Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAPolII CUT&Tag profiles of MDA-MB-231 cell line with repression of CDK genes and PRMT5

ABSTRACT: A clonal doxycycline inducible dCas9-KRAB MDA-MB-231 cell line to control repression of CDK genes and PRMT5. On day 1 of the experiment cells were infected with lentiviruses containing the appropriate targeting/NTC sgRNAs driven by the human U6 promoter at an MOI of ~3 for each virus to ensure all cells were transduced. Cells were transduced in DMEM + 10% FBS with the addition of 8 μg/mL polybrene. 16 hours after the time of transduction, media was changed to DMEM +10% FBS. 24 hours after this, the cell culture media was switched to DMEM + 10%FBS containing 2μg/mL puromycin to ensure no uninfected cells remain. 48 hours after this, cell culture media was changed to DMEM + 10%FBS containing 2 μg/mL puromycin and 1 μg/mL doxycycline to induce dCas9-KRAB expression. 48 hours after this, cells were processed for CUT&Tag library prep following the manufacturer's recommendations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE227432 | GEO | 2023/05/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of a 4 hour treatment of 100 nM endothelin-1 on human primary lung fibroblasts

Project description:primary lung fibroblasts p3 from normal periphery of resected cancer. grown in DMEM 10% FBS, until confluence, then DMEM 0.5% FBS for 18 hours. Media were then changed and incubated for an additional 4 hours in the presence or absence of 100 nM endothelin-1. Data represent two independent experiments performed on two different occasions. Keywords: other

2004-03-12 | GSE1081 | GEO

Cell culture-based model system for FOXO3 activity

Project description:MCF7 and MDA-MB-231 breast cancer cell lines were cultured in DMEM-F12 containing 10% FBS (Lonza) 100U/ml penicillin and 100 µg/ml streptomycin (Lonza). Transfecting third generation packaging vectors using Poly-ethylenimine into HEK293T cells generated lentiviral particles (17). MCF7 and MDA-MB-231 cells were stably transduced with lentivirus containing pINDUCER20-FOXO3.A3, allowing doxycycline induced expression of constitutively active FOXO3 (FOXO3.A3). Cells were treated with 20% FBS or 10 µM PI3K inhibitor LY294002 (Selleckchem) for 16 hours to activate and inactivate the endogenous PI3K pathway, respectively. FOXO3.A3 expression was induced by 16 hours treatment with 10 ng/ml doxycycline.

2018-06-06 | GSE113479 | GEO

DNA methylation analysis of mouse embryonic fibroblasts (MEFs) and Thymidine treatment-induced MEFs (induced cells).

Project description:Investigation of DNA methlation changing in thymidine treatment-induced MEFs. Mouse embryonic fibroblasts (MEFs) were obtained at E14.5 embryos and supplied with Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 15% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin. Potential hematopoietic progenitor cells (CD45+CD41+CD31+c-Kit+) were negatively selected with Biotin labeled anti-CD45, anti-CD31, anti-CD41 and anti-c-Kit antibodies by magnetic beads. Hereafter, treated MEFs are referred to as 4neg MEFs for initiation of induction. 4neg MEFs were seeded on mitomycin (MMC)-treated MEFs as feeder cells and cultured in DMEM with 15% FBS, 100 μg/ml streptomycin, 100 U/ml penicillin, 2 mM L-glutamine, 0.1 mM non-essential amino acids and 100 μM thymidine as induction medium for 2 days followed with analysis

2020-01-28 | GSE144272 | GEO

The CRISPR Screen sequencing raw data

Project description:The hBMEC CRISPR/Cas9 library was seeded in eight T225 flasks with 2 × 107 cells each and incubated for 3 days. The hBMECs doubled every 3 days, generating a total of 3.2 × 108 cells, which were divided into four parts, yielding 8 × 107 cells per experimental condition (~1,000× coverage per perturbation in each library). A quarter of the cells were used as the input library and the remaining three quarters for SzM cytotoxicity screens. The cell libraries were treated with purified SzM protein diluted in DMEM (10% FBS) at a final concentration of 50 μg/ml for 48 hr; when ~50% cells were dead, the surviving cells were out grown in fresh DMEM (10% FBS) without SzM protein. These cells were divided into two parts, one part for genomic DNA extraction, and the other for the next round of screening. The same treatment with 50 μg/ml purified SzM protein for 48 hr was used in the 2nd round and the 3rd rounds, using the same protocol outlined above. After the 3rd round, all cells were harvested for genomic DNA extraction.

2023-05-25 | GSE217997 | GEO

Proteome of CD4 T cells activated through the TCR in the presence of IL2 and IL12 - Part 1

Project description:To activate primary T cells, lymph nodes were removed and disaggregated. Cells were cultured in RPMI 1640 containing L-glutamine, 10% FBS, 50 μM β-mercaptoethanol and penicillin/streptomycin. Cells were stimulated with 1 μg/ml of the CD3 monoclonal antibody (2C11) and 2 μg/ml anti-CD28 (37.51) in the presence of cytokines IL12 (10 ng/ml) and 20 ng/ml IL2 (20 ng/ml). Cells were stimulated for 24 hours. Live TCR activated CD4+ cells were sorted for CD4+ and CD45.1+ expression and DAP1 exclusion prior to collection for proteomics processing. Mice were “wild-type” (ie non-TCR transgenic) from OT-2 CD45.1 expressing C57bl6 background maintained in-house line.

2019-03-29 | PXD012052 | Pride

Endothelin-1 (ET-1) treated lung fibroblasts

Project description:Primary lung fibroblasts were grown to confluence in DMEM 10% FBS, serum starved in DMEM 0.5% FBS for 18 hours. Cells were then treated in the presence or absence of 100 nM ET-1 in the same medium for an additional 4 hours. Keywords: repeat sample

2004-02-28 | GSE981 | GEO

Expression analysis of mouse embryonic fibroblasts (MEFs) and Thymidine treatment-induced MEFs (induced cells)

Project description:Investigation of differentially expressed genes in thymidine treatment-induced MEFs. Mouse embryonic fibroblasts (MEFs) were obtained at E14.5 embryos and supplied with Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 15% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin. Potential hematopoietic progenitor cells (CD45+CD41+CD31+c-Kit+) were negatively selected with Biotin labeled anti-CD45, anti-CD31, anti-CD41 and anti-c-Kit antibodies by magnetic beads. Hereafter, treated MEFs are referred to as 4neg MEFs for initiation of induction. 4neg MEFs were seeded on mitomycin (MMC)-treated MEFs as feeder cells and cultured in DMEM with 15% FBS, 100 μg/ml streptomycin, 100 U/ml penicillin, 2 mM L-glutamine, 0.1 mM non-essential amino acids and 100 μM thymidine as induction medium for 6 days. Cells were then trypsinized and re-seeded to new feeder cells for another 6 days. Cells were positively selected with Biotin labeled anti-CD45 by magnetic beads followed with analysis.

2020-01-11 | GSE143418 | GEO

Fibroblast secretome proteomic analysis

Project description:LV fibroblasts were isolated from control (day 0), and infarcted regions at day 1, day 3, and day 7 after myocardial infarction (MI). Cells were isolated in DMEM in 10% fetal bovine serum and were seeded into 6-well plates and were allowed to grow to 80% confluence in DMEM supplemented with 10% fetal bovine serum (FBS). Cells were serum starved (DMEM + 0.1% FBS) for 18 h and then media was changed and secretome was collected after 24 h. The sample sizes are n=3 biological replicates for each time point.

2019-10-25 | PXD011778 | Pride

Regulation of gene expression by STIM1 and Ca2+ in human T cells

Project description:Human CD4+ T cells were left untreated or stimulated with 5 μg/ml plate-bound anti-CD3 antibody (clone OKT3, 14-0037-82, eBioscience) and 10 μg/ml soluble anti-CD28 antibody (clone CD28.2, 14-0289-82, eBioscience) for 6 h in RPMI1640 medium supplemented with 10% FBS, 1% L-glutamine, and 1% penicillin-streptomycin.

2022-02-02 | GSE179625 | GEO

The effect of MPO inhibitor on the gene expression profiles in HL-60 cell lines exposed to 1, 2, 4,-benzenetriol

Project description:To reveal the gene expression profile changes after exposure to BT, one of benzene metabolites, with or without ABAH, a myeloperoxidase (MPO) inhibitor, and to elucidate how MPO is involved in myelotoxicity of BT, we performed microarray analysis. HL-60 cells suspended in RPMI 1640 containing with 10% of heat-inactivated FBS at 4×10^5/ mL were incubated with or without BT (50 μM) at 37℃ for one or 4 hours. For MPO inhibition experiment, HL-60 (4×10^5 cells/ mL) were pretreatment with 100 μM of ABAH in RPMI 1640/10% of heat-inactivated FBS at 37℃ for 24 hours. Media was then replaced with new media containing the regent plus BT (50 μM) and incubate at 37℃ for one or 4 hours. Unexposed HL-60 cells were used as controls. To validate the microarray results, we selected 22 genes and conducted a real-time PCR.

2013-12-01 | GSE50805 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data