exRNAdisease

Entry Detail

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General Information

Database ID: exR0003077 RNA Name: COL4A2 RNA Type: mRNA Chromosome: chr13 Starnd: + Coordinate: Start Site(bp): 110305812 End Site(bp): 110513209 External Links: ENSG00000134871

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 ABHD10 chr3 111979010 111993368 + ACIN1 chr14 23058564 23095614 - ADNP2 chr18 80109262 80147523 + AF241726.2 chrX 37349330 38687674 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-199a-5p chr1 172144592 172144614 - hsa-miR-199b-5p chr9 128244783 128244805 - hsa-miR-140-5p chr16 69933103 69933124 + hsa-miR-302a-3p chr4 112648186 112648208 - hsa-miR-34c-5p chr11 111513451 111513473 + hsa-miR-299-3p chr14 101023832 101023853 + hsa-miR-302d-3p chr4 112648006 112648028 - hsa-miR-491-5p chr9 20716120 20716141 + hsa-miR-519c-5p chr19 53686484 53686505 + hsa-miR-520a-3p chr19 53690933 53690954 + hsa-miR-526a-5p chr19 53726928 53726949 + hsa-miR-519b-5p chr19 53695225 53695246 + hsa-miR-520c-5p chr19 53707468 53707489 + hsa-miR-518d-5p chr19 53734892 53734913 + hsa-miR-302e chr11 7234771 7234787 + hsa-miR-6850-5p chr8 144791970 144791991 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC009088.1 chr16 31196131 31196963 + 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.