exRNAdisease

Entry Detail

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General Information

Database ID: exR0000142 RNA Name: ACLY RNA Type: mRNA Chromosome: chr17 Starnd: - Coordinate: Start Site(bp): 41866917 End Site(bp): 41930542 External Links: ENSG00000131473

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 AC093155.3 chr1 86993009 87169204 + CTCF chr16 67562467 67639177 + TRMT6 chr20 5937228 5950558 - ADAMTSL4 chr1 150549369 150560937 + PHF1 chr6 33410399 33416453 + LY6E chr8 143017982 143023832 + NOLC1 chr10 102152176 102163871 + CD276 chr15 73683966 73714514 + HSBP1 chr16 83807978 83819737 + INS-IGF2 chr11 2132538 2161209 - RAB8A chr19 16111889 16134234 + HSPA8 chr11 123057489 123063230 - RUVBL2 chr19 48993562 49015970 + ACBD3 chr1 226144679 226186741 - DCAF5 chr14 69050881 69153150 - OAZ1 chr19 2269509 2273490 + ZC3H13 chr13 45954465 46052759 - RNF115 chr1 145738868 145824095 - EEF1D chr8 143579697 143599541 - MTOR chr1 11106535 11262551 - LCOR chr10 96832282 96995959 + TNIP1 chr5 151029945 151093577 - OS9 chr12 57693955 57721557 + IGF2 chr11 2129112 2141238 - HMGA1 chr6 34236873 34246231 + SREBF2 chr22 41833079 41907307 + WDR33 chr2 127701027 127811187 - ATIC chr2 215311956 215349773 + EPHB4 chr7 100802565 100827523 - GUK1 chr1 228139962 228148984 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-22-3p chr17 1713914 1713935 - hsa-miR-27a-3p chr19 13836447 13836467 - hsa-miR-324-3p chr17 7223308 7223330 - hsa-miR-1269a chr4 66276890 66276911 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC007952.4 chr17 19112000 19112636 - AC019205.1 chr6 73263212 73301789 + AL121899.1 chr20 2207217 2213151 + AL132655.2 chr20 58817132 58817725 - AC138761.1 chr17 22266395 22288301 + AL355075.4 chr14 20343048 20343685 - LINC01356 chr1 112820170 112850643 - PURPL chr5 27217714 27496994 + TERC chr3 169764520 169765060 - TMEM161B-AS1 chr5 88268891 88439337 + XIST chrX 73820649 73852723 - 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.