716349 + hsa-miR-1307-5p chr10 103394341 103394361 - hsa-miR-6850-5p chr8 144791970 144791991 - hsa-miR-7111-3p chr6 35470558 35470579 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AD000090.1 chr19 35557956 35581954 + AC026471.1 chr16 31456711 31459736 - AC026362.1 chr12 122975320 122982907 + AC009403.2 chr7 155474256 155644406 - AL022311.1 chr22 37876148 37895563 + AC245014.3 chr1 145281116 145281462 + AC004540.2 chr7 26369310 26376701 - AC132217.1 chr11 2129121 2129964 - AC005618.1 chr5 141326210 141329357 + AC011445.1 chr19 39314651 39320858 - AC091564.7 chr11 6610883 6616594 - AC024940.6 chr12 31280422 31280895 - AC067852.1 chr17 42536510 42562062 + AC093019.2 chr1 100057990 100084471 - AC016876.2 chr17 7581964 7584086 - AL035458.2 chr20 34234840 34281173 - AC022819.1 chr15 99157231 99161140 - AC126365.1 chr17 20788071 20789584 + AL137782.1 chr13 75549773 75807120 + AC011498.6 chr19 4454014 4455286 + AC010331.1 chr19 47607873 47608454 - AC007066.2 chr9 122937623 122940333 + AC009403.1 chr7 155611231 155645205 - AL121992.1 chr1 15586136 15603626 - AC139149.1 chr17 81514047 81527776 + AC245033.4 chr15 82533175 82540008 - AC109460.3 chr16 28974804 28990775 + AC002116.1 chr19 36008638 36014235 - AC092490.1 chr12 8788253 8795789 + AC102953.2 chr7 1464497 1467522 - 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.