Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic

ABSTRACT: Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic

PROVIDER: PRJNA496024 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8042920.fastq.gz	Fastqsanger.gz
	SRR8042930.fastq.gz	Fastqsanger.gz
	SRR8042940.fastq.gz	Fastqsanger.gz
	SRR8042950.fastq.gz	Fastqsanger.gz
	SRR8042960.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic

Project description:MDA-MB-231 (ER-) and T47D (ER+) breast cancer cells were encapsulated in synthetic hydrogels, formed with a multi-arm bioinert polymer poly(ethylene glycol), cell-degradable peptide crosslinks, and receptor-binding pendant peptides, and cultured for 3 days to assess initial cell responses to different matrix compositions. The synthetic matrices had a Young's modulus (E) ~ 0.6 kPa, in the range of bone marrow and healthy mammary tissue, and biochemcial cues to mimic binding sites found in collagen (GFOGER peptide) or laminin (IKVAV peptide). After 3 days in culture, mRNA was collected and RNA-seq performed to compare cell responses between the collagen and laminin mimetic cultures.

2020-02-20 | GSE121179 | GEO

Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic with low and high mechanical properties

Project description:MDA-MB-231 (ER-) and T47D (ER+) breast cancer cells were encapsualted in synthetic hydrogels, formed with a multi-arm bioinert polymer poly(ethylene glycol), cell-degradable peptide crosslinks, and receptor-binding pendant peptides, and cultured for 3 days and up to 40 days to assess initial cell responses to different matrix compositions. The synthetic matrices had a Young's modulus (E) ~ 0.6 kPa (low wt%) and # ~ 5 kPa (high wt%), in the range of bone marrow or healthy mammary tissue and lung tissue, respectively, and Biochemcial cues to mimic binding sites found in collagen (GFOGER peptide) or laminin (IKVAV peptide). After 3 days and 40 days in culture, mRNA was collected and RNA-seq performed to compare cell responses between the collagen and laminin mimetic cultures overtime in both low wt% and high wt% matrices.

2022-03-01 | GSE145696 | GEO

Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic with low and high mechanical properties

Project description:Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic with low and high mechanical properties

| PRJNA607963 | ENA

Transcription profiling of human dermal fibroblasts after 3 hours of cyclic mechanical loading compared with ni loading - collagen 1 hydrogel dynamic loading tests

Project description:Cell viability and global gene expression was anayzed from collagen 1 hydrogel scaffolds following 3 hours of cyclic mechanical loading and compared with non-loaded scaffolds. Experiment Overall Design: 6 samples are analyzed (2 sets in triplicate). The first set is the Loaded condition in which Collagen 1 hydrogels seeded with Human dermal fibroblasts underwent cyclic loading of 0.1Hz for 180 minutes at 37 degrees Celsius. The second set is the control Unloaded condition in which the Collagen 1 hydrogels seeded with Human dermal fibroblasts are incubated at 37 degrees Celsius with no loading.

2008-06-11 | E-GEOD-10125 | biostudies-arrayexpress

Evolutionarily conserved sequence motif analysis guided development of chemically defined hydrogels for therapeutic angiogenesis

Project description:Biologically ligands (e.g., RGDS from fibronectin: Fn-RGD) play a critical role in the development of chemically defined biomaterials. However, there has been limited progress in recent decades towards discovering novel extracellular-matrix-protein-derived ligands for translational applications. Here, by combining motif analysis of evolutionarily conserved RGD-containing regions in laminin (Ln) with functional microarray screening, we identified a Ln-derived angiogenic peptide (LDAP) that showed enhanced proangiogenic activities over commonly used Fn-RGD. Mechanistic studies using RNA-sequencing of LDAP functionalized hydrogels showed an improved angiogenic transcriptome over Fn-RGD functionalized hydrogels and high similarity to Matrigel, attributed to the ability of LDAP to engage both Ln- and Fn-binding integrins. Injectable hydrogels functionalized with LDAP, along with MMP-QK (a VEGF-mimetic peptide), exhibited increased functional recovery over decellularized extracellular matrix (dECM) and alginates functionalized with Fn-RGD and MMP-QK in a mouse ischemic hindlimb model, illustrating the power of the strategy to rapidly develop potent chemically-defined biomaterials for therapeutic applications.

2020-09-21 | GSE126717 | GEO

Collagen bioinks redefined: Optimizing ionic strength and growth factor delivery for cartilage tissue engineering

Project description:This study investigates the impact of ionic strength on the gelation kinetics of collagen biomaterial inks and evaluates the efficiency of TGFβ-1 sequestration within these hydrogels, alongside their compatibility with bioprinting live chondrocyte and adipose-derived stem cell lines for cartilage tissue engineering. By adjusting sodium chloride and phosphate-buffered saline (PBS) concentrations, we demonstrate that reduced ionic strengths accelerate gelation, facilitating high-fidelity bioprinting while supporting high cell viability and post-printing proliferation of chondrocytes. Furthermore, at a 1% collagen concentration, the hydrogel effectively immobilized TGFβ-1, with less than 0.5% released over two weeks, indicating potent sequestration capabilities. Using adipose-derived mesenchymal stem cells, histomorphological and transcriptomic analyses reveal that the presence of TGFβ-1 significantly enhances chondrogenesis. These findings underscore the critical role of ionic strength in optimizing collagen ink properties for advanced bioprinting applications and highlight the potential of collagen hydrogels as effective carriers for sustained growth factor delivery, paving the way for successful cartilage tissue engineering strategies.

2024-10-09 | GSE271638 | GEO

Expression data from fibroblast-like synoviocytes (FLS) transfected with mimic-miR-23b or mimic-NC

Project description:We found microRNA miR-23b was down-regulated in local inflammatory tissues of autoimmune disease such as RA, SLE and related mouse models such as CIA, lpr, EAE. Re-expression of miR-23b significantly inhibits autoimmune pathogenesis of CIA, Lpr and EAE. To identify potential targets of miR-23b, we use microarray gene-expression analysis to identify transcripts which could be repressed by miR-23b. RA: rheumatoid arthritis, CIA: Collagen-induced arthritis, SLE: systemic lupus erythematosus, EAE: experimental autoimmune encephalomyelitis We tansfected fibroblast-like synoviocytes (FLS) with mimic-miR-23b or mimic-NC.Cells were collected and total RNA was extracted for the Affymetrix GeneChipÂ® Human Genome U133 Plus 2.0 Array

2012-12-19 | E-GEOD-37427 | biostudies-arrayexpress

The role of residue chirality of polypeptide hydrogels in regulating local immune microenvironment for anti-tumor immune responses

Project description:The impact of chirality on immune response has attracted great interest in cancer vaccine research recently. However, the study of chiral synthetic polypeptide hydrogels as cancer vaccines as well as of the impact of biomaterials itself for antitumor immunotherapy has rarely been reported. Herein, we demonstrated the key role of residue chirality of polypeptides hydrogels in antitumor immunity and local immune microenvironment regulation. Compared to poly(γ-ethyl-L-glutamate)-based hydrogels (L-Gel), poly(γ-ethyl-D-glutamate)-based hydrogels (D-Gel) induced greater immune cell infiltration. Unexpectedly, D-Gel caused higher levels of suppressive markers on antigen-presenting cells and even induced stronger T cells exhaustion than L-Gel. Finally, D-Gel established a local chronic inflamed and immunosuppressive microenvironment and showed insufficient anti-tumor effects. Conversely, the milder host immune responses induced by L-Gel led to more effective tumor inhibition. This study provides new insights on the role of residue chirality in the regulation of local immune microenvironment and affecting antitumor immune response.

2024-03-14 | GSE261299 | GEO

Laminin binding/non-binding germ cells

Project description:Comparison of laminin binding and laminin non-binding germ cells Keywords: other

2004-03-16 | GSE829 | GEO

Transcription profiling of laminin binding and laminin non-binding germ cells to define the spermatogonial stem cells.

Project description:Comparison of laminin binding and laminin non-binding germ cells.

2007-12-19 | E-GEOD-829 | biostudies-arrayexpress