Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PARCLIP analysis of YBX1, ELAVL1 and ALYREF to detect their binding targets

ABSTRACT: The PAR-CLIP sample was separated by SDS-PAGE, RNA were recovered from the gel by D-tubeTM Dialyzer Midi(Millipore).The mixture were digested by 4 μg/μl proteinase K (Roche, 03115828001) and precipitated in ethanol with the help of glycogen (Thermo, R0551). RNAs in ethanol were used for the small RNA library construction (NEB, E7300L). Finally, the library was sequenced on the Illumina HiSeq X-Ten platform with paired-end 150 bp (PE150) kits. Only the forward reads were used in the data analysis and uploaded. Bowtie was applied to map sequencing reads against hg19 genome with up to two mismatches allowed. PARalyzer software was used to define proteins binding clusters.

ORGANISM(S): Homo sapiens

PROVIDER: GSE133620 | GEO | 2019/07/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

PARCLIP analysis of YBX1, ELAVL1 and ALYREF to detect their binding targets

Project description:PARCLIP analysis of YBX1, ELAVL1 and ALYREF to detect their binding targets

| PRJNA552051 | ENA

RNA-seq of murine bone marrow-derived macrophages (mBMDM) of the wild type (WT) group versus the RBP-J conditionally knockout (CKO) group at 36 hours post HTNV (Hantaan orthohantavirus) infection

Project description:Total RNA was extracted from WT and RBP-JCKO mBMDMs at 36 hpi (HTMV, MOI=1), using TRIzol (Invitrogen). Ribosomal RNA was removed using the Ribo-Zero™ kit (Epicentre Biotechnologies). Fragmented RNA (the average length was approximately 200 bp) was subjected to first-strand and second-strand cDNA synthesis followed by adaptor ligation and enrichment with a low cycle according to the instructions of the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies). The libraries were paired-end sequenced (PE150, sequencing reads were 150 bp) at Guangzhou Ribo Biotechnology (Guangzhou, China) using the Illumina HiSeq 3000 platform. Transgenic mice type: RBP-JCKO (Lyz2-Cre+ RBP-Jfloxed) C57BL/6J Mice.

2022-07-22 | E-MTAB-11926 | biostudies-arrayexpress

Transcriptomics of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues

Project description:RNA was isolated from siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) or HiSeq2500 in paired-read mode, creating reads with a length of 101 or 125 bp. Sequencing chemistry v2 or v4 (Illumina) was used.

2017-04-19 | GSE93750 | GEO

ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

Project description:Epithelial (CD31-CD45-EpCAM+) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (2 biological replicates per genotype). Chromatin from each of the replicates was immunoprecipitated with H3K27me3 antibody (Millipore #07-449) and subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina). Completed libraries from different samples were sequenced on HiSeq 2500 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility.

2015-05-11 | GSE57392 | GEO

ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

2015-05-11 | E-GEOD-57392 | biostudies-arrayexpress

Molecular profiling of Ctcf hemizygous mouse embryonic fibroblasts: ChIP-seq

Project description:CTCF is a highly conserved and ubiquitously expressed protein involved in several fundamental processes such as fine-tuning gene expression, imprinting, X-chromosome inactivation and 3D chromatin organisation. To understand the impact of differences in the concentration of CTCF abundance on these processes, we exploit a CTCF hemizygous mouse model with a stable reduction in the concentration of this protein. We derived twelve independent primary lines of mouse embryonic fibroblasts (MEFs) from six wildtype and six CTCF-hemizygous mouse E13.5 embryos. MEFs were fixed in DMEM containing 1% fresh formaldehyde and incubated at room temperature for 10 min, quenched with 250mM glycine for 10 min, and washed twice with ice cold PBS, before being flash-frozen at -80°C. Cross-linked cells were lysed and sonicated on a Bioruptor Plus (Diagenode) sonicator to fragment chromatin to an average length of 300bp. 10 ug of the following antibodies were used for immunoprecipitation: CTCF (rabbit polyclonal, Merk Millipore 07-729, lot 2517762); H3K4me3 (mouse monoclonal IgG clone CMA304, Merck Millipore 05-1339, lot 2603814); H3K27ac (rabbit polyclonal IgG, Abcam 4729, lot GR244014-1). Immunoprecipitated DNA or 50 ng of input DNA was used for library preparation using the ThruPLEX DNA-Seq library preparation protocol (Rubicon Genomics, UK). Library fragment size was determined using a 2100 Bioanalyzer (Agilent). Libraries were quantified by qPCR (Kapa Biosystems). Pooled libraries were sequenced on a HiSeq4000 (Illumina) according to manufacturer’s instructions using single-end 50 bp reads. On the same MEF lines we have performed RNAseq and HiC (see related accession numbers).

2018-07-29 | E-MTAB-6261 | biostudies-arrayexpress

Global PAS-seq (polyA-site-sequencing) profiling in control and CFIm25 KD human embryonic stem cells (H9 cell line)

Project description:To understand how CFIm25, an mRNA 3' processing regulator, affects global mRNA alternative polyadenylation (APA) profiling in H9 cells. We performed PAS-seq (polyadenylation site sequencing) in control (2 samples) and CFIm25 KD cells (3 samples). PAS-seq library was prepared using a lexogen kit (3'-seq, Catolog. 016.024). Sequencing was performed using Novaseq PE150.

2022-04-21 | GSE176343 | GEO

Transcriptomic profile of a Clostridioides difficile rsbW deletion mutant compared to parental R20291 strain

Project description:RNA-seq was conducted to uncover the regulatory roles of RsbW in the lifestyle of Clostridioides difficile strain R20291. RNA were extracted from planktonic cultures, which were grown in BHI-S (Sigma-Aldrich, USA) to early stationary phase (10h). The cells were re-suspended in LETS buffer and lysed using Fast-prep 24 instrument (MP Bioscience) and RNA was extracted using 1 ml Trizol (Ambion, USA). Samples were cleaned and sequenced by Novogene Company Limited, PE150 with approximately 10 million reads per sample. After QC, reads were aligned to R20291 (NC_013316.1) with Bowtie2 and readcounts were generated with Samtools and Bedtools. Differential gene expression analysis was conducted with DESeq2 with a p-value of 0.05, differential gene expression was determined with ± -2 logFC.

2022-08-22 | E-MTAB-12114 | biostudies-arrayexpress

S. cerevisiae L3262: Control vs. SPT15 multiple point mutant strains, Ets2 and Ets3

Project description:Transcriptional profiling of ethanol tolerant strains Ets2 and Ets3 comparing control Saccharomyces cerevisiae L3262 with ethanol tolerant strains Ets2 and Ets3, through screening a mutant library of SPT15 of Saccharomyces cerevisiae L3262.

2013-09-01 | GSE23965 | GEO

Transcriptomics analysis of gene expression in mouse lung after PM2.5 exposure

Project description:Total RNA was isolated from mouse lung harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

2019-10-24 | GSE122492 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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