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TranscriptomicsImpact 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
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 tis...
ORGANISM(S): Homo sapiens 
2021-08-01 | E-MTAB-10138 | biostudies-arrayexpress
TranscriptomicsHuman-Mouse Mixture experiment to estimate that contribution of Barcode swapping
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.
ORGANISM(S): synthetic construct 
2022-03-10 | E-MTAB-11456 | biostudies-arrayexpress
TranscriptomicsHuman-Mouse Mixture experiment to estimate that contribution of Barcode swapping
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.
ORGANISM(S): Homo sapiens 
2022-03-10 | E-MTAB-11455 | biostudies-arrayexpress
TranscriptomicsBulk RNA-seq of human induced pluripotent stem cells (hIPSC) and neural progenitor cells (NPC) differentiated usind Dual SMAD inhibition using the prime-seq method
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.
ORGANISM(S): Homo sapiens 
2021-08-01 | E-MTAB-10133 | biostudies-arrayexpress
TranscriptomicsBulk RNA-seq of archived Acute Myeloid Leukemia (AML) samples propagated in a mouse Xenograft model over several passages
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.
ORGANISM(S): Homo sapiens 
2021-08-01 | E-MTAB-10175 | biostudies-arrayexpress
TranscriptomicsRNA-seq of human RNA contaminated with different amounts of mouse gDNA to quantify the impact of gDNA contamination in prime-seq
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.
ORGANISM(S): Homo sapiens 
2021-08-01 | E-MTAB-10141 | biostudies-arrayexpress
TranscriptomicsImpact 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.
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 tis...
ORGANISM(S): Homo sapiens 
2021-08-01 | E-MTAB-10142 | biostudies-arrayexpress
TranscriptomicsImpact 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.
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 tiss...
ORGANISM(S): Mus musculus 
2021-08-01 | E-MTAB-10140 | biostudies-arrayexpress
TranscriptomicsRNA-seq of two human and one cynomologous NPC line to assay activity of DNAse1 hypersensitive sites in the proximity of the Trnp1 gene
Homo sapiens and Macaca fascicularis neural progenitor cell lines were transduced with a lentiviral MPRA (Massively Parallel Reporter Assay) library. MPRA barcode sequencing and RNA-seq was performed on the extracted RNA. RNA-seq data was used to confirm transcription factor expression.
ORGANISM(S): Macaca fascicularis 
2021-05-12 | E-MTAB-9951 | biostudies-arrayexpress
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