Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic Characterization of LIPA+/+ and LIPA-/- iPSC-derived Macrophages

ABSTRACT: Using RNA-Seq, we examined the transcriptome profiles of human iPSC-derived macrophage (IPSDM) with knockout of the LIPA gene by CRISPR/Cas9 gene editing technologies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE100260 | GEO | 2020/06/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Bulk RNA sequencing of wildtype and ABCA3 mutant human iPSC-derived mutant containing the ABCA3:GFP fusion reporter

Project description:We performed transcriptomic profiling of induced pluripotent stem cell (iPSC)-derived iAEC2s containing wildtype, E690K homozygous ABCA3 mutantion, and W308R homozygous ABCA3 mutation. We first performed CRISPR-Cas9 gene editing on a wildtype human iPSC line (BU3) to engineer a GFP reporter bi-allelically targeted at the stop codon of the endigenous ABCA3 locus, thus generating an ABCA3:GFP fusion reporter line (as previous published iin Sun. et al, 2021). Next we utilized CRISPR-Cas9 gene-mutagenesis to introduce two homozygous ABCA3 mutations (E690K and W308R), resulting in two, new ABCA3 mutant iPSC lines containg the ABCA3:GFP fusion reporter, totally a total of 3 ABCA3:GFP fusion iPSC lines (wildtype, E690K-AG, W308R-AG). Following triplicate distal lung directed differentiations of all 3 ABCA3:GFP fusion iPSC lines we sorted the ABCA3:GFP positive iAEC2s on day 43 for transcriptomic analyses.

2023-06-01 | GSE205319 | GEO

miRNA-seq of HEK293 cell lines on Illumina iSeq100 instrument

Project description:A validation experiment performed on HEK293 cell lines after genome editing. The design contains three duplicate runs consisted of: HEK293 wild type cell line HEK293 with MIR484 gene knockdown using CRISPR-Cas9 HEK293 with MIR185 gene knockout using CRISPR-Cas9

2023-06-16 | E-MTAB-13009 | biostudies-arrayexpress

RNA-seq of retinal organoids derived from RPGR patient-, control- and mutation-corrected-iPSC at different developmental stages

Project description:Retinitis pigmentosa (RP) is an irreversible and inherited retinopathy. RPGR mutations are the most common causes of this disease. It remains challenging to decipher the mechanism of RPGR mutation because of the lack of appropriate study models. The substitution of patient-specific diseased retina without ethical restrictions is desired and iPSC-derived 3D retina is the best choice. In our experiment, we generated iPSCs from one RP patient with 2-bp frameshift mutation in the exon14 of RPGR gene, which were differentiated into retinal organoids. Also we generated iPSCs from a normal control and differentiated those control-iPSCs into healthy retinal organoids. Samples of patient- and control-retinal organoids at W0, W7, W13 (two replicates), W18 (two replicates) and W22 (two replicates for patient) were collected for RNA-seq. Corrected-iPSC were derived from CRISPR/Cas9-mediated gene correction. Then we collected the corrected-iPSC derived retinal organoids at W0, W7, W13 (two replicates), W18 (two replicates) and W22 (two replicates) for RNA-seq. Through the RNA-seq data, we demonstrate that patient-specific iPSC-dervied 3D retinae can recapitulate disease progress of Retinitis Pigmentosa through presenting defects in photoreceptors' gene profile. CRISPR/Cas9-mediated gene correction can rescue photoreceptor gene profile. Those transcriptome are consistent with the phenotype and function.

2020-02-01 | E-MTAB-6490 | biostudies-arrayexpress

KDM5C safeguards the appropriate timing of early neurodevelopment

Project description:We generated human induced pluripotent cells from intellectual disability patients carrying the c.2T>C mutation in KDM5C (Called “Mutant”). We generated a paired, isogenic human iPS cell line (called “Corrected”) using CRISPR/Cas9 and PiggyBac gene-editing technologies and conducted neuronal differentiation based on “Yichen Shi et al. Nat. Protoc. 7, 1836–1846 (2012)” to define differences in gene expression between the Mutant and Corrected during neurodevelopment.

2023-10-13 | E-MTAB-7551 | biostudies-arrayexpress

CRISPR transduction of iPS cells

Project description:Genome engineering using CRISPR/Cas9 technology enables simple, efficient and precise genomic modifications in human cells. Conventional immortalized cell lines can be easily edited or screened using genome-wide libraries with lentiviral transduction. However, cell types derived from the differentiation of induced Pluripotent Stem Cells (iPSC), which often represent more relevant, patient-derived models for human pathology, are much more difficult to engineer as CRISPR/Cas9 delivery to these differentiated cells can be inefficient and toxic. Here, we present an efficient, lentiviral transduction protocol for delivery of CRISPR/Cas9 to macrophages derived from human iPSC with efficiencies close to 100%. We demonstrate CRISPR/Cas9 knockouts for three non-essential proof-of-concept genes - HPRT1, PPIB and CDK4. We then scale the protocol and validate for a genome-wide pooled CRISPR/Cas9 loss-of-function screen. This methodology enables, for the first time, systematic exploration of macrophage involvement in immune responses, chronic inflammation, neurodegenerative diseases and cancer progression, using efficient genome editing techniques.

| EGAS00001005102 | EGA

A multi-functional AAV-CRISPR-Cas9 and its host response

Project description:CRISPR-Cas9 delivery by AAV holds promise for gene therapy but faces critical barriers due to its potential immunogenicity and limited payload capacity. Here, we demonstrate genome engineering in postnatal mice using AAV-split-Cas9, a multi-functional platform customizable for genome-editing, transcriptional regulation, and other previously impracticable AAV-CRISPR-Cas9 applications. We identify crucial parameters that impact efficacy and clinical translation of our platform, including viral biodistribution, editing efficiencies in various organs, antigenicity, immunological reactions, and physiological outcomes. These results reveal that AAV-CRISPR-Cas9 evokes host responses with distinct cellular and molecular signatures, but unlike alternative delivery methods, does not induce detectable cellular damage in vivo. Our study provides a foundation for developing effective genome therapeutics mRNA-Seq from muscles (9 samples; 3 mice x 3 conditions) and lymph nodes (9 samples; 3 mice x 3 conditions).

2016-07-29 | E-GEOD-84534 | biostudies-arrayexpress

Bacterial Protoplast-Derived Nanovesicles Carrying CRISPR Cas9 Tools Efficiently Re-educate Tumor-Associated Macrophages for Cancer Immunotherapy

Project description:we developed an in vivo CRISPR-Cas9 genome editing system that targets tumor-associated macrophages (TAMs) via bacterial protoplast-derived nanovesicles (NVs) decorated with a pH-responsive PEG conjugated polymer and galactosamine-conjugated ligand

2023-09-20 | PXD045507 | iProX

rRNA 2'-O-methylation profile of SNORD71 knockdown cells

Project description:We generated a SNORD71 KO chondrocyte cell pool using CRISPR/Cas9 gene editing. A CRISPR control cell line was generated and used as a control. Levels of 2’-O-methylation of human rRNAs in SNORD71 KO cell pool and CRISPR control cells were evaluated by RiboMethSeq.

2022-03-05 | E-MTAB-11470 | biostudies-arrayexpress

HBV-KMT2B integrated human induced pluripotent stem cells (KMT2B-Int iPSCs) vs heterozygous mutated KMT2B iPSCs (KMT2B-HT iPSCs) vs homozygous mutated KMT2B iPSCs (KMT2B-KO iPSCs) vs their original iPSCs (KMT2B-WT iPSCs)

Project description:Transcriptional profiling of all KMT2B-WT, HT, KO, Int iPSCs. KMT2B-HT, KO, and Int iPSCs were generated by gene editing using CRISPR/Cas9 and Cre recombinase technologies.

2023-11-15 | GSE217994 | GEO

Gene profiling of HAX1-deficient iPSC-derived CD33-positive promyelocytes and their genetically corrected and wid-type counterparts

Project description:We investigated iPSC-derived granulopoiesis from Kostmann patients (HAX1-deficient iPSCs) and gene corrected isogenic lines generated by CRISPR-Cas9 gene editing. Utilizing neutrophilic differentiation assay, we have successfully modeled the Kostmann hematologic phenotype that is characterized by perturbed granulocytic differentiation and compensatory overproduction of monocytes. We demonstrate that targeted correction of the HAX1-mutation reestablished a HAX1 and HCLS1-centered transcription network in immature myeloid progenitors, which is involved in the regulation of apoptosis and also myeloid differentiation.

2017-04-07 | GSE97414 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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