Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cut&Run of Aldh18a1 using 46C mouse ES cells

ABSTRACT: Using a proteomic approach we identified Aldh18a1 as a protein co-localized with RNA polymerase II. We then carried out Aldh18a1 Cut&Run assays to confirm its co-localization with RNA polymerase II (E-MTAB-11510). As a result, we observed Aldh18a1 is co-localized with RNA polymerase II primarily on transcription start sites.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Mahmoud-reza Rafiee

PROVIDER: E-MTAB-11513 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

TT-seq of mouse embryonic stem cells treated with shAldh18a1 in comparison to the shScramble control.

Project description:Our proteomics data revealed Aldh18a1 is co-localized with RNA polymerase II. To understand the function of Aldh18a1 we knocked it down using 2 different shRNAs. We then isolated newly synthesized RNA using TT-seq procedure, and we compared the result of Aldh18a1 knock down with the scramble controls.

2022-06-01 | E-MTAB-11514 | biostudies-arrayexpress

ChIP-seq of RNA polymerase II using pan-pol II and S2-phosphorylated C-terminal domain antibodies in mouse embryonic stem cells

Project description:Our proteomics data (PXD030253) indicate RNA polymerase II is co-localized with Aldh18a1. To confirm this observation using an orthogonal method we performed ChIP-seq experiments to identify the binding patterns of RNA polymerase II in general, and RNA polymerase II with S2-phosphorylated CTD. We also performed Cut&Run using Aldh18a1 antibody which is submitted separately. To do a ChIP-seq, mES cells (46C) were treated with Accutase to be detached. The cells were fixed by 1.5% formaldehyde in PBS for 15min. Chromatin was fragmented by sonication and sheared to < 500 bp fragments. The cell debris were removed by spinning. The sheared chromatin was treated with 10 ug antibodies (pan-Pol II Bethyl A304-405A, or S2P-Pol II Bethyl A304-407A) overnight at 4 °C. Dynabeads protein A beads (40ul) were added to the samples and the samples were rotated 2-3 hours to perform the immunoprecipitation. The beads were washed 5 times. Chromatin was eluted in a denaturing solution, and proteins were digested using proteinase K. DNA was purified by SPRI beads. The ChIP libraries were prepared using NEBNext Ultra II DNA library prep according to the manufacturer manual. The libraries were sequenced using 150nt reads on paired-end mode by HiSeq4000. Reads were trimmed, aligned to the mouse genome (mm10) using Bowtie2, and duplicated reads were removed with samtools. The ChIP quality was evaluated by cross-correlation using the “SPP'' tool as suggested by ENCODE ChIP-seq guidelines. Peak calling was performed using MACS2.

2022-06-01 | E-MTAB-11510 | biostudies-arrayexpress

mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription

Project description:We report a function of human mRNA decapping factors in control of transcription by RNA polymerase II. Decapping proteins Edc3, Dcp1a and Dcp2 and the termination factor TTF2 co-immunoprecipitate with Xrn2, the nuclear 5'-3' exonuclease torpedo that facilitates transcription termination at the 3' ends of genes. Dcp1a, Xrn2 and TTF2 localize near transcription start sites (TSSs) by ChIP-Seq. At genes with 5' peaks of paused pol II, knockdown of decapping or termination factors, Xrn2 and TTF2, shifted polymerase away from the TSS toward upstream and downstream distal positions. This re-distribution of pol II is similar in magnitude to that caused by depletion of the elongation factor Spt5. We propose that coupled decapping of nascent transcripts and premature termination by the torpedo mechanism is a widespread mechanism that limits bidirectional pol II elongation. Regulated co-transcriptional decapping near promoter-proximal pause sites followed by premature termination could control productive pol II elongation. RNA pol II (GSE30895: GSM766171), Xrn2, TTF2 and Dcp1a were localized by ChIP-Seq in HeLa cells. RNA pol II was localized in control HEK293 cells and cells infected with lentiviruses expressing a scrambled control shRNA (scr), and shRNAs targeting the following proteins: Xrn2, TTF2, Xrn2+TTF2, Edc3, Dcp1a, and Dcp2.

2012-04-04 | E-GEOD-36185 | biostudies-arrayexpress

ChIP-Seq of Dazl in mouse embryonic stem cells

Project description:We developed a method to identify chromatin-associated proteins by mass spectrometry. In addition to many known DNA and chromatin-binders, we identified several RNA-binding proteins in the chromatin composition of mouse embryonic stem cells (mESC). Interestingly, we found Dazl as a RBP that specifically binds to chromatin in mESC grown in 2iL condition. So far, Dazl was reported as a RBP that regulates the stability of transcripts in cytoplasm. To identify the binding sites of Dazl on the genome, we carried out a ChIP-seq experiment. As a result, we detected about 1300 reproducible Dazl ChIP-seq peaks. Interestingly, most of the peaks are located close to the transcription start sites of developmental and pluripotency-related genes.

2020-12-25 | E-MTAB-9302 | biostudies-arrayexpress

ALDH18A1promotes the tumor progression of esophageal cancer by binding to and regulating genes associated with tumorigenesis [RNA-Seq]

Project description:Esophageal cancer is a common tumor in the digestive system. Every year, approximately 300 000 people worldwide die due to esophageal cancer. As a potential RNA binding protein (RBP), ALDH18A1 binds to RNAs to regulate a series of biological processes. To reveal the effect of ALDH18A1 on gene expression and alternative splicing (AS) as well as its function in the occurrence and development of esophageal cancer, we used RNA-seq to analyze the ALDH18A1-alternative splicing events in ALDH18A1-silenced and control KYSE150 cells. The results showed that ALDH18A1 mediates global AS dysregulation in KYSE150 cells. We performed improved RNA immunoprecipitation and sequencing for ALDH18A1 and found that ALDH18A1 has extensive RNA binding activity and preferentially binds to the GUAAUCC and UAGCUGG motifs on RNAs. The ALDH18A1-bound transcripts highly overlap with AS genes, indicating that ALDH18A1 can globally regulate AS by binding to the transcripts in KYSE150 cells. The overlapped genes between ALDH18A1-bound and AS genes are mainly involved in transcriptional regulation, RNA splicing, DNA repair, and nuclear mRNA splicing through spliceosome. In this work, we determined that ALDH18A1 affects cell invasion and metastasis by binding to mRNA and controlling the expression of regulator gene and the level of AS, thus playing a role in the development of esophageal carcinogenesis. The findings enhance the understanding of ALDH18A1 as an RBP in AS and tumor regulation.

2024-06-02 | GSE249813 | GEO

ALDH18A1promotes the tumor progression of esophageal cancer by binding to and regulating genes associated with tumorigenesis [IRIP-seq]

2024-06-02 | GSE249244 | GEO

POLII localization in HeLa cells

Project description:RNA polymerase II (POLR2A; POLII) was localized via ChIP-chip using N20 Ab-mediated pull-down of POLII Keywords: ChIP-chip

2006-03-09 | GSE4337 | GEO

POLII localization in HeLa cells

Project description:RNA polymerase II (POLR2A; POLII) was localized via ChIP-chip using N20 Ab-mediated pull-down of POLII Classical design; ChIP-chip of POLII in ENCODE regions

2010-07-01 | E-GEOD-4337 | biostudies-arrayexpress

CRISPR RNA-seq from K562 (ENCSR642RCV)

Project description:RNA-seq on K562 cells treated with a CRISPR gRNA against ALDH18A1. (ALDH18A1-BGKcLV26) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2022-12-04 | GSE219575 | GEO

Chd1 co-occupancy with early transcription elongation factors

Project description:We report the genome-wide Chd1 co-occupancy with early transcription elongation factors ChIP-seq for Chd1 and elongating RNA polymerase II

2014-10-23 | E-GEOD-56061 | 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