Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq for PHF8-knockout CT26 cell and parental cell.

ABSTRACT: CT26 cells with or without PHF8 knockout were processed using the High-Sensitivity Open Chromatin Profile Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.

ORGANISM(S): Mus musculus

PROVIDER: GSE313944 | GEO | 2026/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cut&tag of H4K20me1 for PHF8-knockout CT26 cell and parental cell.

Project description:CT26 cells with or without PHF8 knockout were processed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.

2026-01-01 | GSE313899 | GEO

ATAC-seq for PHF8-knockout CT26 cell and parental cell.

Project description:ATAC-seq for PHF8-knockout CT26 cell and parental cell.

| PRJNA1387406 | ENA

Cut&tag of H4K20me1 for PHF8-knockout CT26 cell and parental cell.

Project description:Cut&tag of H4K20me1 for PHF8-knockout CT26 cell and parental cell.

| PRJNA1387222 | ENA

TCR variable regions transcripts of CT26-shppp2r1a and CT26-scr samples

Project description:TCR variable regions transcripts of three CT26-shppp2r1a samples and three CT26-scr samples

2021-11-20 | GSE189092 | GEO

RNA-seq data of PHF8 wild-type and PHF8 knockout TRAMP mouse

Project description:RNA-seq analysis were applied to elucidate the transcriptional differences of PHF8 wild-type and PHF8 knockout TRAMP mouse. A total of 2,092 differentially expressed genes (Fold Change > 2, or Fold Change＜0.5; FDR < 0.05) with 623 down- and 1469 up-regulated genes were identifed in Phf8-KO TRAMP mice.

2020-09-26 | GSE157621 | GEO

RNA sequencing of mouse CT26 knockout Pd-l1 cells rescued with WT or K262Q Pd-l1

Project description:Although membrane-anchored Pd-l1 has been well-studied for its engagement with PD-1 on T cells to evade anti-tumor immunity, whether Pd-l1 regulate oncogenic signaling pathways in tumor cells remains elusive. In this experiment, to further dissect roles of the K262 residue acetylation for Pd-l1 nuclear function, we profiled RNA expression of WT or K262Q mutant mouse Pd-l1 re-expressed in CT26 KO Pd-l1 cells. Methods: Total RNA fromCT26/Vector, CT26/WT or CT26 Pd-l1 KO cells was purified using Qiagen RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Library preparation and sequenceing analysis were performed by BGI-Hong Kong Co. Ltd. Conclusions: Our study indicates that Pd-l1 acetylation modification may affect its function in nuclear.

2020-06-07 | GSE146557 | GEO

The histone demethylase PHF8 is essential for cytoskeleton dynamics

Project description:PHF8 is a histone demethylase associated with X-linked mental retardation (XLMR). It has been described as a transcriptional coactivator involved in cell cycle progression, but its physiological role is still poorly understood. Here we show that PHF8 controls the expression of genes involved in cell adhesion and cytoskeleton organization such as RhoA, Rac1 and GSK3M-NM-2. A lack of PHF8 not only results in a cell cycle delay but also in a disorganized actin cytoskeleton and impaired cell adhesion. Our data demonstrate that PHF8 directly regulates the expression of these genes by demethylating H4K20me1 at promoters. Moreover, c-Myc transcription factor interacts with PHF8 and binds to the analyzed promoters, suggesting that c-Myc is involved on PHF8 recruitment to these promoters. Further analysis in the neuroblastoma cell line SH-SY5Y and in cortical neurons shows that depletion of PHF8 results in deficient neurite elongation. Overall, our results suggest that the mental retardation phenotype associated with loss of function of PHF8 could be due to abnormal neuronal connections as a result of alterations in cytoskeleton function. HeLa cells were transfected with either control or PHF8 siRNAs. Experiments were performed in biological triplicates. RNA were extracted and sujected to microarray analysis.

2012-07-31 | E-GEOD-38175 | biostudies-arrayexpress

APOC2 increase PHF8 binding on chromatin

Project description:We performed PHF8 ChIP-seq analysis of APOC2 overexpressed RKO cells and control cells to identify high-confident PHF8 regulated targets.

2021-05-07 | GSE114089 | GEO

RNA sequencing of PD-L1 knock out human MDA-MB231 cells and mouse CT26 cells

Project description:Although membrane-anchored PD-L1 has been well-studied for its engagement with PD-1 on T cells to evade anti-tumor immunity, whether PD-L1 regulate oncogenic signaling pathways in tumor cells remains elusive. Methods: Total RNA from MDA-MB-231 wild type (WT) , MDA-MB-231 PD-L1 knock-out (KO), CT26 WT or CT26 Pd-l1 KO cells was purified using Qiagen RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Library preparation and sequenceing analysis were performed at the Molecular Genetics Core facility in Dana-Farber Cancer institute. RNA-seq data was aligned using STAR v2.5.4a. Conclusions: Our study indicates that PD-L1 may regulate genes that are involved in immune response regulating pathways.

2020-06-07 | GSE134510 | GEO

RNA-seq data of 786-O cells transfected with control-sgRNA (Control) and PHF8-sgRNA (PHF8-KO)

Project description:RNA-seq analysis were applied to elucidate the transcriptional differences between 786-O cell lines transfected with control-sgRNA (Control) and PHF8-sgRNA (PHF8-KO). A total of 3575 differentially expressed genes (Fold Change > 2, or Fold Change＜0.5; FDR < 0.05) with 2097 down- and 1478 up-regulated genes were identified in PHF8-KO 786-O cells

2022-10-08 | GSE214183 | GEO

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