exRNAdisease

Entry Detail

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General Information

Database ID: exR0000171 RNA Name: ACSL1 RNA Type: mRNA Chromosome: chr4 Starnd: - Coordinate: Start Site(bp): 184755595 End Site(bp): 184826818 External Links: ENSG00000151726

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 ACOT7 chr1 6264269 6394391 - ACP6 chr1 147629652 147670524 - ALMS1 chr2 73385758 73625166 + APOBEC3G chr22 39077067 39087743 + BCAT2 chr19 48795062 48811029 - CCL22 chr16 57358783 57366189 + CHST12 chr7 2403588 2448484 + CPNE1 chr20 35626031 35664956 - DDB1 chr11 61299451 61342596 - DPYSL2 chr8 26514031 26658178 + ENOSF1 chr18 670318 712662 - FADS2 chr11 61792980 61867354 + FBL chr19 39834458 39846379 - HNRNPH1 chr5 179614178 179634784 - IMP3 chr15 75639085 75648706 - LPXN chr11 58526871 58578220 - NAA16 chr13 41311267 41377030 + POLL chr10 101578882 101588270 - PTDSS2 chr11 448268 491399 + TMEM170A chr16 75443054 75465497 - TWNK chr10 100987367 100994403 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-34a-5p chr1 9151735 9151756 - hsa-miR-205-5p chr1 209432166 209432187 + hsa-miR-34c-5p chr11 111513451 111513473 + hsa-miR-337-3p chr14 100874553 100874574 + hsa-miR-449a chr5 55170586 55170607 - hsa-miR-449b-5p chr5 55170706 55170727 - 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.