exRNAdisease

General Information

Database ID:

exR0006399

RNA Name:

HMGA1

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

34236873

End Site(bp):

34246231

External Links:

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
ACTR2	chr2	65227753	65271253	+
ADNP	chr20	50888916	50931437	-
AKR7A2	chr1	19303965	19312146	-
ADH5	chr4	99070978	99088801	-
ADM	chr11	10305073	10307397	+
AC008982.1	chr19	38817471	38840178	-
ADGRL1	chr19	14147743	14206187	-
AGPAT1	chr6	32168212	32178096	-
ADGRA3	chr4	22345071	22516066	-
AGFG2	chr7	100539203	100568220	+
ACLY	chr17	41866917	41930542	-
AJUBA	chr14	22971177	22982551	-
AK4	chr1	65147549	65232145	+
AAMP	chr2	218264123	218270257	-
AC009133.6	chr16	29812261	29820092	+
AHCYL2	chr7	129225023	129430211	+
AC068547.1	chr2	151802651	151973949	-
AC015813.2	chr17	57989038	58007246	-
AKAP13	chr15	85380571	85749358	+
AFTPH	chr2	64524305	64593005	+
AK5	chr1	77282019	77559966	+
ADRM1	chr20	62302093	62308862	+
ACER3	chr11	76860867	77026797	+
AL121594.1	chr14	35122549	35317474	+
ACTA1	chr1	229431245	229434098	-
AHCY	chr20	34280268	34311802	-
ABRACL	chr6	139028745	139043302	+
ADARB1	chr21	45073853	45226560	+
AL136454.1	chr1	192716132	192716653	+
ACAD10	chr12	111686056	111757107	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-let-7a-5p	chr9	94175962	94175983	+
hsa-let-7d-5p	chr9	94178841	94178862	+
hsa-let-7e-5p	chr19	51692793	51692814	+
hsa-miR-21-5p	chr17	59841273	59841294	+
hsa-miR-138-5p	chr16	56858527	56858549	+
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-1321	chrX	85835832	85835849	+
hsa-miR-3654	chr7	133034860	133034878	-
hsa-miR-6835-3p	chr6	34240714	34240736	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007952.4	chr17	19112000	19112636	-
AC010331.1	chr19	47607873	47608454	-
AC016876.2	chr17	7581964	7584086	-
AC019205.1	chr6	73263212	73301789	+
AC020663.1	chr16	4730115	4752565	-
AC020928.2	chr19	36773712	36775908	-
AC025271.4	chr15	57553955	57555680	+
AC079781.5	chr7	97851688	97972985	-
AC104971.1	chr18	58670009	58671877	-
AC126365.1	chr17	20788071	20789584	+
AC132217.1	chr11	2129121	2129964	-
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL117378.1	chr6	131901963	131920565	+
AL132780.1	chr14	22929607	22956374	+

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.