# _embedded.samples[].characteristics.sample source name[].text
kidney epithelial cells expressing viral Nsp11

# _embedded.samples[].characteristics.secondary description[].text
kidney epithelial cells expressing viral Nsp11

# _embedded.samples[].organization[].Name
University of Illinois at Champaign-Urbana

# _embedded.samples[].characteristics.description[].text
Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on plastic dishes

# _embedded.samples[].characteristics.sample characteristics[].text
SATB1-knocked down (by shRNA) human breast cancer cell line

# _embedded.samples[].characteristics.sample source name[].text
SATB1-shRNA trasnfected MDA-MB-231 cells grown on 2D culture

# _embedded.samples[].characteristics.description[].text
Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on matrigel coated dishes

# _embedded.samples[].characteristics.sample characteristics[].text
SATB1-knocked down (by shRNA) human breast cancer cell line

# _embedded.samples[].characteristics.sample source name[].text
SATB1-shRNA trasnfected MDA-MB-231 cells grown on 3D culture

# _embedded.samples[].characteristics.submission description[].text
The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of this mechanism is unclear. Here we show that nuclear rearrangement of repressive histone marks H3K9me3 and H3K27me3 into non-overlapping structural layers characterizes senescence-associated heterochromatic foci (SAHF) formation in human fibroblasts. However, the global landscape of these repressive marks remains unchanged upon SAHF formation, suggesting that in somatic cells heterochromatin can be formed through the spatial repositioning of pre-existing repressively marked histones. This model is reinforced by the correlation of pre-senescent replication timing with both the subsequent layered structure of SAHFs and the global landscape of the repressive marks, allowing us to integrate microscopic and genomic information. Furthermore, modulation of SAHF structure does not affect the occupancy of these repressive marks nor vice versa. These experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events. Profile comparison of normal growing (control) and Ras-induced senescent IMR90 cells.

# _embedded.samples[].characteristics.submission title[].text
Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

# _embedded.samples[].organization[].Name
University of Medicine and Dentistry of New Jersey

# _embedded.samples[].characteristics.description[].text
Gene expression data from parental-adherent considered as cells commited to differentiation

# _embedded.samples[].characteristics.sample source name[].text
PCSC-3 parental cultures in PCSCs medium

# _embedded.samples[].organization[].Name
University of Medicine and Dentistry of New Jersey

# _embedded.samples[].characteristics.sample source name[].text
Late-replicating DNA of Ras-induced senescent IMR90 cells

# _embedded.samples[].characteristics.sample title[].text
Replication timing of Ras-induced senescent IMR90 cells

# _embedded.samples[].characteristics.description[].text
Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on matrigel coated dishes (3D)

# _embedded.samples[].characteristics.sample characteristics[].text
SATB1-knocked down (by shRNA) human breast cancer cell line

# _embedded.samples[].characteristics.sample source name[].text
SATB1-shRNA trasnfected MDA-MB-231 cells grown on 3D culture

# _embedded.samples[].characteristics.submission description[].text
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. 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.

# _embedded.samples[].characteristics.submission title[].text
Expression data of control-shRNA and SATB1-shRNA expressing MDA-MB-231 cells from 2D and 3D culture system

# _embedded.samples[].characteristics.description[].text
Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on plastic dishes

# _embedded.samples[].characteristics.sample characteristics[].text
SATB1-knocked down (by shRNA) human breast cancer cell line

# _embedded.samples[].characteristics.sample source name[].text
SATB1-shRNA trasnfected MDA-MB-231 cells grown on 2D culture

# _embedded.samples[].characteristics.sample source name[].text
Early-replicating DNA of Ras-induced senescent IMR90 cells

# _embedded.samples[].characteristics.sample title[].text
Replication timing of Ras-induced senescent IMR90 cells

# _embedded.samples[].characteristics.sample source name[].text
Early-replicating DNA of normal IMR90 cells

# _embedded.samples[].characteristics.sample title[].text
Replication timing of normal growing IMR90 cells

# _embedded.samples[].characteristics.description[].text
Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on matrigel coated dishes (3D)

# _embedded.samples[].characteristics.sample characteristics[].text
SATB1-knocked down (by shRNA) human breast cancer cell line

# _embedded.samples[].characteristics.sample source name[].text
SATB1-shRNA trasnfected MDA-MB-231 cells grown on 3D culture