Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq with metabolic labelling of human breast cancer cell line MCF7 treated with a panel of 40 different cancer drugs and untreated controls

ABSTRACT: This experiment has utilized metabolic labeling coupled with RNA-sequencing to identify directly responding genes after perturbing breast cancer targets.

INSTRUMENT(S): DNBSEQ-G400, Silica-coated MagPrep magnetic beads (Sigma)

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-14924 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-13091

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq with metabolic labelling of human lymphoblast cell line K562 treated with a panel of 83 different epigenetically active compounds and untreated controls

Project description:This experiment has utilized metabolic labeling coupled with RNA-sequencing to identify directly responding genes after perturbing cellular enzymes affecting epigenetic modifications.

2024-01-01 | E-MTAB-13091 | biostudies-arrayexpress

RNA-seq of human cell lines K562 and HEK293FT treated with vorinostat and untreated controls

Project description:This experiment has utilized RNA-sequencing to identify responding genes after histone deacelyate pertubation using vorinostat and two different cell lines and with two different treatment times.

2025-02-17 | E-MTAB-14822 | biostudies-arrayexpress

Deep RNA-seq of Universal Human Reference RNA mixed with external spike in molecules ERCC mix 1 using prime-seq. This sample is anologous to sample A in the MAQC-III study, while the mixing ratios and the input was the same 1000th of the total input was used here.

Project description:Here a part of the MAQC-III study was repeated with the prime-seq method to have a dataset to compare to this gold standard RNA-seq dataset using power simulations.

2021-08-01 | E-MTAB-10139 | biostudies-arrayexpress

Human-Mouse Mixture experiment to estimate that contribution of Barcode swapping

Project description:Here we test the impact of barcode swapping in prime-seq. To this end we isolated RNA from human iPSCs and mouse ESCs, processed them separately using prime-seq but pooled them for cDNA amplification.

2022-03-10 | E-MTAB-11456 | biostudies-arrayexpress

Human-Mouse Mixture experiment to estimate that contribution of Barcode swapping

Project description:Here we test the impact of over-/under-amplification on barcode swapping in prime-seq. To this end we isolated RNA from human iPSCs and mouse ESCs, processed them separately using prime-seq but pooled them for cDNA amplification.

2022-03-10 | E-MTAB-11455 | biostudies-arrayexpress

RNA-seq of human RNA contaminated with different amounts of mouse gDNA to quantify the impact of gDNA contamination in prime-seq

Project description:The impact of gDNA contamination on RNA-seq experiments performed with the prime-seq method was assessed by introducting artifical contamination using mouse gDNA this enables us to identify contamination by species specific assignment of mapped reads.

2021-08-01 | E-MTAB-10141 | biostudies-arrayexpress

Bulk RNA-seq of human induced pluripotent stem cells (hIPSC) and neural progenitor cells (NPC) differentiated usind Dual SMAD inhibition using the prime-seq method

Project description:Five hiPSC lines from four individuals were differentiated to neural progenitor cells. The two cell types were compared in regards to marker gene expression of known cell type markers to show that the used bulk RNA-seq protocol, called prime-seq can capture known biological differences.

2021-08-01 | E-MTAB-10133 | biostudies-arrayexpress

Impact of RNA isolation methods for RNA-seq on gene expression. Here RNA was isolated from human peripheral blood mono nuclear cells (PBMCs) using either Columns or magnetic beads and the isolated RNA was processed using prime-seq

Project description:Here silica column and bead based RNA isolation was performed. The two methods were compared using prime-seq to determine the effect of the RNA isolation method on gene expression quantification. This was tested for three different types of input samples, PBMCs, HEK293T cells and striatal mouse tissue to compare the RNA isolation over a range of inputs. For each sample and experimental condition 8 technical replicates were performed.

2021-08-01 | E-MTAB-10138 | biostudies-arrayexpress

Impact of RNA isolation methods for RNA-seq on gene expression. Here RNA was isolated from HEK293T cells using either Columns, magnetic beads with/without proteinase K or magnetic beads without proteinase K but heating. RNA was processed using prime-seq.

Project description:Here silica column and bead based RNA isolation was performed. The two methods were compared using prime-seq to determine the effect of the RNA isolation method on gene expression quantification. This was tested for three different types of input samples, PBMCs, HEK293T cells and striatal mouse tissue to compare the RNA isolation over a range of inputs. The RNA isolation was performed with either 1000 or 10000 cells input. For each sample and experimental condition 8 technical replicates were performed.

2021-08-01 | E-MTAB-10142 | biostudies-arrayexpress

Impact of RNA isolation methods for RNA-seq on gene expression. Here RNA was isolated from mouse striatal tissue using either Columns or magnetic beads and the isolated RNA was processed using prime-seq.

2021-08-01 | E-MTAB-10140 | biostudies-arrayexpress