LSD1 inhibitor-induced changes in gene expression profile in T-cell acute lymphoblastic leukemia cells
ABSTRACT: We screened for the changes in gene expression induced by an LSD1 inhibitor to elucidate the mechanism of its cytotoxic effect on T-cell acute lymphoblastic leukemia (T-ALL). Overall design: We isolated mRNA from the T-ALL cell line MOLT4 cultured with vehicle alone or LSD1 inhibitor, and subjected them to gene expression profiling using an Agilent GeneChip Array. Please note that experiments were technically performed as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed dat was provided for each single channel (Cy3 and Cy5 signals; i.e. one raw data file for two sample records).
INSTRUMENT(S): Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version)
Project description:We treated the T-ALL cell line MOLT4 with a novel LSD inhibitor and performed ChIP-seq analysis using anti-histoneH3K27ac antibody to assess the enhancer function. Overall design: We isolated fixed chromatin from MOLT4 cells treated with the LSD1 inhibitor S2157 and performed immunoprecipitation with anti-H3K27ac antibody, followed by deep sequencing.
Project description:Transcriptional profiling of SMMC-7721 cells comparing control untreated with sub-lethal heat treated cells (50°C for 10 min). Differentially expressed lncRNA and mRNA were measured with an Agilent Human lncRNA+mRNA Array V4.0 (4 × 180 K format) containing 41,000 lncRNAs and 34,000 mRNAs. Goal was to determine the effects of sub-lethal heat treatment on global hepatoma carcinoma cells gene expression. Overall design: Two-condition experiment, sub-lethal heat treated vs. untreated cells. Biological replicates: 3 control replicates, 3 experimental replicates. Please note that experiments were carried out technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the data was processed as though they are single channel (Cy3 and Cy5 signals are calculated insted of Cy3/Cy5 ratios). Therefore three raw data files (for total 6 samples) are linked as Series supplementary files and the corresponding raw data file is indicated in the sample description field.
Project description:Bacteria commonly adapt to stresses by altering gene expression. To understand the response of M. tuberculosis (MTB) to bedaquiline, we performed transcriptomics over a time-course on MTB bacilli exposed to the drug. Overall design: Bacteria were harvested at 1, 6, 24, 48, 96 hrs after being exposed to concentrations of bedaquiline (no drug, 1.5μM, 15μM) during a 7-day drug exposure time course experiment (as indicated in each sample title). RNA was isolated and applied to custom Agilent tiled arrays. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel (Cy3 and Cy5 signals are calculated). Therefore, there are two sample records per each raw data file and the raw data file associated with each sample is indicated in the corresponding sample description field.
Project description:Long noncoding RNAs (lncRNAs), which are noncoding RNAs (ncRNAs) with length more than 200 nucleotides (nt), have been demonstrated to be involved in various types of cancer. In this study, a custom designed microarray platform covering both mRNAs and lncRNAs was applied to tumor tissues of gastric, colon, liver and lung. 316 and 157 differential expressed (DE-) protein coding genes and lncRNAs common to these four types of cancer were identified respectively. Overall design: The expression profiles of cancer and adjacent normal tissues form 76 patients (20 with gastric cancer, 20 with colon cancer, 16 with liver cancer and 20 with lung cancer) were studied by microarray and a set of lncRNAs as well as PCGs were identified as potential biomarkers general to different types of cancer. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed though they are single channel (total 152 sample records for 76 raw data files; Cy3 and Cy5 signals are calculated). Therefore, raw data file for each sample was duplicated and linked to each paired sample records. For example, the raw data files for the 'Normal_tissue_Colon_cancer_patient_01'(Cy5) sample and 'Cancer_tissue_Colon_cancer_patient_01'(Cy3) sample are identical.
Project description:Many long noncoding transcripts are involved in cancer progression. Here, we utilized high-throughput microarray to compare the transcriptome alterations between the SNHG1 knockdown or control in HCT116 cell lines. Two independent siRNAs were designed against the SNHG1 cDNA sequence. Thus, we identified 302 genes which were expressionally changed. Moreover, Gene Ontology and pathway enrichment analysis revealed that several gene signature were significantly enriched, such as MAPK signaling pathway, growth factor activity and transcriptional corepresssor activity. Further, GSEA analysis suggested NF-kB signaling pathway, PI3K/Akt pathway were markedly associated with SNHG1-reuglated genes. The present study indicated that SNGH1 regulated both the local and distal genes in cancer progression. Overall design: HCT116 cells with SNHG1 knockdown and control. Three biological replicates of each condition were analyzed on Agilent microarray. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated). Thus, the raw data files (one file per two sample records) were linked as Series supplementary file and are indicated in the corresponding sample 'description' field.
Project description:Analysis of gene expression profile of Tibialis anterior (TA) skeletal muscle tissues with Notch1 intracellular domain (N1ICD) overexpression. Skeletal myogenesis involves sequential activation, proliferation, self-renewal/differentiation and fusion of myogenic stem cells (satellite cells). Notch signaling is known to be essential for the maintenance of satellite cells, but its function in late-stage myogenesis, i.e. post-differentiation myocytes and post-fusion myotubes, is unknown. Here we use muscle creatine kinase (MCK)-Cre to induce N1ICD expression in multinucleated myotubes. We found that myotube-specific Notch1 activation improved muscle regeneration and exercise performance of mdx mice, a model of Duchenne Muscular Dystrophy (DMD). Agilent microarray was performed to compare gene expression in mdx control and N1ICD-overexpressing mdx muscles. The results may provide mechanistic insights into how Notch1 activation in myotubes modulate muscle function. Overall design: Two-condition experiment, mdx muscle vs. N1ICD-mdx muscle. Biological replicates: 3 mdx TA muscles and 3 N1ICD-mdx TA muscles. Please note that experiments were performed technically as dual channel (eg, Cy3-labeled-mdx and Cy5-labeled-N1ICD samples hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated).
Project description:Human embryonic stem cell derived retinal pigmented epithelial cells (hESC-RPE) are in clinical trials for the treatment of macular diseases. Currently, these cells take over three months to derive and subsequent months to mature and characterize. After only five to six passages the cells begin to undergo an epithelial-to-mesenchymal transition and are unsuitable for cellular therapies. We describe a novel passaging protocol and show that inhibition of Rho-associated, coiled coil containing protein kinases (ROCK1 and ROCK2) using Y-27632, allows extended passage of hESC-RPE in serum-free culture with maintenance of the RPE phenotype. After 30 population doublings, hESC-RPE at passage 13 maintain normal karyotype, display typical, polarized epithelial morphology, and continue to express RPE-specific genes. Passage 13 hESC-RPE show protein localization patterns similar to passage 2 cells, and display similar levels of growth factor secretion and phagocytosis of photoreceptor outer segments. Microarray analysis from day 2 cells shows several key pathways are altered by ROCK inhibition, including stimulation of the cell cycle and suppression of TGFβ and Wnt signaling. These findings describe a means to greatly increase the yield of functional hESC-RPE for use in research and clinical trials. Two-condition experiment, Control vs Y-27632 treated hESC-RPE passage 5. Biological replicates: 4 control, 4 Y-27632. The experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as though they are single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated). Therefore, there are 4 raw data files for total 8 samples.
Project description:Contains 90 Sinperca chuatsi miRNAs identified in fast and slow muscle fibers, and 60 miRNAs showed significantly different levels of expression. Overall design: In this experiment, six Samples are analyzed with 3 replicates are included.The miRNA microarrays were used to analyze miRNA expression patterns in the white muscle and red muscle (LC-Bio Hangzhou, China). Chip hybridizations were performed overnight on a μParaflo microfluidic chip using a microcirculation pump (Atactic Technologies). Based on mature miRNA sequences of zebrafish downloaded in miRBase Release 19.0 (http://microrna.sanger.ac.uk/), 246 probes were designed to detect S. chuatsi miRNAs on microarray chips. In addition, the arrays contained 95 probes complementary to the miRNA in S. chuatsi, positive control probes for zebrafish 5s rRNA, and negative controls for normalizing data with low-density signals. Sufficient RNA was extracted to hybridize in triplicate with three biological repeats to ensure microarray reproducibility. After hybridization, signals were detected using tag-specific Cy3 and Cy5 dyes. Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices, Sunnyvale, CA, USA) and digitized by Array-Pro image analysis software (Media Cybernetics, Bethesda, MD, USA). Finally, hybridization signals were detected and quantified, and data were analyzed by first subtracting the background and then normalizing the signals with a cyclic LOWESS filter (Locally-weighted Regression). Please note that the experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel (Cy3 and Cy5 signals are calculated). Therefore there are total 3 raw data files for 6 samples, and the corresponding raw data file is indicated in the sample description field.
Project description:RNA-Seq for Lsd1-deficient TSCs or treated with Lsd1 inhibitor for 24hrs Overall design: TSC were treated with Lsd1 inhibitor or DMSO in stemness conditions for 24hrs; media and inhibitor where replaced every 12hrs along the duration of the experiment; 2 replicates were used for treatment together with 2 control replicates in stemness; DFKZ genomics and proteomics. Please note that strain and targeting strategy had been described in the previous PMID: 24448552 publication
Project description:Several studies have indicated an important role for miR-155 in the pathogenesis of B-cell lymphoma. Highly elevated levels of miR-155 were indeed observed in most B-cell lymphomas with the exception of Burkitt lymphoma (BL). However, the molecular mechanisms that underlie the oncogenic role of miR-155 in B-cell lymphoma are not well understood. To identify the miR-155 targets relevant for B-cell lymphoma, we performed RNA immunoprecipitation of Argonaute 2 in Hodgkin lymphoma (HL) cells upon miR-155 inhibition and in BL cells upon ectopic expression of miR-155. We identified 54 miR-155-specific target genes in BL cells and confirmed miR-155 targeting of DET1, NIAM, TRIM32, HOMEZ, PSIP1 and JARID2. Five of these targets are also regulated by endogenous miR-155 in HL cells. Both overexpression of miR-155 and inhibition of expression of the novel miR-155 target gene NIAM increased proliferation of BL cells. In primary B-cell lymphoma NIAM-positive cases have significant lower levels of miR-155 as compared to NIAM-negative cases, suggesting that NIAM is also regulated by miR-155 in primary B-cell lymphoma. Thus, our data indicate an oncogenic role for miR-155 in B-cell lymphoma which involves targeting the tumor suppressor NIAM. Overall design: Gene expression profiles were performed in KM-H2 Hodgkin lymphoma cell line in 4 samples: KM-H2 EV (empty pMSCV-PIG vector) total cell lysate, KM-H2 miR-155-sp (KM-H2 with miR-155 sponge) total cell lysate, KM-H2 EV Ago2-IP, KM-H2 miR-155-sp Ago2-IP. Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed though they are single channel (total 8 sample records for 4 raw data files; Cy3 and Cy5 signals are calculated). Therefore, the raw data files for paired samples (e.g.KM-H2 EV Total Cy3 and KM-H2 EV IP Cy5 samples) are identical.