Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12543000_1.fastq.gz | Fastqsanger.gz | |||
| SRR12543000_2.fastq.gz | Fastqsanger.gz | |||
| SRR12543001_1.fastq.gz | Fastqsanger.gz | |||
| SRR12543001_2.fastq.gz | Fastqsanger.gz | |||
| SRR12543002_1.fastq.gz | Fastqsanger.gz |
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Project description:Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. Aberrant hypermethylation in the promoter region of some known or putative tumor suppressor genes (TSGs) occurs frequently during the development of various cancers including head and neck squamous cell carcinoma (HNSCC). In this study we used an expanded mRNA expression profiling approach followed by microarray expression analysis to identify epigenetically inactivated genes in HNSCC. Two HNSCC cell lines were treated with 5-aza-2M-bM-^@M-^Y-deoxycytidine followed by microarray analysis to identify epigenetically silenced genes in HNSCC. 1960, 614, and 427 genes were upregulated in HNSCC cell lines JHU-012, JHU-011 and the combination of both cell lines, respectively. HNSCC tumor and normal mucosal samples were used for gene profiling by a 47K mRNA gene expression array and we found, 7140 genes were downregulated in HNSCC tumors compared to normal mucosa as determined by microarray analysis and were integrated with cell line data. Integrative analysis defined 126 candidate genes, of which only seven genes showed differentially methylation in tumors and no methylation in normal mucosa after bisulfite sequencing. After validation by QMSP, one gene, GNG7, was confirmed as being highly methylated in tumors and unmethylated in normal mucosal and salivary rinse samples demonstrating cancer-specific methylation in HNSCC tissues. TXNIP and TUSC2 were partially methylated in tumors and normal salivary rinses but unmethylated in normal mucosa. We concluded GNG7 as a highly specific promoter methylated gene associated with HNSCC. In addition, TXNIP and TUSC2 are also potential biomarkers for HNSCC. We performed pharmacological unmasking analysis on two HNSCC cancer cell lines JHU-O11 and JHU-O12 by treating cells with or without 5-aza-dC, followed by RNA extraction and microarray analysis using Affymetrix U133 Plus 2.0. The array data were analyzed by initially dChip and then SAM. We performed a four-phase strategy to obtain the unmasked genes in the cells treated with 5-aza and downregulated genes in primary tumors. In the first phase, we compared the cell lines, either JHU-012 or JHU-011, before treatment to the cell lines treated with 5-aza, in order to identify genes that were reexpressed M-bM-^IM-% 2 fold. We found 1960 genes that were upregulated by 5-aza-dC in JHU-O12 cell line. SAM output was obtained at a delta value of 2.05 with a false discovery rate (FDR) of 10% and the d-score cut-off was 1.17. 614 reexpressed genes were found in 5 aza-treated JHU-O11 (SAM output; delta: 2.089, FDR%: 10, d-score cut-off: 2.8). 427 genes were commonly upregulated in both cell lines when the cell lines were normalized and analyzed together (SAM output; delta: 1.44, FDR%: 10, d-score cut-off: 1.88). In the second phase of our analysis, we further extracted RNA and performed the 47K mRNA expression array analysis on 13 primary HNSCC tumors samples and 5 normal mucosa samples from non-cancer control patients. After initial dChip and SAM analysis (SAM output; delta: 1.247, FDR%: 5.24, d-score cut-off:0.24), we found 7140 downregulated genes in primary HNSCC tumors compared with normal mucosa. In the third phase, we investigated these three data sets: a) SAM output of 1960 upregulated genes after 5-aza treatment of JHU-012 vs SAM output of 7140 downregulated genes in primary HNSCC: We found that 210 genes that were upregulated by 5-aza-dC in the JHU-O12 cell line and showed downregulation in tumor samples, b) SAM output of 614 upregulated genes after 5-aza treatment of JHU-011 vs SAM output of 7140 downregulated genes in primary HNSCC: We found 79 genes that were upregulated by 5-aza-dC in the JHU-O11 cell line and showed downregulation in tumor samples, c) SAM output from analyzing both cell lines together in the same SAM computation, of 427 upregulated genes after 5-aza treatment of JHU-011 and JHU-012 vs SAM output of 7140 downregulated genes in primary HNSCC: We found 44 genes that were upregulated by 5-aza-dC in JHU-O11 and JHU-012 cell lines and showed downregulation in tumor samples, suggesting that methylation might be involved in gene downregulation. In the fourth phase of our strategy, we rank-ordered the results of upregulated genes obtained from these 3 data sets and found 126 common genes. We then examined promoter regions of the 126 genes for CpG islands and performed bisulfite sequencing analysis of the promoter region of these genes. We found that 7 genes showed a differential methylation pattern between normal and neoplastic samples. After validation of these genes in a cohort of 33 HNSCC patients and normal salivary and mucosal samples from healthy people by QMSP, we found 3 genes of interest.
2014-05-01 | E-GEOD-29330 | biostudies-arrayexpress
Project description:Bacillus cereus strain:JHU | isolate:JHU Genome sequencing and assembly
| PRJNA591929 | ENA
Project description:TCGA Analysis of DNA Methylation Using Illumina Infinium Human DNA Methylation 27 platform laird-00224 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_OV.HumanMethylation27.1.adf, jhu-usc.edu_OV.HumanMethylation27.v2 Organism: Homo sapiens (ncbitax) Tissue Sites: Ovary, Ovary, NOT SPECIFIED, PERITONEUM (OVARY), OMENTUM Material Types: Control Cell Line, Solid normal_tissue, organism_part, Primary solid_tumor, whole_organism, Recurrent Solid Tumor Disease States: Serous Cystadenocarcinoma, Serous cystadenocarcinoma, NOT SPECIFIED
2015-11-21 | E-GEOD-75268 | biostudies-arrayexpress
Project description:A whole genome PCR amplicon DNA microarray for B. mallei were fabricated as previously described [7]. Total RNA was isolated from in vitro cultures in LBG medium of B. mallei ATCC 23344, FMH, and JHU. The OD600 of the samples at harvest were all 0.55. The RNAs from FMH and JHU were labeled and hybridized to the array using the ATCC 23344 RNA as the reference using protocols as described. Flip-dye replicates were performed for all analyses. Two B. mallei ATCC 23344 samples grown to an O.D.600 of 1.0 on separate days and total RNA was extracted. These RNA samples were hybridized against each other as a control for the JHU vs. ATCC 23344 hybridization and the FMH vs. ATCC 23344 hybridization.
2006-09-22 | E-MEXP-853 | biostudies-arrayexpress
Project description:Extended pluripotent stem cells (EPSCs) derived from mice and humans showed an enhanced potential for chimeric formation. By exploiting transcriptomic techniques, we assessed the differences in gene expression profile between extended EPSCs derived from mice and humans, and those newly derived from the common marmoset (marmoset; Callithrix jacchus). Although the marmoset EPSC-like cells displayed a unique colony morphology distinct from murine and human EPSCs, they displayed a pluripotent state akin to embryonic stem cells (ESCs), as confirmed by gene expression and immunocytochemical analyses of pluripotency markers and three-germ-layer differentiation assay. Importantly, the marmoset EPSC-like cells showed interspecies chimeric contribution to mouse embryos, such as E6.5 blastocysts in vitro and E8.5 epiblasts in vivo in mouse development. Also, we discovered that the perturbation of gene expression of the marmoset EPSC-like cells from the original ESCs resembled that of human EPSCs. Thus, we established the efficacy of the method for the derivation of marmoset EPSCs
2022-01-01 | GSE189633 | GEO
Project description:We report the liver progenitor cell related gene expression of established marmoset liver progenitor cell line and provide the whole gene expression transcriptomes of marmoset liver.
2018-01-01 | GSE99168 | GEO
Project description:Mutations in non-coding regulatory DNA such as enhancers underlie a wide variety of diseases including developmental disorders and cancer. As enhancers rapidly evolve, understanding their function and configuration in non-human disease models can have important clinical applications. Here, we analyze enhancer configurations in tissues isolated from the common marmoset, a widely used primate model for human disease. Integrating these data with human and mouse data, we find that enhancers containing trait-associated variants are preferentially conserved. In contrast, most human-specific enhancers are highly variable between individuals, with a subset failing to contact promoters. These are located further away from genes and more often reside in inactive B-compartments. Our data show that enhancers typically emerge as instable elements with minimal biological impact prior to their integration in a transcriptional program. Furthermore, our data provide insight into which trait variations in enhancers can be faithfully modeled using the common marmoset.
2020-05-15 | GSE141563 | GEO
Project description:The analysis compares primary fibroblasts initially used for reprogramming, established marmoset ES cells and a marmoset iPS cell line which was generated witha non-viral approach using a six-factor-in-one-vector approach
2015-04-08 | GSE64966 | GEO
Project description:We derive experimental conditions for the derivation of marmoset trophoblast like cells. Marmoset naïve PSC form extraembryonic mesoderm in human TSC conditions, whilst TGFβ/NODAL, FGF/ERK and WNT signalling control marmoset peri- and postimplantation trophoblast identity.
2024-11-21 | E-MTAB-12463 | biostudies-arrayexpress
Project description:Hypervariable regions V3-V5 of bacterial 16S rRNA genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-03-14 | E-ERAD-254 | biostudies-arrayexpress