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 CSMD1 enhancer CRISPRi in LUHMES cells and differentiated neurons

ABSTRACT: we performed lentiviral CRISPR interference (CRISPRi) by recruiting dCas9 fused with the KRAB domain to the CSMD1 enhancer (fam3) in the neuronal precursor cell line – Lund human mesencephalic (LUHMES). Given that the expression of CSMD1 was not detectable in LUHMES cells we differentiated these cells into neurons. Differentiated neurons with CRISPRi of CSMD1 enhancer showed significantly higher expression of CSMD1 than control.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Santosh Atanur

PROVIDER: E-MTAB-8027 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of human cell line HeLa after depletion of a lncRNA with three different loss-of-function methods

Project description:Long noncoding RNAs (lncRNAs) are a major transcriptional output of the mammalian genome, and their cellular roles are typically assayed by a variety of loss-of-function approaches. This study aims to identify the best current method to deplete nuclear lncRNAs. Small interfering RNAs (RNAi), antisense oligonucleotides (LNAs) and CRISPR interference (CRISPRi) were applied to knock down loc100289019 (a typical nuclear lncRNA, referred to as lnc289) in HeLa cells. We generated sequencing libraries after performing each step of each method, up to and including depletion of lnc289. Differential expression analyses between libraries generated before and after each step allowed us to evaluate the effect of that step on gene expression. The transcriptional effect of lncRNA depletion was then compared to the magnitude of off-target effects inherent to each method.

2017-05-31 | E-MTAB-5308 | biostudies-arrayexpress

ATAC-seq of wildtype or Dppa2 knockout ESC upon release of the epigenetic editing trigger

Project description:Chromatin accessibility was assayed in wildtype or Dppa2 knockout ESC after 26 days of release of the trigger imposed by epigenetic editing. Samples were collected in two clonal knockout and wildtype lines after sorting at FACS of cells which maintained a repressive Esg1-tdTomato (TOMneg) reporter expression after 26 days of DOX washout (release of the trigger).

2021-11-23 | E-MTAB-10522 | biostudies-arrayexpress

RNA-seq following enhancer repression

Project description:Using RNA-seq to identify genes regulated by dCas9-KRAB mediated enhancer repression in NCI-H2009 lung adenocarcinoma cells NCI-H2009 cells were first transfected with dCas9-KRAB fusion and subsequently transfected with no guide RNA (Empty), a guide RNA that has no target in the human genome (Dummy), and two separate guide RNAs (e3 #1 and e3 #2) recognizing the enhancer region of our study.

2015-10-26 | E-GEOD-72001 | biostudies-arrayexpress

ATAC-seq of ESC or in vitro differentiated endoderm cells after epigenetic editing and upon release of the trigger

Project description:Chromatin accessibility was assayed in ESC after epigenetic editing with dCas9::KRAB (or dCas9::GFP as a control) and subsequently in ESC and Endoderm differentiated cells upon release of the trigger. Samples were collected in two biological replicates after 7 days of DOX induction in ESC (epigenetic editing) and after 7 days of DOX washout (release of the trigger) in ESC and Endoderm cells.

2021-11-23 | E-MTAB-10523 | biostudies-arrayexpress

Enhancers

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-10-27 | E-GEOD-72002 | biostudies-arrayexpress

CUT&RUN-seq of H3K9me3, H4K20me3 or H3K4me3 in mESC after epigenetic editing and upon release of the trigger

Project description:Enrichment of histone marks was assessed by CUT&RUN-sequencing after epigenetic editing with dCas9::KRAB (or dCas9::GFP as a control) and subsequently upon release of the trigger. Samples were collected after 7 days of DOX induction (epigenetic editing) and after 4 and 7 days of DOX washout (release of the trigger).

2021-11-23 | E-MTAB-10525 | biostudies-arrayexpress

CUT&RUN-seq of DPPA2 in Esg1-tdTomato reporter mESC line

Project description:Enrichment of DPPA2 was assessed by CUT&RUN-sequencing in wildtype Esg1-tdTomato reporter mESC line.

2021-11-23 | E-MTAB-11182 | biostudies-arrayexpress

Reconstructing the RUNX2 transcriptional hierarchy in thyroid cancer using a multi-layered network- based approach

Project description:The aim of this experiment was to identify the RUNX2-dependent transcriptional program in thyroid cancer. To this end TPC1 cell line was infected with dCas9-KRAB and sgRNA targeting RUNX2 distal promoter or a non-targeting sgRNA as control. RNA was collected 10 days after infection and changes in gene expression were evaluated by mRNA-seq. Three replicates were analyzed.

2023-10-20 | E-MTAB-11049 | biostudies-arrayexpress

MND1 and PSMC3IP control PARP inhibitor sensitivity in mitotic cells

Project description:CRISPR screen data

2023-05-31 | E-MTAB-12929 | biostudies-arrayexpress

RNA-seq of thyroid cancer cell line upon silencing of RAIN, a RUNX2 associated intergenic lncRNA, and RUNX2

Project description:The aim of this experiment was to identify the RUNX2- and RAIN-dependent transcriptional program in thyroid cancer. TPC1 and MDA-T41 cell line were infected with dCas9-KRAB and sgRNA targeting the gene of interest (RAIN or RUNX2 respectively) or a non-targeting (NT) sgRNA as control. RNA was collected 10 days after infection and changes in gene expression were evaluated by total RNA-seq.

2024-09-12 | E-MTAB-13777 | 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