exRNAdisease

Entry Detail

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General Information

Database ID: exR0011377 RNA Name: PRRC2B RNA Type: mRNA Chromosome: chr9 Starnd: + Coordinate: Start Site(bp): 131373636 End Site(bp): 131500197 External Links: ENSG00000130723

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 AAK1 chr2 69457997 69674349 - ABCB6 chr2 219209772 219218994 - ABLIM1 chr10 114431113 114768061 - AC011511.4 chr19 10315471 10320678 - AC068946.2 chr2 219209772 219222738 - AC245033.1 chr15 82536788 82573194 - ACTN4 chr19 38647649 38731589 + ACTR2 chr2 65227753 65271253 + ADIPOR1 chr1 202940826 202958572 - AFDN chr6 167826922 167972023 + AFF4 chr5 132875395 132963634 - AGAP5 chr10 73674285 73698159 - AGRN chr1 1020120 1056118 + AHCY chr20 34280268 34311802 - AHNAK2 chr14 104937244 104978374 - AKT2 chr19 40230317 40285536 - AL024498.2 chr6 10747794 10930423 + AL121594.1 chr14 35122549 35317474 + ALCAM chr3 105366909 105576900 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-31-5p chr9 21512158 21512178 - hsa-miR-147a chr9 120244985 120245004 - hsa-miR-217-5p chr2 55983020 55983042 - hsa-miR-135a-5p chr12 97563834 97563856 + hsa-miR-135b-5p chr1 205448361 205448383 - hsa-miR-483-3p chr11 2134142 2134162 - hsa-miR-520a-5p chr19 53690895 53690915 + hsa-miR-525-5p chr19 53697547 53697567 + hsa-miR-650 chr22 22822791 22822811 + hsa-miR-423-5p chr17 30117095 30117117 + hsa-miR-541-3p chr14 101064548 101064569 + hsa-miR-1286 chr22 20249145 20249165 - hsa-miR-1294 chr5 154347153 154347174 + hsa-miR-1321 chrX 85835832 85835849 + hsa-miR-5100 chr10 42997630 42997651 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC005082.1 chr7 23205787 23208045 + AC022400.3 chr10 73674295 73730466 - AC109460.3 chr16 28974804 28990775 + AD000090.1 chr19 35557956 35581954 + 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.