Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome 3' end profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination.

ABSTRACT: Transcriptome 3' end profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination.

PROVIDER: PRJEB23802 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2214600.fastq.gz	Fastqsanger.gz
	ERR2214610.fastq.gz	Fastqsanger.gz
	ERR2214601.fastq.gz	Fastqsanger.gz
	ERR2214611.fastq.gz	Fastqsanger.gz
	ERR2214602.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Transcriptome 3' end profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination.

Project description:We performed mRNA 3'end sequencing experiments on three biological replicates of HeLa cells depleted of MATR3, PTBP1/2, controls, or combined depletion of MATR3/PTBP1/2. Cells were fractionated into cytoplasmic and nuclear RNAn and only the nuclear RNA was used. Library preparation was done with the QuantSeq library kit (Lexogen) according to manufacturer’s recommendations. Replicates 1 and 2 were prepared with the QuantSeq forward library kit, replicates 3 and 4 with the QuantSeq reverse library kit. All libraries were sequenced on Illumina HiSeq2 machines in a single-end manner with a read length of 100 nt.

2018-05-01 | E-MTAB-6287 | biostudies-arrayexpress

Transcriptome profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination by siRNA.

Project description:We performed RNA-seq experiments on three biological replicates of HeLa cells depleted of MATR3, PTBP1/2, controls, or combined depletion of MATR3/PTBP1/2. Cells were fractionated into cytoplasmic and nuclear RNA. Library preparation was done with the TruSeq stranded RNAseq library kit (Illumina) according to manufacturer’s recommendations; RNA was depleted of rRNA using the RiboZero kit (Epicentre). All libraries were sequenced on Illumina HiSeq2 machines in a single-end manner with a read length of 100 nt.

2018-05-01 | E-MTAB-6204 | biostudies-arrayexpress

Transcriptome profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination by siRNA.

Project description:Transcriptome profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination by siRNA.

| PRJEB23439 | ENA

4SU-iCLIP of PTBP1 from HEK293 cells with or without MATR3 depletion

Project description:The aim of the experiment was to compare binding of PTBP1 in presence and absence of MATR3. HEK293T cells were transfected with siRNA targeting MATR3 or control sequences and labelled with 4thio-uridine for 8 hours (100µM, crosslinking 2x400mJ/cm2 365nm UV light).

2018-05-01 | E-MTAB-6286 | biostudies-arrayexpress

4SU-iCLIP of MATR3 from HEK293 cells with or without PTBP1 depletion

Project description:The aim of the experiment was to compare binding of MATR3 in presence and absence of PTBP1. HEK293T cells were transfected with siRNA targeting PTBP1 and PTBP2 or control sequences and labelled with 4thio-uridine for 8 hours (100µM, crosslinking 2x400mJ/cm2 365nm UV light).

2018-05-01 | E-MTAB-6267 | biostudies-arrayexpress

MATR3

Project description:MATR3

| PRJNA823719 | ENA

4SU-iCLIP of PTBP1 from HEK293 cells with or without MATR3 depletion

Project description:4SU-iCLIP of PTBP1 from HEK293 cells with or without MATR3 depletion

| PRJEB23801 | ENA

4SU-iCLIP of MATR3 from HEK293 cells with or without PTBP1 depletion

Project description:4SU-iCLIP of MATR3 from HEK293 cells with or without PTBP1 depletion

| PRJEB23752 | ENA

The nuclear matrix protein MATR3 maintains higher-order chromatin architecture [Hi-C]

Project description:The chromatin structure in eukaryotic nucleus is highly ordered and organized in hierarchical frameworks. We performed Hi-C assay in WT and MATR3-depleted AML12 cells to reveal the MATR3's role in AML12 cells.

2023-06-28 | GSE200243 | GEO

Genome-wide maps of nuclear lamina interactions in AML12 cells upon MATR3 KD [DamID-Seq]

Project description:We performed DamID-seq assay in WT and MATR3-depleted AML12 cells to investigate the Lamina-associated-domains (LADs) affected by loss of MATR3.

2025-03-14 | GSE200242 | 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