Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq study on MLL-AF9 leukemia cells harboring JMJD1C sgRNAs targeting jumonji and zinc finger domains.

ABSTRACT: We transduced clonally MLL-AF9 leukemia cells expressing cas9 with sgRNA targeting the jumonji and zinc finger domains of JMJD1C. GFP (MLL-AF9) and TdTomato (sgRNA) double positive cells were sorted on Day 6 after transduction. Total RNA was isolated followed by mRNA selection. cDNA libraries were generated and NextGen Sequencing was performed.

ORGANISM(S): Mus musculus

PROVIDER: GSE129660 | GEO | 2019/04/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

ChIP-seq of histone marks H3K36, H3K27, and H3K9 in JMJD1C knockout or mutated MLL-AF9 leukemia cells

Project description:We performed genome-wide profiling of H3K9me3, H3K9me1, H3K27me3, and H3K36me3 by ChIP-seq in JMJD1C knockout or mutated MLL-AF9 leukemia cells. For ChIP-seq in JMJD1C mutated cells, we transduced sgRNA targeting the zinc finger, jumonji domain of JMJD1C or Renilla control and sorted on day 6 for GFP (MLL-AF9) Tdtomato (sgRNA) double positive cells. For ChIP-seq in JMJD1C knockout cells, we transduced Jmjd1c flox/flox MLL-AF9 leukemia cells with CRE TdTomato and sorted on day 6 for GFP (MLL-AF9) Tdtomato (CRE) double positive cells. These cells were subjected to ChIP-seq analysis with either H3K27me3, H3K9me3, H3K9me1 (JMJD1C knockout cells) or H3K36me3 (both knockout and mutated cells) antibody. We found increased H3K36me3 level at promoters of differentially expressed genes between control and JMJD1C loss or mutated leukemia cells.

2019-04-12 | GSE129661 | GEO

Single-cell sequencing of JMJD1C Jumonji domain mutated MLL-AF9 Leukemia cells

Project description:We performed single-cell sequencing on mouse MLL-AF9-cas9 leukemia cells 7 days after transduction with sgRNA against Renilla or JMJD1C JmjC domain. We revealed heterogeneity within each population.

2019-04-12 | GSE129662 | GEO

RNA-seq study on MLL-AF9 leukemia cells harboring JMJD1C sgRNAs targeting jumonji and zinc finger domains.

Project description:RNA-seq study on MLL-AF9 leukemia cells harboring JMJD1C sgRNAs targeting jumonji and zinc finger domains.

| PRJNA532409 | ENA

Effect of loss of Jmjd1c on MLL-AF9 leukemia

Project description:Analysis of gene expression profile of MLL-AF9 leukemia cells 6 days after loss of Jmjd1c. Loss of Jmjd1c induces differentiation and apoptosis in MLL-AF9 leukemia cells. These results provide insight into the role of Jmjd1c in MLL leukemia.

2016-06-09 | GSE75576 | GEO

Single-cell sequencing of JMJD1C Jumonji domain mutated MLL-AF9 Leukemia cells

Project description:Single-cell sequencing of JMJD1C Jumonji domain mutated MLL-AF9 Leukemia cells

| PRJNA532410 | ENA

Effect of loss of Jmjd1c on H3K9me2 level across the genome

Project description:Analysis of H3K9me2 level in MLL-AF9 leukemia cells upon deletion of Jmjd1c. Jmjd1c has been shown to be a H3K9me1/2 demethylase and these results provide insight into its role in MLL-Af9 leukemia

2016-06-09 | GSE75577 | GEO

shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance (Agilent)

Project description:We used a mouse model of human AML induced by the MLL-AF9 fusion oncogene, and an epigenetic shRNA library to screen for novel potential drug targets. One of the best candidate drug targets identified in these screens was Jmjd1c. Depletion of Jmjd1c impairs growth and colony formation of mouse MLL-AF9 cells in vitro, as well as establishment of leukemia after transplantation. Depletion of JMJD1C impairs expansion and colony formation of human leukemic cell lines, with the strongest effect observed in the MLL-rearranged ALL cell line, SEM. In both mouse and human leukemic cells, the growth defect upon JMJD1C depletion appears to be primarily due to increased apoptosis, which implicates JMJD1C as a potential therapeutic target in leukemia. To assess the effect of JMJD1C depletion on transcription, we compared the transcriptome of shJMJD1C- and shScr-transduced mouse MLL-AF9 transformed cells 48h after infection. A total of 451 transcripts were detected as changing between the two conditions (FDR<0.25)

2014-01-23 | E-GEOD-54311 | biostudies-arrayexpress

shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance

2013-08-22 | GSE50048 | GEO

shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance (Agilent)

2014-01-23 | GSE54311 | GEO

shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance

Project description:We used a mouse model of human AML induced by the MLL-AF9 fusion oncogene, and an epigenetic shRNA library to screen for novel potential drug targets. One of the best candidate drug targets identified in these screens was Jmjd1c. Depletion of Jmjd1c impairs growth and colony formation of mouse MLL-AF9 cells in vitro, as well as establishment of leukemia after transplantation. Depletion of JMJD1C impairs expansion and colony formation of human leukemic cell lines, with the strongest effect observed in the MLL-rearranged ALL cell line, SEM. In both mouse and human leukemic cells, the growth defect upon JMJD1C depletion appears to be primarily due to increased apoptosis, which implicates JMJD1C as a potential therapeutic target in leukemia. To assess the effect of JMJD1C depletion on transcription, we compared the transcriptome of shJMJD1C- and shScr-transduced SEM cells soon after induction of shRNA expression by addition of IPTG to the growth medium. To ensure detecting early changes, 48h was selected as the earliest timepoint displaying JMJD1C depletion and detectable phenotype as monitored by PARP and Caspase 3 cleavage. These observations were consistent across triplicate samples. A total of 138 transcripts were detected as changing between the two conditions (FDR<0.05)

2013-08-22 | E-GEOD-50048 | 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