exRNAdisease

Entry Detail

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General Information

Database ID: exR0000201 RNA Name: ACTR10 RNA Type: mRNA Chromosome: chr14 Starnd: + Coordinate: Start Site(bp): 58200080 End Site(bp): 58235636 External Links: ENSG00000131966

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 HIBCH chr2 190189735 190344193 - CCNG1 chr5 163437569 163446151 + PPP2CA chr5 134194332 134226073 - TOMM20 chr1 235109341 235128837 - ACTB chr7 5527148 5563784 - APP chr21 25880550 26171128 - PTK2B chr8 27311482 27459391 + CTDSP2 chr12 57819927 57846729 - SLC6A9 chr1 43991500 44031467 - B2M chr15 44711487 44718877 + RPS20 chr8 56067295 56074581 - NUDC chr1 26900238 26946871 + AURKA chr20 56369389 56392337 - PABPC3 chr13 25095868 25099254 + TUBA3C chr13 19173772 19181824 - UBA6 chr4 67612652 67701155 - CAND1 chr12 67269358 67319953 + MGRN1 chr16 4616493 4690974 + ARF1 chr1 228082660 228099212 + ALDOA chr16 30064164 30070457 + MTRNR2L12 chr3 96617188 96618236 - PBX1 chr1 164555584 164899296 + PRKCI chr3 170222424 170305977 + LRRC20 chr10 70298970 70382650 - CCNC chr6 99542387 99568825 - SMARCC1 chr3 47585269 47782106 - TSPAN15 chr10 69451465 69507666 + NID1 chr1 235975830 236065109 - CAMK2G chr10 73812501 73874591 - AIF1L chr9 131096476 131123152 + 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.