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ABSTRACT: HI-TOM NGS

PROVIDER: PRJNA486598 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			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

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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

scRNAseq analysis of hepatocytes from p16-Tom mice following CCl4 treatment

Project description:We used the Flex single-cell RNA sequencing platform (10x Genomics) to investigate the transcriptomic differences between p16high (Tom+) and p16low (Tom-) hepatocytes from p16-CreERT2/R26-LSL-tdTomato mice following 4 weeks of CCl4 treatment.

2026-03-02 | GSE312805 | 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

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