# _embedded.samples[].characteristics.description[].text
The HCC patients had not received adjuvant chemotherapy.

# _embedded.samples[].organization[].Name
Liver Cancer Institute, Zhongshan Hospital, Fudan University;

# _embedded.samples[].characteristics.description[].text
Gene expression data from E. coli in early logarithmic growth

# _embedded.samples[].organization[].Name
University of Pennsylvania, School of Medicine

# _embedded.samples[].characteristics.description[].text
normalized using 14028s total RNA isolated from the equvalent condition.

# _embedded.samples[].characteristics.organism[].text
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

# _embedded.samples[].characteristics.description[].text
Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled

# _embedded.samples[].characteristics.sample source name[].text
reference commercial genomic DNA (Promega), labeled with Cyanine-5 (green).

# _embedded.samples[].characteristics.sample type[].text
reference commercial genomic DNA (Promega)

# _embedded.samples[].characteristics.submission description[].text
High-throughput sequencing of Drosophila melanogaster small RNAs from S2R+ cells. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Small RNAs were sequenced from D. melanogaster S2R+ cells. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt.

# _embedded.samples[].characteristics.submission title[].text
High-throughput sequencing of Drosophila melanogaster small RNAs from S2R+ cells

# _embedded.samples[].organization[].Name
Genomics Institute of the Novartis Research Foundation

# _embedded.samples[].characteristics.description[].text
Gene expression data from monocytes after 7 days in vitro macrophage differentiation

# _embedded.samples[].characteristics.sample title[].text
Newborn cord blood gDNA for sample_X18_a

# _embedded.samples[].characteristics.submission description[].text
Background: Global DNA methylation contributes to genomic integrity by supressing repeat associated transposition events. Several chromatin factors are required in addition to DNA methyltransferases to maintain DNA methylation at intergenic and satellite repeats. Embryos lacking Lsh, a member of the SNF2 superfamily of chromatin helicases, are hypomethylated. The interaction of Lsh with the de novo methyltransferase, Dnmt3b, facilitates the deposition of DNA methylation at stem cell genes. We wished to determine if a similar targeting mechanism operates to maintain DNA methylation at repetitive sequences. Results: We used HELP-seq to map genome wide DNA methylation patterns in Lsh-/- and Dnmt3b-/- somatic cells. DNA methylation is predominantly lost from specific genomic repeats in Lsh-/- cells: LTR-retrotransposons, LINE-1 repeats and mouse satellites. RNA-seq experiments demonstrate that specific IAP (Intracisternal A-type particle) LTRs and satellites, but not LINE-1 elements, are aberrantly transcribed inLsh-/- cells. LTR hypomethylation in Dnmt3b-/- cells is moderate and hypomethylated repetitive elements (IAP, LINE-1 and satellite) are silent. Chromatin immunoprecipitation (ChIP) indicates that repressed LINE-1 elements gain H3K4me3, but H3K9me3 levels are unaltered in Lsh-/- cells, indicating that DNA hypomethylation alone is not permissive for their transcriptional activation. Mis-expressed IAPs and satellites lose H3K9me3 and gain H3K4me3 in Lsh-/- cells. Conclusions: Our study emphasizes that regulation of repetitive elements by DNA methylation is selective and context dependent. We propose a model where Lsh is specifically required at a precise developmental window to target de novo methylation to repeat sequences, which is subsequently maintained by Dnmt1 in somatic cells to enforce repeat silencing thus contributing to genomic integrity. Two pairs of genomic samples compared: WT and Lsh-/- DNA isolations from tail-tip fibroblasts; WT and Dnmt3b knockout DNA isolations from mouse embryonic fibroblasts.

# _embedded.samples[].characteristics.submission title[].text
Lsh regulates LTR retrotransposon repression independent of Dnmt3b function (HELP-seq)

# _embedded.samples[].characteristics.description[].text
normalized using 14028s total RNA isolated from the equvalent condition.

# _embedded.samples[].characteristics.organism[].text
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

# _embedded.samples[].characteristics.description[].text
Gene expression data from freshly isolated monocytes

# _embedded.samples[].characteristics.submission description[].text
Transcriptome analysis of EYA2 non-expressing pancreatic cancer cell lines with stable transfectant overexpressing EYA2 We analyzed Panc2.5 and Panc3.014 stable transfectant (overexpressing EYA2) and control (empty pcDNA6.2/cLumio-DEST vector) cell transcriptomes using the Affymetrix Exon Array ST1.0 platform. Statistical analysis of gene expression array data was completed with Partek Genomic Suite 6.4 software.

# _embedded.samples[].characteristics.submission title[].text
Transcriptome analysis of EYA2 non-expressing pancreatic cancer cell lines with stable transfectant overexpressing EYA2

# _embedded.samples[].characteristics.description[].text
The HCC patients had not received adjuvant chemotherapy.

# _embedded.samples[].characteristics.sample type[].text
Reference RNA pool from 20 normal livers

# _embedded.samples[].organization[].Name
Liver Cancer Institute, Zhongshan Hospital, Fudan University;

# _embedded.samples[].characteristics.description[].text
The HCC patients had not received adjuvant chemotherapy.

# _embedded.samples[].characteristics.sample type[].text
Reference RNA pool from 20 normal livers

# _embedded.samples[].organization[].Name
Liver Cancer Institute, Zhongshan Hospital, Fudan University;