Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: InnateDB library HEK293T

PROVIDER: PRJNA1235432 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32725483_1.fastq.gz	Fastqsanger.gz
	SRR32725483_2.fastq.gz	Fastqsanger.gz
	SRR32725484_1.fastq.gz	Fastqsanger.gz
	SRR32725484_2.fastq.gz	Fastqsanger.gz
	SRR32725485.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

Evaluation of single cell classifiers for single cell RNA-seq datasets

Project description:Three human cell lines, K562, HEK293T and A431, and one murine cell line, L929, are mixed with equal proportion in two experiments. One mixture, named Mix3, consists of K562, HEK293T and L929. The other, named Mix4, consists of K562, HEK293T, A431 and L929. These cell lines were processed with the Singleron GEXSCOPETM protocol using GEXSCOPETM Single Cell RNA Library Kit (Singleron) and sequenced on an Illumina Xten. FASTQ data were preprocessed using fastp and STAR.

2019-11-27 | GSE128982 | GEO

satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect

Project description:We use stable expression of a cystathionine-beta synthase (CBS) variant library in HEK293T cells to identify CBS coding sequence variants that alter mRNA abundance

2022-04-22 | GSE201057 | GEO

LL10000 hybridization

Project description:The screening of a previously reported fluorescein labelled 10,000 member PNA encoded peptide library allowed information on the interaction between the peptide-ligands and the cell surface receptors to be extracted, identified new peptide ligands for cell surface receptors, and gave crucial information about consensus sequences. A novel indirect amplification of the PNA signal by amplification of the PNA-complementary DNA library was developed to screen PNA-encoded peptide library against D54, HEK293T, and HEK293T-CCR6 cells. This work generates a new approach to biological discovery and an expansion of modern microarray techniques. In addition, the microarray approach facilitates screening for differences in surface-receptor ligands and/or receptor expression between various cell types including diseased and normal cells.

2011-11-08 | E-MEXP-3104 | biostudies-arrayexpress

Analysis of transcriptome of mouse melanoma cells co-cultured with HEK293T cells expressing mouse Siglec1.

Project description:To evaluate the effect of mouse Siglec1 on B16F10 melanoma we used co-culture methos where HEK293T cells were transiently transfected with plasmid containg mouse Siglec1 or empty plasmid (mock). These HEK293T cells were cultured with B16F10-GFP mouse melanoma cells for 18 hours in low binding plates. After 18 hours of incubation on 37°C, 5% CO2, melanoma cells were FACS sorted based on GFP expression and total RNA was isolated and used for TruSeq RNA library construction for transcriptome analysis. Samples were from 3 independent experiments. The library preparation and NGS data aquisition were performed by Macrogen (Macrogen, Inc., Korea)

2019-12-22 | GSE109077 | GEO

Whole genome inducible CRISPR KO screens for HIFa activity

Project description:Hypoxic inducible factors control the cellular response low oxygen by transcription regulation of gene programs. In order to understand the genes that control HIFa transcription factor regulated gene expression we generated dual fluorescent dFLASH-HIF reporter cells lines in HEK293T and U2OS cells to monitor HIFa activity. We then generated dox-inducible Cas9-TagBFP expressing reporter lines and performed 3 replicate genome wide KO gain- or loss- of function screens for HIF activity in U2OS and HEK293T reporter cell lines using the Brunello sgRNA KO library (~79,000 sgRNA, covering ~19,000 genes). High throughput sequencing was used to identify sgRNAs in enriched vs library samples and sgRNA enrichment quantified by either DEseq2 or MAGeck.

2025-03-21 | GSE290538 | GEO

Temporal Insights into Molecular and cellular responses during rAAV production in HEK293T cells

Project description:To understand the dynamic role of HEK293T cells at different cellular states post-transfection we have performed a comprehensive comparative proteome profiling of the host cell system post-transfection at 24, 48, and 72 hpt. For this study, we developed an in-house label-free HEK293T-AAV spectral library

2024-08-09 | PXD046574 | Pride

Using mitoribosomal profiling to investigate human mitochondrial translation

Project description:Human 143B.206 Rho+ cells (depleted mitochondrial DNA) and cytoplasts (derived from mitochondrial patient fibroblast containing C1624T mutation in mitochondrial tRNAVal ) were previously used to generated transmitochondrial cybrid lines. Hek293T cells,143B cells and cybrid cells were cultured in DMEM supplemented with 10% FCS in 5% CO2 at 37 °C. Cells were treated with Chloramphenicol (100 μg/ ml) for 15 min before harvest. Cells were then lysed and RNase I digested. Lysates were then loaded on a sucrose gradient (7%-47%). Fractions containing mito-monosomes were used to isolated RNA which were used to generate the library for deep sequencing. Mitoribosomal profiling were generated for both control (143B and Hek293T) and cybrid cells to reveal aspects of mitoribosome behaviour.

2017-12-01 | E-MTAB-6284 | biostudies-arrayexpress

The novel lysine deacetylase ABHD14B regulates transcription of metabolic genes

Project description:Purpose: To understand the role of ABHD14B in cellular metabolism by regulation of transcription. To address this, we performed a RNA-seq experiment with stable knockdowns of ABHD14B in HEK293T cells generated by lentivirus-based shRNA technology. Methods: Four biological replicates of HEK293T wild-type control, non-targeting shRNA control (NT), and two knockdowns (KD_2 and KD_3) of ABHD14B cells were collected and total RNA was extracted in QIAzol. The total RNA was used to generate a cDNA library using Quantseq 3' mRNA kit Fwd. Results: Transcriptional profiling revealed that genes involved in cellular metabolism are differentially regulated in HEK293T ABHD14B knockdown cells. Conclusions: Our study demonstrates the first extensive transcriptomics analysis of mammalian cells upon knocking down ABHD14B, and finds that loss of ABHD14B results in altered expression of glucose and lipid metabolic genes. This observation was complemented by changes in the levels of key intermediates of glucose metabolic pathways and triglycerides. Together, our findings illuminate an important metabolic role played by the KDAC ABHD14B.

2022-06-10 | GSE196907 | GEO

Phosphoproteome-derived peptide libraries derived from human cell lines for phosphatase profiling

Project description:This dataset contains raw data corresponding to analysis of phosphoproteome-derived peptide libraries derived from untreated HEK293T cells and pervanadate-treated HEK293T, Jurkat, and K562 cells. It also contains a timecourse of lambda phosphatase treatment of a phosphoproteome-derived peptide library derived from pervanadate-treated HEK293T cells.

2025-08-11 | MSV000098786 | MassIVE

ChIP-seq on ZNF506 overexpression HEK293T to verify ZNF506 binding capacity at PBS-Pro sites.

Project description:To identify ZNF506 genome-wide target sites, we performed ChIP-seq assay and found that ZNF506 binding sites enriched at PBS-Pro-containing ERV subfamilies (ERVPs) and further motif calling analysis showed that ZNF506 binds to PBS-Pro sequences, promoting formation of H3K9me3 modifications at binding regions. And ChIP-seq assay also indicated that the distinction of H3K9me3 signals closed to ZNF506 peak regions between ZNF506 overexpressing (OE) HEK293T cells and ZNF506 Knockout (KO) HEK293T cells was correlated with the different recruitment of corepressor KAP1. The ChIP-seq experiments using GFP antibodies and H3K9me3 antibodies on ZNF506-GFP OE HEK293T cell lines, and ZNF417-GFP OE HEK293T cell lines were used as controls for H3K9me3 ChIP. Also, the ChIP-seq experiments were performed using H3K9me3 antibodies and KAP1 antibodies on ZNF506 KO HEK293T cells and ZNF506 OE HEK293T cells.

2023-07-26 | GSE209826 | 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