exRNAdisease

Entry Detail

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General Information

Database ID: exR0000372 RNA Name: AGGF1 RNA Type: mRNA Chromosome: chr5 Starnd: + Coordinate: Start Site(bp): 77029251 End Site(bp): 77065234 External Links: ENSG00000164252

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 ASPM chr1 197084127 197146694 - RPL27A chr11 8682788 8714759 + PGK1 chrX 77910739 78129295 + TUBA1B chr12 49127782 49131397 - EIF5A chr17 7306999 7312463 + FP565260.6 chr21 5155499 5165472 - MYL6 chr12 56158161 56163496 + FP565260.2 chr21 5116343 5133805 - ESRP1 chr8 94641074 94707466 + SUB1 chr5 32531633 32604079 + BZW2 chr7 16646131 16706523 + ACTA1 chr1 229431245 229434098 - B2M chr15 44711487 44718877 + NEDD4L chr18 58044226 58401540 + HLA-A chr6 29941260 29945884 + MARCKSL1 chr1 32333839 32336233 - RPS9 chr19 54200809 54249003 + AC008581.2 chr5 77030902 77152155 + KIFC3 chr16 57758217 57863053 - SMC4 chr3 160399274 160434954 + PRRC1 chr5 127517609 127555089 + TCEAL4 chrX 103576231 103587736 + PPP2R5B chr11 64917553 64934475 + ERAL1 chr17 28855010 28861061 + PBX1 chr1 164555584 164899296 + ID1 chr20 31605283 31606515 + CCPG1 chr15 55340032 55408510 - RPL23A chr17 28719985 28724359 + ACTN1 chr14 68874143 68979440 - MIF chr22 23894383 23895227 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand FGD5-AS1 chr3 14920347 14948424 - 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.