exRNAdisease

Entry Detail

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General Information

Database ID: exR0000153 RNA Name: ACOT7 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 6264269 End Site(bp): 6394391 External Links: ENSG00000097021

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 HMGA1 chr6 34236873 34246231 + CHAMP1 chr13 114314482 114337626 + ANKZF1 chr2 219229783 219236679 + PRR7 chr5 177446445 177456286 + PGS1 chr17 78378649 78425114 + GYPC chr2 126656133 126696667 + UBP1 chr3 33388336 33441371 - TRIP10 chr19 6737925 6751530 + MTRNR2L11 chr1 237943724 237945275 - CCT7 chr2 73233420 73253021 + SEMA7A chr15 74409289 74433958 - TLE3 chr15 70047790 70098176 - GJA1 chr6 121435595 121449727 + NAP1L1 chr12 76036585 76084958 - UBE2D2 chr5 139526431 139628434 + PPP6R1 chr19 55229779 55259017 - CUL4A chr13 113208193 113267108 + EPB41L3 chr18 5392381 5630700 - FXR1 chr3 180868141 180982753 + CSNK2A1 chr20 472498 543835 - ELP2 chr18 36129444 36180557 + OGT chrX 71533104 71575892 + EEF2 chr19 3976056 3985463 - MLYCD chr16 83899115 83951445 + ZNF675 chr19 23525631 23687220 - SHC1 chr1 154962298 154974395 - SLC25A6 chrX 1386152 1392113 - ZNF333 chr19 14689801 14733746 + RBM15B chr3 51391285 51397908 + TRIM11 chr1 228393673 228406835 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-155-5p chr21 25573983 25574006 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC116407.1 chr17 32141226 32143135 - AL117378.1 chr6 131901963 131920565 + AC009119.2 chr16 83929796 83931223 - AL139393.2 chr6 160926269 160943110 + DANCR chr4 52712404 52720351 + FGD5-AS1 chr3 14920347 14948424 - MIR155HG chr21 25561909 25575168 + TUG1 chr22 30969245 30979395 + 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.