exRNAdisease

Entry Detail

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General Information

Database ID: exR0000470 RNA Name: AKTIP RNA Type: mRNA Chromosome: chr16 Starnd: - Coordinate: Start Site(bp): 53491040 End Site(bp): 53504411 External Links: ENSG00000166971

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 AHCYL1 chr1 109984765 110023742 + AP002990.1 chr11 62559603 62591531 - ATXN2L chr16 28823035 28837237 + EEF1G chr11 62559596 62574086 - EI24 chr11 125569280 125584684 + EIF3H chr8 116642130 116766925 - ERG28 chr14 75649791 75660876 - FGF2 chr4 122826708 122898236 + FLRT3 chr20 14322985 14337614 - FRAS1 chr4 78057323 78544269 + HILPDA chr7 128455849 128458418 + HMGN3 chr6 79201245 79234738 - MT-CO3 chrMT 9207 9990 + NAPG chr18 10525905 10552764 + PIGX chr3 196639775 196736007 + PPP4R3B chr2 55547292 55618880 - PTGES3 chr12 56663341 56688408 - SH3KBP1 chrX 19533977 19887600 - SLC7A5 chr16 87830023 87869507 - TMCO3 chr13 113491021 113554590 + TMX1 chr14 51240162 51257655 + TRIM71 chr3 32817997 32897824 + TSPAN6 chrX 100627108 100639991 - TUFM chr16 28842411 28846348 - UQCR10 chr22 29767369 29770413 + VCPIP1 chr8 66628487 66667231 - 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.