exRNAdisease

Entry Detail

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General Information

Database ID: exR0000270 RNA Name: ADAMTSL4 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 150549369 End Site(bp): 150560937 External Links: ENSG00000143382

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 BAG6 chr6 31639028 31652705 - POLR2C chr16 57462660 57472009 + LMNA chr1 156082573 156140089 + EIF3L chr22 37848868 37889407 + NSD1 chr5 177133025 177300215 + ZIC2 chr13 99981784 99986765 + BST2 chr19 17402939 17405630 - NENF chr1 212432920 212446379 + TAF1D chr11 93729948 93784391 - URM1 chr9 128371361 128392016 + CNN2 chr19 1026586 1039068 + PABPC1 chr8 100685816 100722809 - ORC6 chr16 46689643 46698394 + ZNF678 chr1 227563543 227677443 + NFS1 chr20 35668052 35699355 - FLNA chrX 154348524 154374638 - VPS4A chr16 69311350 69326939 + TIAL1 chr10 119571802 119597029 - SMARCD2 chr17 63832081 63843065 - ZDHHC18 chr1 26826688 26857604 + UBE2V2 chr8 48008415 48064708 + ANKFY1 chr17 4163821 4263995 - FAR1 chr11 13668668 13732346 + RANGAP1 chr22 41245611 41286251 - SH3KBP1 chrX 19533977 19887600 - SFPQ chr1 35176378 35193145 - EIF4H chr7 74174245 74197101 + ARF4 chr3 57571363 57598220 - LIN28B chr6 104936616 105083332 + IGF2 chr11 2129112 2141238 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC132217.1 chr11 2129121 2129964 - AP001372.2 chr11 74493366 74498533 + 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.