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Series GSE5417

Query DataSets for GSE5417

Status

Public on Jan 31, 2008

Title

Expression data of control-shRNA and SATB1-shRNA expressing MDA-MB-231 cells from 2D and 3D culture system

Organism

Experiment type

Expression profiling by array

Summary

We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells.
Keywords: Comparative studies on Control_shRNA and SATB1_shRNA1 expressing MDA-MB-231 from 2D or 3D culture.

Overall design

We examined control_shRNA-MDA-MB-231 cells and SATB1_shRNA1-MDA-MB-231 cells under two culture condition;on plastic dish(2D culture) and on Matrigel coated dish(3D culture). When SATB1 was depleted by RNAi technology, these normally aggressive cells exhibited normal breast like morphology on 3D. We used two different microarray platforms (Codelink and Affymetrix) to make expression data. Initial analysis of data and cross-platform comparison were performed using Codelink expression analysis and GeneSpring software. We provide ratio for control_shRNA/SATB1_shRNA1-MDA-MB-231 cells for 2D and 3D on this series.

Contributor(s)

Hye-Jung H, Yoshinori K, Terumi K

Citation(s)

Submission date

Jul 31, 2006

Last update date

Jan 17, 2017

Contact name

Terumi Kohwi-shigematsu

E-mail(s)

terumiks@lbl.gov

Phone

510-486-4983

Fax

510-486-4545

Organization name

LBNL

Department

Life Science

Street address

1 Cyclotron road

City

Berkeley

State/province

CA

ZIP/Postal code

94720

Country

USA

Platforms (2)

GPL3921	[HT_HG-U133A] Affymetrix HT Human Genome U133A Array
GPL4044	CodeLink UniSet Human 20K I Bioarray

Samples (12)

More...

GSM124327	SATB1_shRNA1-MDA-MB-231_2D
GSM124328	SATB1_shRNA1-MDA-MB-231_3D
GSM124329	Control_shRNA-MDA-MB-231_2D

Relations

BioProject

Significantly-regulated gene list header descriptions
ID_REF	ProbeSet ID
2D VALUE	Ratio of normalized expression measurement of control_shRNA cells to SATB1_shRNA cells cultured on plastic dish
3D VALUE	Ratio of normalized expression measurement of control_shRNA cells to SATB1_shRNA cells cultured on matrigel coated dish
GENE SYMBOL	Gene symbol
GENE DESCRIPTION	Gene product
NCBI ACCESSION ID	NCBI accession ID

Data table
ID_REF	2D VALUE	3D VALUE	GENE SYMBOL	GENE DESCRIPTION	NCBI ACCESSION ID
211337_s_at	1.406	1.582	76P	Gamma Tubulin Ring Complex Protein (76P Gene)	NM_014444
213266_at	0.694	1.625	76P	Gamma Tubulin Ring Complex Protein (76P Gene)	BF592982
205969_at	0.809	0.59	AADAC	Arylacetamide Deacetylase (Esterase)	NM_001086
201000_at	1.483	1.458	AARS	Alanyl-Trna Synthetase	NM_001605
222064_s_at	0.85	1.561	AARSD1	Alanyl-Trna Synthetase Domain Containing 1	AI093187
NM_025267.1_PROBE1	0.96	2.36	AARSD1	Alanyl-Trna Synthetase Domain Containing 1	NM_025267
210852_s_at	0.569	1.456	AASS	Aminoadipate-Semialdehyde Synthase	NM_005763
214829_at	0.534	1.086	AASS	Aminoadipate-Semialdehyde Synthase	NM_005763
218991_at	1.118	1.514	ABC1	Amplified In Breast Cancer 1	NM_022070
65493_at	1.023	1.504	ABC1	Amplified In Breast Cancer 1	AA555088
214209_s_at	1.009	1.79	ABCB9	ATP-Binding Cassette, Sub-Family B (Mdr/Tap), Member 9	BE504895
208161_s_at	0.622	1.5	ABCC3	ATP-Binding Cassette, Sub-Family C (Cftr/Mrp), Member 3	NM_020037
NM_005688.1_PROBE1	0.47	0.83	ABCC5	ATP-Binding Cassette, Sub-Family C (Cftr/Mrp), Member 5	NM_005688
NM_000033.2_PROBE1	1.93	2.17	ABCD1	ATP-Binding Cassette, Sub-Family D (Ald), Member 1	NM_000033
NM_001090.1_PROBE1	0.78	2.30	ABCF1	ATP-Binding Cassette, Sub-Family F (Gcn20), Member 1	NM_001090
AF261091_PROBE1	0.46	1.06	ABCF2	ATP-Binding Cassette, Sub-Family F (Gcn20), Member 2	NM_007189
202394_s_at	1.451	1.288	ABCF3	ATP-Binding Cassette, Sub-Family F (Gcn20), Member 3	NM_018358
204567_s_at	0.801	0.559	ABCG1	ATP-Binding Cassette, Sub-Family G (White), Member 1	NM_004915
957502.1_PROBE1	1.16	2.18	ABHD14B	Abhydrolase Domain Containing 14B	NM_032750
213805_at	0.737	0.607	ABHD5	Abhydrolase Domain Containing 5	AI692428

Total number of rows: 3692

Table truncated, full table size 288 Kbytes.

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE5417_RAW.tar	24.8 Mb	(http)(custom)	TAR (of CEL, TXT)
Processed data included within Sample table

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