exRNAdisease

Entry Detail

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General Information

Database ID: exR0000296 RNA Name: ADD2 RNA Type: mRNA Chromosome: chr2 Starnd: - Coordinate: Start Site(bp): 70607618 End Site(bp): 70768225 External Links: ENSG00000075340

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 COL21A1 chr6 56056590 56394094 - PRKD3 chr2 37250502 37324808 - SMIM20 chr4 25861830 25929874 + CNN3 chr1 94896949 94927223 - SHISA5 chr3 48467798 48504826 - PRUNE1 chr1 151008420 151035713 + FUBP3 chr9 130578965 130638352 + YWHAB chr20 44885702 44908532 + USP40 chr2 233475520 233566782 - DYNC1H1 chr14 101964573 102056443 + YIPF4 chr2 32277904 32316594 + RPS6 chr9 19375715 19380236 - C12orf75 chr12 105235290 105396097 + AC138894.1 chr16 28456371 28492098 - PPID chr4 158709127 158723396 - P4HB chr17 81843161 81860624 - CMSS1 chr3 99817837 100181732 + HSP90AB1 chr6 44246166 44253888 + TREX2 chrX 153444720 153470587 - AAK1 chr2 69457997 69674349 - RPL11 chr1 23691742 23696835 + MAP3K3 chr17 63622415 63696303 + ANKRD13C chr1 70258999 70354734 - ATP5F1D chr19 1241746 1244825 + GDF11 chr12 55743122 55757264 + ZMIZ2 chr7 44748581 44769881 + SRSF9 chr12 120461672 120469748 - SHMT1 chr17 18327860 18363563 - RPL4 chr15 66498015 66524532 - GTPBP1 chr22 38705742 38738299 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC245014.3 chr1 145281116 145281462 + AL356489.2 chr9 33697459 33700986 + FOXD3-AS1 chr1 63320884 63324441 - 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.