exRNAdisease

Entry Detail

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General Information

Database ID: exR0000181 RNA Name: ACSS1 RNA Type: mRNA Chromosome: chr20 Starnd: - Coordinate: Start Site(bp): 25006230 End Site(bp): 25058980 External Links: ENSG00000154930

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 CTSB chr8 11842524 11869448 - RPL13 chr16 89560657 89566828 + RPL3 chr22 39312882 39320389 - MX1 chr21 41420304 41459214 + MKI67 chr10 128096659 128126423 - PTK2B chr8 27311482 27459391 + CLPTM1L chr5 1317752 1345099 - DIMT1 chr5 62347284 62403939 - LCP1 chr13 46125920 46211871 - CD79A chr19 41877279 41881372 + CMC4 chrX 155061622 155071136 - PHC3 chr3 170086732 170181749 - SASH3 chrX 129779949 129795201 + PAICS chr4 56435741 56464579 + PGM2 chr4 37826660 37862937 + MTRNR2L8 chr11 10507894 10509186 - AC092073.1 chr19 34396315 34409364 + ARL6IP6 chr2 152717893 152761253 + RPS29 chr14 49570984 49599164 - MTCP1 chrX 155064034 155147937 - GPI chr19 34359480 34402413 + CASP8 chr2 201233443 201287711 + MSL3 chrX 11758159 11775772 + EEF2 chr19 3976056 3985463 - SFPQ chr1 35176378 35193145 - TNFRSF14 chr1 2555639 2565382 + ACAD8 chr11 134253495 134265855 + RPL14 chr3 40457292 40468587 + PPP2R1A chr19 52190048 52229518 + SYVN1 chr11 65121780 65134533 - miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.