exRNAdisease

Entry Detail

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General Information

Database ID: exR0000106 RNA Name: ABTB2 RNA Type: mRNA Chromosome: chr11 Starnd: - Coordinate: Start Site(bp): 34150987 End Site(bp): 34358010 External Links: ENSG00000166016

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 ACAA2 chr18 49782164 49813953 - AL136454.1 chr1 192716132 192716653 + ATE1 chr10 121740421 121928801 - CEP104 chr1 3812086 3857214 - CYP4X1 chr1 47023669 47050751 + ECE1 chr1 21217247 21345572 - EEF2 chr19 3976056 3985463 - FAM118A chr22 45308968 45341955 + FASN chr17 82078338 82098294 - GAPDH chr12 6534512 6538374 + ID3 chr1 23557926 23559501 - KRAS chr12 25205246 25250936 - NPAT chr11 108157215 108222638 - PDIA4 chr7 149003062 149028662 - PHC3 chr3 170086732 170181749 - PTTG1IP chr21 44849585 44873903 - RAB1B chr11 66268590 66277492 + RBBP4 chr1 32651142 32686211 + RPL22 chr1 6185020 6209389 - RPS18 chr6 33272075 33276511 + RUSC1 chr1 155320894 155331114 + SERP1 chr3 150541998 150603228 - SHISA5 chr3 48467798 48504826 - SRGN chr10 69088103 69104805 + SRP68 chr17 76038775 76072517 - STAT6 chr12 57095408 57132139 - TBC1D2B chr15 77984036 78077724 - TUBB chr6 30720352 30725426 + TWNK chr10 100987367 100994403 + ZFYVE9 chr1 52142094 52346686 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AP003392.4 chr11 119065263 119065677 - 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.