exRNAdisease

Entry Detail

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General Information

Database ID: exR0000355 RNA Name: AFTPH RNA Type: mRNA Chromosome: chr2 Starnd: + Coordinate: Start Site(bp): 64524305 End Site(bp): 64593005 External Links: ENSG00000119844

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 BID chr22 17734138 17774770 - YWHAQ chr2 9583967 9630997 - CLEC2D chr12 9664969 9699553 + NAP1L1 chr12 76036585 76084958 - DTYMK chr2 241675747 241686944 - TWSG1 chr18 9334767 9402420 + TUBA1B chr12 49127782 49131397 - LAMC1 chr1 183023420 183145592 + BIRC2 chr11 102347211 102378670 + CUL3 chr2 224470150 224585397 - PGK1 chrX 77910739 78129295 + HLA-A chr6 29941260 29945884 + HEXA chr15 72340919 72376476 - STRN4 chr19 46719511 46746994 - RPUSD4 chr11 126202096 126211692 - HLA-F chr6 29722775 29738528 + BRPF3 chr6 36196744 36232790 + CD48 chr1 160678746 160711831 - ATP5MG chr11 118401606 118431496 + LCP1 chr13 46125920 46211871 - ATP8B2 chr1 154325553 154351304 + NCL chr2 231453531 231483641 - AKIRIN2 chr6 87674860 87702233 - HNRNPU chr1 244840638 244864560 - HDAC2 chr6 113933028 114011308 - PHF20 chr20 35771974 35950370 + RPL32 chr3 12834485 12841582 - MRPL4 chr19 10251901 10260055 + RPL27 chr17 42998273 43002959 + YWHAH chr22 31944522 31957603 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand LINC01405 chr12 110934590 110959093 + 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.