Entry Detail



General Information

Database ID:exR0000374
RNA Name:AGL
RNA Type:mRNA
Chromosome:chr1
Starnd:+
Coordinate:
Start Site(bp):99850361End Site(bp):99924023
External Links:ENSG00000162688



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 SymbolChromosomeStart Site(bp)End Site(bp)Strand
FSD1
chr19
4304598
4323843
+
ATP5F1B
chr12
56638175
56645984
-
MRPL16
chr11
59806140
59810778
-
CTPS1
chr1
40979688
41012565
+
MARCKSL1
chr1
32333839
32336233
-
ERCC6
chr10
49454470
49539538
-
APP
chr21
25880550
26171128
-
CRLS1
chr20
6006093
6040053
+
NAT10
chr11
34105617
34147670
+
EEF1A1
chr6
73515750
73523797
-
PTOV1
chr19
49850735
49860744
+
NUCKS1
chr1
205712822
205750182
-
KLHL15
chrX
23983720
24027186
-
PPIA
chr7
44796680
44824564
+
RPS8
chr1
44775251
44778779
+
POLD3
chr11
74493851
74669117
+
ANXA7
chr10
73375101
73414076
-
TBKBP1
chr17
47694081
47712050
+
CARD10
chr22
37490362
37519542
-
IQSEC1
chr3
12897043
13283281
-
BEX4
chrX
103215108
103217246
+
MRPL13
chr8
120380761
120445402
-
CIAPIN1
chr16
57428187
57447420
-
MIGA2
chr9
129036621
129072082
+
KIF3C
chr2
25926598
25982749
-
DTL
chr1
212035553
212107400
+
KHDRBS1
chr1
32013868
32060850
+
UHMK1
chr1
162497251
162529631
+
AURKAIP1
chr1
1373730
1375495
-
PARP1
chr1
226360691
226408093
-
miRNA targets:
miRNA SymbolChromosomeStart Site(bp)End Site(bp)Strand
hsa-miR-302b-3p
chr4
112648489
112648511
-
circRNA targets:NA
lncRNA targets:
lncRNA SymbolChromosomeStart Site(bp)End Site(bp)Strand
LINC00910
chr17
43338741
43389199
-
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.