exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000040 RNA Name: ABCB4 RNA Type: mRNA Chromosome: chr7 Starnd: - Coordinate: Start Site(bp): 87401697 End Site(bp): 87480435 External Links: ENSG00000005471

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 ABCB1 chr7 87503017 87713323 - AP1G2 chr14 23559565 23568070 - BASP1 chr5 17065598 17276843 + CENPV chr17 16342534 16353656 - CLDN6 chr16 3014712 3020071 - CUL5 chr11 108008898 108107761 + DDX5 chr17 64498254 64508199 - EIF5A chr17 7306999 7312463 + FXR2 chr17 7591230 7614897 - HNRNPDL chr4 82422564 82430408 - HSPA8 chr11 123057489 123063230 - HTATSF1 chrX 136497079 136512346 + KIF5B chr10 32009015 32056425 - MAF1 chr8 144104461 144107611 + NUAK1 chr12 106063340 106140033 - PAM chr5 102753981 103031105 + PHF14 chr7 10973336 11169630 + RPL5 chr1 92832013 92841924 + SERF2 chr15 43777087 43802589 + SLC39A1 chr1 153959099 153968184 - SNX18 chr5 54517759 54546586 + SPOCK2 chr10 72059034 72089032 - STX7 chr6 132445867 132513198 - TMEM167A chr5 83052846 83077863 - TPT1 chr13 45333471 45341370 - ZNF136 chr19 12163064 12189871 + ZNF385A chr12 54369133 54391298 - miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.