Entry Detail



General Information

Database ID:exR0000062
RNA Name:ABCF1
RNA Type:mRNA
Chromosome:chr6
Starnd:+
Coordinate:
Start Site(bp):30571393End Site(bp):30597179
External Links:ENSG00000204574



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
HLA-DRB1
chr6
32578769
32589848
-
ZNF501
chr3
44729596
44737083
+
TMEM250
chr9
136114581
136118875
-
MT-CO1
chrMT
5904
7445
+
GLUL
chr1
182381704
182392206
-
CIC
chr19
42268537
42295797
+
MTRNR2L8
chr11
10507894
10509186
-
MYLIP
chr6
16129086
16148248
+
IFIT3
chr10
89327997
89340971
+
ZNF581
chr19
55635459
55645623
+
MAU2
chr19
19320829
19358754
+
CERS2
chr1
150960583
150975004
-
TNRC6A
chr16
24610209
24827632
+
PDP2
chr16
66878589
66895754
+
BSG
chr19
571277
583493
+
EEF1G
chr11
62559596
62574086
-
PTBP1
chr19
797075
812327
+
AP1S2
chrX
15825806
15854931
-
FTL
chr19
48965309
48966879
+
IQGAP1
chr15
90388242
90502239
+
SURF4
chr9
133361450
133376166
-
SELENON
chr1
25800176
25818221
+
RPS6
chr9
19375715
19380236
-
PDCD6IP
chr3
33798571
33869707
+
GPC6
chr13
93226807
94408020
+
VPS26A
chr10
69123512
69174412
+
CYFIP2
chr5
157266079
157395595
+
MFSD5
chr12
53251251
53254405
+
AC005832.4
chr12
4604944
4662643
+
BZW2
chr7
16646131
16706523
+
miRNA targets:
miRNA SymbolChromosomeStart Site(bp)End Site(bp)Strand
hsa-miR-302c-3p
chr4
112648366
112648388
-
circRNA targets:NA
lncRNA targets:
lncRNA SymbolChromosomeStart Site(bp)End Site(bp)Strand
AC000068.1
chr22
19447893
19450105
+
AC010642.2
chr19
58309727
58327248
-
DANCR
chr4
52712404
52720351
+
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.