Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: HI-TOM NGS

PROVIDER: PRJNA486598 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7716362_1.fastq.gz	Fastqsanger.gz
	SRR7716362_2.fastq.gz	Fastqsanger.gz
	SRR7716363.fastq.gz	Fastqsanger.gz
	SRR7716363_1.fastq.gz	Fastqsanger.gz
	SRR7716363_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

Project description:Hi-tom NGS

| PRJNA481881 | ENA

Project description:Hi-tom NGS of gene editing by CRISPR-SaCas9 system

| PRJNA496604 | ENA

Project description:293T-cells-Hi-Tom-data

| PRJNA674944 | ENA

scRNAseq of sorted splenic MHCII+ cells from 9 day-old female Clec9a-Cre/Cre Rosa-tdTomato/tdTomato mice after exclusion of CD19+ B cells and autofluorescence+F4/80hi macrophages

Project description:We use scRNA sequencing of MHCII+ cells in the neonatal spleen to elucidate the heterogeneity in young cDC populations and their potential ontogenetic relationship with MHCII-expressiong ILCs. Additionally, we aim to uncover the transcriptomic differences of TOM+ cDC2 and TOM- DC2 in the single cell level. Our data reveal that the neonatal spleen consists of the same cDC1 and cDC2 subsets that comprise the adult cDC compartment. Additionallu, ILCs do not seem to relate otogenetically with TOM- DC2.In the cDC2 clusters, TOM+/- cells are evenly distributed indicative of their transciptomic resemblance. A unique and distinct cluster of TOM- DC2 is observed.

2020-11-06 | GSE151592 | GEO

Comparative transcriptome analysis between two tomato materials under cold stress

Project description:RNA sequencing was performed to investigate the the response mechanism of tomato response to cold stress.“Micro-TOM-EX” is the 'Micro-TOM' plants overexpressing a GATA transcription factor gene.

2020-04-19 | GSE148887 | GEO

RNAseq of splenic dendritic cells from 1 week-old and adult Clec9a-Cre Rosa-Tomato mice

Project description:We use bulk RNA sequencing of sorted cells to characterize the gene expression profiles of splenic TOM+ cDC2 and TOM- DC2 from 1 week-old mice as well and of TOM+ cDC2 from adult mice. We aim to reveal transcriptional differences based on ontogeny and developmental age. Sequencing results revealed that the developmental age rather than cell origin is a major determinantof the transcriptomic differences observed between young and adult cDC2.

2020-11-06 | GSE151593 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of effect of knockdown of GATA2 on AR binding sites

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare AR binding activity in LNCaP cells with and without knockdown of GATA2. Methods: LNCaP cells between passage number 32-34 were used for assay. Cells are transfected with GATA2 specific or nonspecific siRNA and ChIP was performed, the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks. Results: GATA2 knockdown lead to changes of AR binding activity , in most AR binding sites, AR shows decreased bindig activity. Only small percent sites show increased binding. Conclusions: Our study represents the first detailed analysis of the relationship between GATA2 and AR binding in whole genomic DNA.These results demostrate GATA2 play a critical role in AR activity in prostate cancer. LNCaP cells was used as cell model were treated with specific GATA2 siRNA.Library was sequenced using Illumina HI-seq 2500.

2014-01-21 | E-GEOD-52725 | biostudies-arrayexpress

Comparative analysis of drought-responsive transcriptome in soybean lines contrasting for canopy wilting

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of abiotic stress molecular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of contrasting slow wilting lines to quantify transcript abumdance under drought stress condition Methods: The three biological replicates of DS line, Pana (control and drought samples) and DT line, PI 567690 (control and drought samples) leaf sample RNA were multiplexed and sequenced on an Illumina Hi-Seq 2000 platform. The RNA concentration of each sample was approximately 200ng/µl with a quantity of 50 µl.isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

2015-08-31 | E-GEOD-70310 | biostudies-arrayexpress

The Myc-Associated Zinc Finger Protein (MAZ) Works Both Independently and Together with CTCF to Control Cohesin Positioning and Genome Organization

Project description:Purpose: The objectives of this study are to evaluate the roles of MAZ in cellular processes using the NGS-deriveed ChIP-seq, RNA-seq and Hi-C profiles in K562 wild type and siRNA MAZ knockdown cells Methods: ChIP-Seq and Hi-C profiles of K562 wild-type (WT) and siRNA MAZ knockdown cells were generated by deep sequencing in duplicate or triplicate using Illumina GAIIx. The ChIP-seq sequence reads were analyzed with Burrows–Wheeler Aligner (BWA) followed by MACS software; The Hi-C sequence reads were analyzed with Juicer and HiC-Pro software. Results: Comparative analysis of the ChIP-seq, RNA-seq and Hi-C data between K562 wild type and siRNA MAZ knockdown cells indicates that 1.MAZ colocalizes with CTCF in the genome, and helps stabilize CTCF binding; 2. MAZ is able to arrest the cohesin complex independently of CTCF and contributes additively to cohesin localization when it is associated with CTCF; 3. MAZ, similarly to CTCF, acts as an insulator protein to block interaction between promoter and enhancer ; 4. MAZ can pause the elongating form of RNA Pol II; and 5. MAZ helps control local chromatin organization and some aspects of TAD structure. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2021-01-01 | GSE143937 | GEO

Calcium treatment can delay tomato (Solanum lycopersicum L.) fruit senescence

Project description:In the present study, we demonstrated that application of CaCl2 to ‘Micro Tom’ tomato fruit (mature green stage) delayed fruit senescence and mature.

2017-09-28 | GSE73520 | 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