Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER: Lucas Esteban Wange

PROVIDER: E-MTAB-10133 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

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 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

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

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

Bulk RNA-seq of archived Acute Myeloid Leukemia (AML) samples propagated in a mouse Xenograft model over several passages

Project description:Cryopreserved AML PDX samples were collected with minimal harm to the sample by taking a biopsy punch from the vial of cell and transfering it into lysis buffer. 96 AML PDX samples collected in such manner were processed using prime-seq to generate high quality expression profiles.

2021-08-01 | E-MTAB-10175 | biostudies-arrayexpress

RNA-seq of TET1 knockout, catalytic mutant and wild type mESCs

Project description:Investigation of TET1 non-catalytic functions in mESCs cultured in serum + LIF (primed)

2022-07-29 | E-MTAB-10937 | biostudies-arrayexpress

Single cell RNA-seq of perinatal mouse hematopoietic stem cells

Project description:Molecular characterization of perinatal liver HSCs.

2023-09-30 | E-MTAB-13293 | biostudies-arrayexpress