exRNAdisease

Entry Detail

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General Information

Database ID: exR0000481 RNA Name: ALDH1B1 RNA Type: mRNA Chromosome: chr9 Starnd: + Coordinate: Start Site(bp): 38392702 End Site(bp): 38398661 External Links: ENSG00000137124

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 UPF1 chr19 18831938 18868236 + ISG20L2 chr1 156721891 156728799 - STAU1 chr20 49113339 49188367 - SNURF chr15 24954986 24977850 + P4HB chr17 81843161 81860624 - GLYR1 chr16 4803203 4847288 - POLRMT chr19 617221 633537 - C9orf129 chr9 93318199 93346414 - LSP1 chr11 1852970 1892267 + HNRNPU chr1 244840638 244864560 - TPCN1 chr12 113221050 113298585 + LRG1 chr19 4536402 4540036 - RNF150 chr4 140859807 141212877 - CLDN6 chr16 3014712 3020071 - TXNDC5 chr6 7881517 7910788 - SSBP1 chr7 141738334 141787922 + PPP1R12A chr12 79773563 79935460 - YIPF1 chr1 53851719 53889798 - BLOC1S5-TXNDC5 chr6 7881522 8064364 - WDR70 chr5 37379285 37753435 + SPOP chr17 49598884 49678163 - TP53 chr17 7661779 7687550 - SNRPN chr15 24823637 24978723 + NOLC1 chr10 102152176 102163871 + TMEM132B chr12 125186836 125662377 + HMGA1 chr6 34236873 34246231 + LY75 chr2 159803355 159904756 - PTP4A1 chr6 63521746 63583436 + HSP90AB1 chr6 44246166 44253888 + KLC2 chr11 66257294 66267860 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC020663.1 chr16 4730115 4752565 - AP003175.1 chr11 75069243 75096964 - SNHG3 chr1 28505980 28510892 + XIST chrX 73820649 73852723 - 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.