Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of two human and one cynomologous NPC line to assay activity of DNAse1 hypersensitive sites in the proximity of the Trnp1 gene

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Macaca fascicularis

SUBMITTER: Lucas Esteban Wange

PROVIDER: E-MTAB-9951 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

MPRA of two human and one cynomologous NPC line to assay activity of DNAse1 hypersensitive sites in the proximity of the Trnp1 gene

Project description: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. MPRA data was used to compare activity of regulatory sequences across 75 mammalian species with a focus on primates and correlate these activities with the Phenotype of gyrencephaly.

2021-05-12 | E-MTAB-9952 | biostudies-arrayexpress

RNA-seq of of human (Homo sapiens), gorilla (Gorilla gorilla) and cynomolgus macaque (Macaca fascicularis) iPSC and iPSC-derived NPC cell lines

Project description:RNA-seq samples from 3 species across a differentiation from induced pluripotent stem cells to neural progenitor cells were generated to study gene expression evolution. Briefly, previously generated urinary stem cell derived iPSCs of 3 human (Homo sapiens) individuals (3 clones), 1 gorilla (Gorilla gorilla) individual and fibroblast derived cynomolgus macaque (Macaca fascicularis) iPSCs of 2 individuals (4 clones) (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). Bulk RNA-seq libraries of iPSCs and NPCs were generated using prime-seq protocol (Janjic et al. 2022).

2023-11-23 | E-MTAB-13494 | 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

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

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

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 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

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

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