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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiling of Chinese Hamster Ovary production cell lines

ABSTRACT: The dataset set consists of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that varied in terms of seeding density, temperature, medium, feed medium, culture duration and product type. Cells were sampled for gene expression analysis at various stages of the culture and bioprocess-relevant characteristics including cell density, growth rate, viability, lactate, ammonium and cell specific productivity (Qp) were determined A total of 295 microarray samples were assayed. In addition 9 continous bioprocess variables were also measured.

ORGANISM(S): Cricetulus griseus

SUBMITTER: Colin Clarke

PROVIDER: E-GEOD-30321 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity.

Clarke Colin C Doolan Padraig P Barron Niall N Meleady Paula P O'Sullivan Finbarr F Gammell Patrick P Melville Mark M Leonard Mark M Clynes Martin M

Journal of biotechnology 20110727 3

Weighted gene coexpression network analysis (WGCNA) was utilised to explore Chinese hamster ovary (CHO) cell transcriptome patterns associated with bioprocess relevant phenotypes. The dataset set used in this study consisted of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that v ...[more]

PMID: 21801763

Similar Datasets

Gene expression profiling of Chinese Hamster Ovary production cell lines

Project description:The dataset set consists of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that varied in terms of seeding density, temperature, medium, feed medium, culture duration and product type. Cells were sampled for gene expression analysis at various stages of the culture and bioprocess-relevant characteristics including cell density, growth rate, viability, lactate, ammonium and cell specific productivity (Qp) were determined

2011-07-28 | GSE30321 | GEO

Gene expression profiling of Fast vs. Slow Chinese Hamster Ovary cell lines using Wye3aHamster array

Project description:A 3rd generation Wye3aHamster microarray chip was used to carry out a differential expression microarray study of a panel of 30 slow- and fast-growing production cell lines, identifying a priority list of 240 transcripts (110 Up; 130 Down) that passed a statisical filter (ANOVA p-value <0.05, 1.3 fold-change) when the samples were grouped into fast versus slow and pairwise compared and a minimum Pearson Correlation Coefficent (PCC) of >0.7 when growth rate was used as a continuous variable (i.e. included genes have to satisfy BOTH criteria, not just one). This yielded a list of 240 genes. The 240-member genelist yielded 223 Annotated IDs, 203 of which are Unique and all of which are associated with contributing to a high rate of growth in production CHO cell lines. Prospective samples were isolated from 2 distinct groups of clones (slow growers and fast growers), all chosen from the same project (transfection of product transgene into parent line) generated at Pfizer Inc., Bioprocess R&D, Andover, MA, USA. Each group comprised 5 distinct clones, all of which had comparable Qp characteristics. The clones were passaged for 3 or 4 passages over 3-4 days to stabilise the phenotype and freeze stocks. Samples for array hybridization were generated in batch shake flask culture (60ml working volume) with AS1 medium and without feeds or temperature shift. Samples were collected at a single time point (72hrs - mid/late log) and each clone was grown in triplicate flasks, yielding a total of 30 samples for collection and processing. Two bioprocess-relevant variables, viable cell density (VCD) and viability were measured. From the VCD, the growth rate (h-1) was calculated.

2013-01-01 | E-GEOD-37251 | biostudies-arrayexpress

Response of Bacillus halodurans C-125 wild-type and OLE-OAP knockout cells to acute ethanol stress

Project description:OLE RNA (Ornate, Large, Extremophilic RNA) is a large, noncoding RNA from extremophilic and/or anaerobic Firmicutes that binds to an integral membrane protein (OAP, OLE-Associated Protein) and localizes to the cell membrane. It is highly abundant in cells, and knockouts show increased sensitivity to short-chain alcohols, especially ethanol. We treated Bacillus halodurans C-125 cells (both wild-type and OLE-OAP knockouts) with 5% (v/v) ethanol for 3 hours to determine differences in their response to this stress. There are almost no significant differences between cells before ethanol stress, while after ethanol stress a small number (~40) genes show differences in expression between the two strains. These genes show little connection between their function, however, leading us to conclude that the majority of differential adaptation in kncokouts may occur at an earlier time or at the post-trancriptional level. These data also serve as a reference for a Gram-positive alkaliphile's response to acute ethanol stress. Examination of wild-type and OLE-OAP knockout cells before and after ethanol stress, in duplicate (8 samples total)

2012-06-15 | E-GEOD-33303 | biostudies-arrayexpress

Single cell RNA-seq of in vitro cultured human embryos

Project description:Human embryogenesis is characterised by a series of coordinated cell fate specification events. Upon implantation on day 7, the three cell lineages forming the human blastocyst undergo major morphogenetic and transcriptomic changes. Using single-cell RNA sequencing, we reconstruct the molecular events driving post-implantation development of the human embryo at day 9 and 11. Our study provides the first molecular map of gene expression patterns in early post-implantation human embryos, unveiling how signalling interactions between embryonic and extra-embryonic tissues drive human embryogenesis.

2021-06-11 | E-MTAB-8060 | biostudies-arrayexpress

Establishment of trophoblast stem cells under defined culture conditions in mice

Project description:The inner cell mass (ICM) and trophoblast cell lineages duet early embryonic development in mammals. After implantation, the ICM forms the embryo proper as well as some extraembryonic tissues, whereas the trophoectoderm (TE) exclusively forms the fetal portion of the placenta and the trophoblast giant cells. Although embryonic stem (ES) cells can be derived from ICM in cultures of mouse blastocysts in the presence of LIF and/or combinations of small-molecule chemical compounds, and the undifferentiated pluripotent state can be stably maintained without use of serum and feeder cells, defined culture conditions for derivation and maintenance of undifferentiated trophoblast stem (TS) cells have not been established. Here, we report that addition of FGF2, activin A, XAV939, and Y27632 are necessary and sufficient for derivation of TS cells from both of E3.5 blastocysts and E6.5 early postimplantation extraembryonic ectoderm. Moreover, the undifferentiated TS cell state can be stably maintained in chemically defined culture conditions. Cells derived in this manner expressed TS cell marker genes, including Eomes, Elf5, Cdx2, Klf5, Cdh1, Esrrb, Sox2, and Tcfap2c; differentiated into all trophoblast subtypes (trophoblast giant cells, spongiotrophoblast, and labyrinthine trophoblast) in vitro; and exclusively contributed to trophoblast lineages in chimeric animals. This delineation of minimal requirements for derivation and self-renewal provides a defined platform for precise description and dissection of the molecular state of TS cells. Total RNA was purified by using RNeasy Mini kit (QIAGEN). Microarray targets from 200 ng total RNA were synthesized and labelled using the Low RNA Input Linear Amp Kit (Agilent) and hybridized to Mouse 4x44K Ver.2.0 arrays. Arrays were scanned on an Agilent Technologies Microarray scanner and signal intensities were calculated in Agilent Feature Extraction 10.7.3.1 software.

2014-07-08 | E-GEOD-59107 | biostudies-arrayexpress

Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast [MeDIP-Seq]

Project description:Reprogramming of ES cells towards the trophoblast lineage, and specifally into self-renewing TS cells, can seemingly be achieved by manipulation of transcription factors such as Cdx2 and Oct4, or modulation of signalling cascades, notably Ras signalling. Here we analyze the arising cells from such treatment in detail for the efficiency and completeness of the reprogramming process. We find that the reprogrammed cells retain an epigenetic and transcriptional memory of their ES cell origin and are not equal to bona fide trophectoderm-derived TS cells. DNA methylation analysis in conventional ES and TS cells and various ES-to-TS reprogramming models

2014-11-24 | E-GEOD-62138 | biostudies-arrayexpress

Transcriptomes of miR-290-295 KO mESCs treated with siPOOLs for three different transcription factors and a negative control

Project description:In order to identify direct microRNA targets in mouse embryonic stem cells (mESCs), we generated miR-290-295 KO mutant cell lines, assessed their transcriptomes. We identified novel transcription factors (TF) as potential direct and functional targets of miR-290-295. To assess the role of these TFs, we rescued their expression in the miR-290-295 KO cell line using siPOOLs and profiled their transcriptomes.

2022-07-15 | GSE179451 | GEO

Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-24 | E-GEOD-62150 | biostudies-arrayexpress

Breast Cancer Gene Expression Analysis

Project description:Analysis of 104 breast cancer biopsies (removed prior to any treatment with tamoxifen or chemotherapeutic agents) from patients aged between 31 years and 89 years at the time of diagnosis (mean age = 58 years). Twenty were less than 50 years and seventy-seven women were 50 years, or older, at diagnosis. The size of the tumours ranged between 0.6 cm and 8.0 cm (mean = 2.79 cm). Eighteen tumours were T1 (<2 cm) in maximal dimension; 83 were T2 (2M-bM-^@M-^S5 cm) and 3 tumours were T3 (>5 cm). Eighty-two were invasive ductal carcinoma, 17 were invasive lobular and five were tumours of special type (two tubular and three mucinous). Eleven tumours were grade 1; 40 were grade 2; and 53 were grade 3. Sixty-seven tumours were oestrogen receptor (ER) positive and 34 were ER negative (ER status was determined by Enzyme Immuno-Assay (EIA); a positive result was defined as more than 200 fmol/g protein). ER status was not available for 3 patients. Forty-five tumours had no axillary metastases and 59 tumours had metastasised to axillary lymph nodes. Sixty-nine women were treated with post-operative tamoxifen; 26 did not receive tamoxifen. Fifty patients were treated with adjuvant systemic chemotherapy (CMF +/M-bM-^HM-^R adriamycin); 45 patients did not receive chemotherapy. Details regarding tamoxifen and systemic chemotherapy were not available for 9 patients. Maximal follow-up was 3,026 days with a mean follow-up of 1,887 days. 17 normal breast tissues were also assayed. Gene expression profiling of 104 breast cancer and 17 normal breast biopsies.

2013-05-26 | E-GEOD-42568 | biostudies-arrayexpress

Expression and ChIP-seq analyses of embryonic stem cells, extraembryonic endoderm stem cells, and trophoblast stem cells

Project description:Bivalent histone domains have been proposed to contribute to pluripotency in embryonic stem cells, suggesting an epigenetic mechanism may regulate stem cell behavior in general. Here we compare histone modifications in two other stem cells derived from the blastocyst. We show that extraembryonic stem cells have little repressive lysine 27 trimethylation and few bivalent domains. Thus, bivalent domains are not a common mechanism for maintaining the undifferentiated state in blastocyst-derived stem cells and alternative mechanisms must mediate transcriptional repression in extraembryonic cells. We show that lysine 9 trimethylation, but not DNA methylation, is likely to fulfill this role. Intriguingly, although we do detect bivalent domains in pluripotent cells in the early mouse embryo, the epigenetic status of extraembryonic cells does not entirely reflect their in vitro stem cell counterparts. Therefore, differences in epigenetic regulation between lineage progenitors in vivo and in vitro may arise during selection for self-renewal in vitro. Expression profiles [GSM388878-GSM388881] of three different stem cells (R1 embryonic stem cells, trophoblast stem cells, extraembryonic endoderm stem cells) were generated for comparison to CHIP-seq data [GSM392044-GSM392055] of the same three stem cell lines to observe correlations with Histone 3 K4 and K27 trimethylation patterns. CHIP-seq details: R1 embryonic stem cells, trophoblast stem cells or extraembryonic endoderm stem cells were grown, lysed and chromatin purified. The chromatin was immunoprecipitated for either histone 3 K4 trimethylation or histone 3 K27 trimethylation and the immunoprecipitate was subjected to purification and high-throughput Illumina-based sequencing.

2010-05-16 | E-GEOD-15519 | biostudies-arrayexpress

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