exRNAdisease

Entry Detail

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General Information

Database ID: exR0000160 RNA Name: ACP1 RNA Type: mRNA Chromosome: chr2 Starnd: + Coordinate: Start Site(bp): 264140 End Site(bp): 278283 External Links: ENSG00000143727

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 PIP4K2A chr10 22534854 22714578 - XPO6 chr16 28097979 28211920 - UBP1 chr3 33388336 33441371 - CST3 chr20 23626706 23638473 - RPS4X chrX 72255679 72277248 - ENSA chr1 150600851 150629612 - PTOV1 chr19 49850735 49860744 + SMC5 chr9 70258978 70354873 + TUFM chr16 28842411 28846348 - DTD2 chr14 31446036 31457506 - B2M chr15 44711487 44718877 + NUDT5 chr10 12165330 12196144 - SCD chr10 100347233 100364826 + VSIG10 chr12 118063593 118136026 - TBX6 chr16 30085793 30091887 - AC009133.6 chr16 29812261 29820092 + BORCS5 chr12 12357078 12471233 + ARPC2 chr2 218217141 218254356 + TOP2A chr17 40388525 40417896 - MT-CO1 chrMT 5904 7445 + EIF3CL chr16 28379579 28403879 - EIF3H chr8 116642130 116766925 - POLH chr6 43576185 43620523 + TUBB chr6 30720352 30725426 + CHMP1A chr16 89644435 89657721 - MOB3A chr19 2071036 2096673 - LYRM4 chr6 5102593 5260939 - TP53 chr17 7661779 7687550 - ORMDL3 chr17 39921041 39927601 - MSH2 chr2 47403067 47663146 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-let-7b-5p chr22 46113691 46113712 + hsa-let-7d-5p chr9 94178841 94178862 + hsa-let-7f-5p chrX 53557246 53557267 - hsa-miR-196a-5p chr17 48632532 48632553 - hsa-let-7g-5p chr3 52268336 52268357 - hsa-let-7i-5p chr12 62603691 62603712 + hsa-miR-151a-3p chr8 140732587 140732607 - hsa-miR-196b-5p chr7 27169528 27169549 - hsa-miR-519c-5p chr19 53686484 53686505 + hsa-miR-519b-5p chr19 53695225 53695246 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC126365.1 chr17 20788071 20789584 + AL139819.1 chr10 100335563 100346390 - 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.