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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cross-species meta-analysis of regulatory networks of the Pax5 transcription factor

ABSTRACT: Transcription profiling of chicken Pax5 deficient DT40 B cell line to investigate the targets of Pax5 which is required for B-cell differentiation Used in cross-species comparison to investigate evolutionarily conserved regulatory circuits in B cell development Pax5 deficient DT40 B cells (3 biological replicates) were compared to DT40 wild-type cells (3 biological replicates).

ORGANISM(S): Gallus gallus

SUBMITTER: Pekka Kohonen

PROVIDER: E-GEOD-34687 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of chicken Pax5 deficient DT40 B cell line

Project description:PAx5 is indispensible for the committment if early lymphoid progenitors to the B cell lineage as well as for the development and maintenance of B cells. To better understand the functional importance of Pax5 in the later stages of B cell development and investigate the targets of Pax5 regulation, we established a novel Pax5 deficient DT40 B cell line.

2005-04-17 | E-MEXP-270 | biostudies-arrayexpress

Transcription profiling of chicken Bcl6 deficient DT40 B cell line to investigate the targets of Bcl6 which is required for germinal center formation

Project description:The transcription factor Bcl6 is required for germinal center formation and deregulated expression of Bcl6 has been observed in lymphomas. To gain insight to the function of Bcl6 in terminal differentiation of B cells to plasma cells and to investigate the targets of Bcl6, we established a Bcl6 deficient DT40 B cell line.

2010-02-17 | E-MEXP-2062 | biostudies-arrayexpress

Transcription profiling by array of chicken wild type and tumor supressor 53Bp1 knockout lymphoblast cells

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2011-05-07 | E-MEXP-2721 | biostudies-arrayexpress

Transcription profiling of chicken histone H1 null mutant cells

Project description:In chicken DT40 cells, there are six linker histone H1 variants and 12 of coding genes. We have previously reported of 11 out of 12 H1 knock out DT40 cells (Takami et al., Genes to Cell 1997 [PMID:9491804]) but complete H1 null DT40 cells could not established, so far. We identified one of the H1 variant, H1R was involved in genomic instabilities (Hashimoto et al., DNA repair (2007) [17613284]), so we re-introduced floxed H1R-eGFP and mer-cre-mer into 11 out of 12 H1 knock out DT40 cells. Then we targeted last enedogenous H1, we successfully established conditional H1 KO cells (K11). Next we treated with tamoxifen to loop out floxed H1R-eGFP, and cloning H1 completely null cells (K11-5, and K11-7). We analysis those gene expression pattern in wild-type, K11, and K11-5 cells Experiment Overall Design: Apoptosis is induced in H1 null cells, so we inhibit apoptosis with pan-caspase inhibitor, Z-VAD-FMK and extract RNAs.

2008-11-04 | E-GEOD-8483 | biostudies-arrayexpress

RNA-seq of H3.3 knockout and wild type chicken DT40 cells

Project description:RNA-seq was performed for transcriptional analysis of wild-type DT40 cells (Gallus gallus, B-cell line) and a H3.3 knockout line (h3.3a-/-, h3.3b-/-). H3.3 is a H3 histone variant encoded on two genes (H3.3A and H3.3B) in chickens.

2014-08-31 | E-MTAB-2754 | biostudies-arrayexpress

Condensin plays a role in both interphase nuclei and premature chromosome condensation

Project description:Purpose: to identify how condensin I removal affects gene expression globally. Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation. Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated. Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase. Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.

2017-05-03 | E-GEOD-74892 | biostudies-arrayexpress

Expression profiling of DT40 chicken B cell line by RNA-seq

Project description:A single replicate of exponentially growing DT40 CL18 chicken B lymphoma cells were harvested and extracted RNA was subjected to Illumina GAIIx paired-end sequencing to determine global gene expression. Single replicate RNA-seq expression analysis of DT40 cells.

2015-09-04 | E-GEOD-58766 | biostudies-arrayexpress

PAX5 overexpression is not enough to reestablish the mature B-cell phenotype in classical Hodgkin lymphoma (ChIP-Seq)

Project description:In lymphomas derived from mature B cells the expression of the transcription factor PAX5 is maintained whereas classical Hodgkin lymphoma displays significantly reduced PAX5 expression despite its derivation from mature B cells. To elucidate the functional role of PAX5 in classical Hodgkin lymphoma, we re-established the PAX5 expression in the Hodgkin cell line L428 with and without epigenetic modulation. To this end, we stably transfected the Hodgkin cell line L428 with an inducible PAX5 expression construct. Although the overexpressed PAX5 was transcriptionally active as demonstrated by synthetic reporter constructs, no induction of the B-cell phenotype was achieved. PAX5 chromatin immunoprecipitation with subsequent next generation sequencing in B-cell lines and the PAX5 overexpressing L428 cell line showed different binding patterns. Since epigenetic restrictions might affect PAX5 binding, combined DNA demethylation and histone acetylation was performed. However, no re-expression of B-cell genes was observed also under these conditions. Thus, PAX5 is not sufficient for the re-activation of the B-cell program in Hodgkin cells despite epigenetic opening of the chromatin. This clearly indicates that the repression of the B-cell identity of the Hodgkin cells is caused and secured by complex molecular mechanisms. Analysis of genome-wide PAX5 binding sites in B-cell lines (Raji, Namalwa) and the PAX5-producing Hodgkin cell line L428-PAX5 by ChIP-Seq

2013-07-30 | E-GEOD-44551 | biostudies-arrayexpress

Profile of gene expression signatures on DT40 cell for bursal-derived peptides

Project description:To further elucidate the mechanism of bursal-derived bioactive peptides on avian B cell proliferation on the broad molecular level, we have employed whole genome microarray expression profiling as a discovery platform to examine gene expression patterns during BP5 and BSP-II treatment in DT40 cell culture system. Analysis of our expression microarray data in this manner defined 3163 genes up-regulated and 3539 genes down-regulated by BP5 treatment and 3117 genes up-regulated and 3531 genes down-regulated by BSP-II treatment at 95% confidence, with a commonly regulated gene set of 2253 upregulated genes and 2083 downregulated genes. Various pathways were significantly impacted by BP5 and BSP-II treatment, and gene Ontology annotations show changes in the expression of molecules involved in DT40 cell with BP5 and BSP-II treatment. Expression of 12 genes (FGF3, RAP1B, TCEB1, CSNK2A1, DNMT1, HIF1A, HDAC1, FZR1, GDF3, FGF8, IRF7, and SKP1) from this signature was quantified in the RNA samples by QRT-PCR, confirming low variability between the predicted response patterns. BP5 and BSP-II induced gene expressions in DT40 cell were measured at 4 hours after exposure to doses of 0.02ug/ml and 2ug/ml, respectively. Two independent experiments were performed using different cells for each experiment.Three independently generated populations of cells were used for these experiments.

2011-07-06 | E-GEOD-30396 | biostudies-arrayexpress

PAX5 overexpression is not enough to reestablish the mature B-cell phenotype in classical Hodgkin lymphoma

Project description:In lymphomas derived from mature B cells the expression of the transcription factor PAX5 is maintained whereas classical Hodgkin lymphoma displays significantly reduced PAX5 expression despite its derivation from mature B cells. To elucidate the functional role of PAX5 in classical Hodgkin lymphoma, we re-established the PAX5 expression in the Hodgkin cell line L428 with and without epigenetic modulation. To this end, we stably transfected the Hodgkin cell line L428 with an inducible PAX5 expression construct. Although the overexpressed PAX5 was transcriptionally active as demonstrated by synthetic reporter constructs, no induction of the B-cell phenotype was achieved. PAX5 chromatin immunoprecipitation with subsequent next generation sequencing in B-cell lines and the PAX5 overexpressing L428 cell line showed different binding patterns. Since epigenetic restrictions might affect PAX5 binding, combined DNA demethylation and histone acetylation was performed. However, no re-expression of B-cell genes was observed also under these conditions. Thus, PAX5 is not sufficient for the re-activation of the B-cell program in Hodgkin cells despite epigenetic opening of the chromatin. This clearly indicates that the repression of the B-cell identity of the Hodgkin cells is caused and secured by complex molecular mechanisms. 2 Burkitt lymphoma cell lines (Raji, Namalwa), the Hodgkin lymphoma cell line L428 and the PAX5-producing L428 (L428-PAX5) with or without 5-aza-2M-bM-^@M-2-deoxycytidine/Trichostatin A treatment were analysed in triplicate.

2013-07-30 | E-GEOD-44244 | biostudies-arrayexpress

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