Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

WUYAO-Lindera aggregata (Sims) Kosterm.

ABSTRACT: WUYAO-Lindera aggregata (Sims) Kosterm. For analysis the raw and processed Lindera aggregata (Sims) Kosterm. 2022.10.17

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Lindera Aggregata (sims) Kosterm.

SUBMITTER: Songhong Yang

PROVIDER: MSV000091210 | MassIVE | Mon Feb 06 08:34:00 GMT 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Differential effects of two catalytic mutations on full-length PRDM9 and its isolated PR/SET domain reveal a case of pseudo-modularity

Project description:The locations of mammalian recombination hotspots are determined by PRDM9, a zinc finger histone methyltransferase that locally trimethylates histone H3 at residues K4 and K36. We previously reported two hypomorphic catalytic mutations, Prdm9-EP and Prdm9-EK, with different phenotypic effects. Prdm9-EP, but not Prdm9-EK, is compatible with female sub-fertility, while both mutations phenocopy the Prdm9-null condition in males. Here we directly compare and contrast the enzymatic effects of the two mutations in vitro and in vivo. We previously performed two biological H3K4me3 ChIP-seq replicates in spermatocytes isolated from Prdm9-EP homozygous males (GSE144144; SRX8588740 and SRX8588741), and re-processed previously reported H3K4me3 ChIP-seq data from spermatocytes isolated from wild-type B6 males (GSE52628; SRX381465 and SRX381466). We used those raw and processed files for this study (GSE144144). We also previously performed one biological H3K4me3 replicate in spermatocytes isolated from Prdm9-EP homozygous males (GSE112110; SRX4136625). We report an additional replicate here, and merged the two replicates for analysis; raw and processed files are reported here. We also performed ChIP-seq for H3K36me3 in both Prdm9-EP and Prdm9-EK homozygous spermatocytes. Raw and processed files are available here. For comparison, we re-mapped and re-analyzed H3K36me3 ChIP-seq data we previously reported from wild-type B6 spermatocytes (GSE76416; SRX1508234); processed files are available here.

2021-10-11 | GSE181479 | GEO

Mapping genotypes to chromatin accessibility profiles in single cells [Genotyping GoT-ChA amplicon]

Project description:Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments

2024-05-08 | GSE204911 | GEO

Single-cell RNA-seq of brassinosteroid response in Arabidopsis roots

Project description:We report both raw and processed scRNA-seq data profiling brassinosteroid response and related mutants in Arabidopsis roots

2022-09-14 | GSE212230 | GEO

Mapping genotypes to chromatin accessibility profiles in single cells [scATAC-seq; Pt01-19;Pt-02 DOGMAseq]

Project description:Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments

2024-05-08 | GSE203251 | GEO

Single-cell RNA-seq data of Arabidopsis root

Project description:We report both raw and processed scRNA-seq data that are used to build transcriptomic atlas of Arabidopsis root.

2020-07-02 | GSE152766 | GEO

Single-cell RNA-seq of rice roots grown in gel, non-compacted soil and compacted soil conditions

Project description:We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress

2024-02-01 | GSE251706 | GEO

RNAseq in Arabidopsis prefoldin mutants

Project description:This GEO submission includes RNAseq raw data (fastq.gz) and processed data (using DESeq2) from samples obtained in the wild type and the pfd4 and 6x_pfd mutants

2020-12-22 | GSE138432 | GEO

Tandem mass tag (TMT) quantification data from knee chondrocytes for 12 osteoarthritis patients, comparing disease tissue against control tissue in each individual

Project description:This data set is made up of 4 experiments (batches) analysing chondrocytes from healthy and diseased knees in 12 patients with osteoarthritis. There are 6 samples (from 3 patients) for each batch, where diseased and control samples were extracted from each patient and compared within patient. The batches were necessary due to the maximum sample capacity (6) of the mass spectrometer. The raw data files were deposited at EBI PRIDE database under accession number PXD002014 ( http://www.ebi.ac.uk/pride/archive/projects/PXD002014 ). This ArrayExpress record contains sample meta-data and processed data in the form of ratios and the log2 fold changes. The ratios were calculated for each patient as diseased vs control (the reference). Please note that one patient (number 52) was excluded from the fold change analysis as no proteins showed any significant change which suggests the samples were not correct or something went wrong with them. There is also the median and standard deviation across the patients.

2017-10-01 | E-PROT-4 | biostudies-arrayexpress

Transcriptome profiling of A549 RB1 wild-type/knockout cell lines

Project description:A549 cells were co-transfected with CRISPR/Cas9 (containing sgRNA and GFP) and HDR donor plasmids (containing RFP and puromycin). The genetic editing cells were selected by puromycin. And then, we performed RNA sequencing for transcription profiling of A549 RB1 RB1 wild-type/knockout cell lines. The raw data were processed with Tophat and cuffdiff for gene expression analysis.

2020-08-25 | GSE132722 | GEO

Proteomic profiling of NCI60 cell lines from Cancer Cell Line Encyclopedia

Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.

2017-01-27 | E-PROT-2 | biostudies-arrayexpress

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