exRNAdisease

Entry Detail

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General Information

Database ID: exR0012415 RNA Name: RPS6 RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 19375715 End Site(bp): 19380236 External Links: ENSG00000137154

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 ALDH5A1 chr6 24494867 24537207 + AL365205.1 chr6 41780349 41790141 + AC093668.1 chr7 102541501 102592444 - AKR1E2 chr10 4786629 4848062 + ADCY5 chr3 123282296 123449758 - AC093155.3 chr1 86993009 87169204 + ACTR2 chr2 65227753 65271253 + ABCF1 chr6 30571393 30597179 + AC138696.1 chr8 143247110 143276403 + ALDOA chr16 30064164 30070457 + AATF chr17 36948954 37056871 + AC105052.1 chr7 102582523 102642869 - ABCF3 chr3 184186023 184194012 + AL136454.1 chr1 192716132 192716653 + ADIPOR1 chr1 202940826 202958572 - ALDH6A1 chr14 74056847 74084492 - AARD chr8 116938207 116944487 + ACOT13 chr6 24667035 24705065 + ACKR3 chr2 236567787 236582354 + AHSA1 chr14 77457870 77469472 + AL139300.1 chr14 103562962 103685924 + ABHD14B chr3 51968510 51983409 - AGAP3 chr7 151085831 151144436 + AL136295.3 chr14 24120956 24131829 + AC040162.1 chr16 67929614 67936017 - AL121594.1 chr14 35122549 35317474 + ACO2 chr22 41469117 41528989 + AC009133.6 chr16 29812261 29820092 + ALDH9A1 chr1 165662216 165698863 - AARSD1 chr17 42950526 42964498 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-26a-2-3p chr12 57824620 57824641 - hsa-miR-4426 chr1 192716333 192716349 + hsa-miR-7705 chr8 100703002 100703024 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC005899.4 chr17 32328441 32329395 + AC012236.1 chr15 31221999 31230838 - AC016044.1 chr15 52800168 52805972 - AC016876.2 chr17 7581964 7584086 - AC023509.1 chr12 53441741 53467528 + AC115284.1 chr3 51961212 51974031 - AC135048.1 chr16 30948386 30956511 + AC245014.3 chr1 145281116 145281462 + AC245033.4 chr15 82533175 82540008 - AL022311.1 chr22 37876148 37895563 + 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.