Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: 4x-6x genome expression

PROVIDER: PRJNA657699 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12464136_1.fastq.gz	Fastqsanger.gz
	SRR12464136_2.fastq.gz	Fastqsanger.gz
	SRR12464137_1.fastq.gz	Fastqsanger.gz
	SRR12464137_2.fastq.gz	Fastqsanger.gz
	SRR12464138_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 56

Similar Datasets

Altered H3K27 trimethylation contributes to flowering time variations in polyploid Arabidopsis thaliana ecotypes

Project description:Polyploidy is a widespread phenomenon in flowering plant species. Polyploid plants frequently exhibit considerable transcriptomic alterations after whole-genome duplication (WGD). It is known that the transcriptomic response to tetraploidization is ecotype-dependent in Arabidopsis. Nevertheless, the biological significance and the underlying mechanism are unknown. Here, we showed that 4x Col-0 and 4x Ler presented different flowering times, with a delayed flowering time in 4x Col-0 but not in 4x Ler. We found that the expression of FLOWERING LOCUS C (FLC), the major repressor of flowering, was significantly increased in 4x Col-0 but subtle change in 4x Ler. Moreover, the level of a repressive epigenetic mark, trimethylation of histone H3 at lysine 27 (H3K27me3), was significantly decreased in 4x Col-0 but not in 4x Ler, potentially leading to different transcription levels of FLC and flowering time in 4x Col-0 and 4x Ler. Apart from the FLC locus, hundreds of genes showed differentially H3K27me3 alterations in 4x Col-0 and 4x Ler. Comparably, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) and transcription factors required for H3K27me3 deposition presented differential transcriptional changes between 4x Col and Ler, potentially account for differential H3K27me3 alterations in 4x Col-0 and Ler. Last, we found that the natural 4x Arabidopsis ecotype Wa-1 presented early flowering time, associated with low expression and high H3K27me3 of FLC. Taken together, our results showed a role of H3K27me3 alterations in response to genome duplication in Arabidopsis autopolyploids and that flowering time variation potentially functions in autopolyploid speciation.

2022-01-01 | GSE185114 | GEO

The acute milk yield response to frequent milking in early lactation is mediated by genes transiently regulated by milk removal.

Project description:Milking dairy cows four times daily (4X) instead of twice daily (2X) during early lactation stimulates an increase in milk yield that partly persists through late lactation; however, the mechanisms behind this response are unknown. We hypothesized that the acute mammary response to regular milkings would be transient and would involve different genes from those that may be specifically regulated in response to 4X. Nine multiparous cows were assigned at parturition to unilateral frequent milking (UFM; 2X of the left udder half, 4X of the right udder half). Mammary biopsies were obtained from both rear quarters at 5 days in milk (DIM), immediately after 4X glands had been milked (Experiment 1; n = 4 cows), or 2.5 h after both udder halves had last been milked (Experiment 2; n = 5 cows). Affymetrix GeneChip® Bovine Genome Arrays were used to measure gene expression. Eight hundred and fifty five genes were differentially expressed in mammary tissue between 2X vs. 4X glands of cows in experiment 1 (FDR ≤ 0.05), whereas none were differentially expressed in experiment 2 using the same criterion. We conclude that there is an acute transcriptional response to milk removal, but 4X milking did not elicit differential expression of unique genes. Therefore, there does not appear to be a sustained transcriptional response to 4X milking on day 5 of lactation. Using a differential expression plot of data from both experiments, as well as qRT-PCR, we identified at least two genes that may be responsive to both milk removal and to 4X milking. Therefore, the milk yield response to 4X milking may be mediated by genes that are acutely regulated by removal of milk from the mammary gland.

2012-02-27 | GSE27380 | GEO

Anti-GCGR antibody treatment in db/db mice

Project description:Gene expression of liver tissue from db/db untreated (6x replicates) and db/db treated with 5mg/kg of 3c7.v44 mAb (6x replicates). Anti-GCGR antibody treatment in db/db mice: fig 2b in Solloway et al.

2015-06-02 | GSE68142 | GEO

FB-IIN-GNPS Bile acids animal extracts 88 pos

Project description:analysis of 88 bile acid animal extracts; methanol extraction (6x diluted); Kinetex Polar C18 separation; qTOF MS/MS detection; standards - methanolic solutions 1mg/ml 4x diluted (resulting conc. 62.5ug/ml); spiked with 2uM sulfamethazine as int. standard. Lock mass-corrected.

2019-08-06 | MSV000084170 | GNPS

GNPS - BileAcid - AnimalExtracts_88_positive

2018-10-03 | MSV000082996 | GNPS

TR study of ‘A multi-center proof-of-concept phase2 study of encorafenib + binimetinib + cetuximab in patients with BRAF non-V600E mutated metastatic colorectal cancer (BIGBANG study)&quot

Project description:Primary outcome(s): Cancer related genome analysis, gene expression and molecular characterization analysis

| 2647002 | ecrin-mdr-crc

Project description:SGRP-4X Rna-seq

| PRJNA379146 | ENA

Gene expression changes between wildtype (WT) Nicotiana benthamiana plants with and without infection with Potato Spindle Tuber Viroid (PSTVd)

Project description:WT plants (at the five-leaf stage) were infected with PSTVd strain NB by agroinfiltration. Three weeks post infection (3 wpi) young leaves were collected from infected and uninfected (control) WT plants and used in a custom genome-wide gene expression microarray (4x 180K Sureprint G3 microarray, Agilent)

2016-09-19 | GSE81923 | GEO

Genomic methylation variation during grape genome duplication

Project description:WGBS was used to assess gene expression variation between 2X and 4X grape

2020-06-10 | GSE119632 | GEO

The acute milk yield response to frequent milking in early lactation is mediated by genes transiently regulated by milk removal.

Project description:Milking dairy cows four times daily (4X) instead of twice daily (2X) during early lactation stimulates an increase in milk yield that partly persists through late lactation; however, the mechanisms behind this response are unknown. We hypothesized that the acute mammary response to regular milkings would be transient and would involve different genes from those that may be specifically regulated in response to 4X. Nine multiparous cows were assigned at parturition to unilateral frequent milking (UFM; 2X of the left udder half, 4X of the right udder half). Mammary biopsies were obtained from both rear quarters at 5 days in milk (DIM), immediately after 4X glands had been milked (Experiment 1; n = 4 cows), or 2.5 h after both udder halves had last been milked (Experiment 2; n = 5 cows). Affymetrix GeneChipM-BM-. Bovine Genome Arrays were used to measure gene expression. Eight hundred and fifty five genes were differentially expressed in mammary tissue between 2X vs. 4X glands of cows in experiment 1 (FDR M-bM-^IM-$ 0.05), whereas none were differentially expressed in experiment 2 using the same criterion. We conclude that there is an acute transcriptional response to milk removal, but 4X milking did not elicit differential expression of unique genes. Therefore, there does not appear to be a sustained transcriptional response to 4X milking on day 5 of lactation. Using a differential expression plot of data from both experiments, as well as qRT-PCR, we identified at least two genes that may be responsive to both milk removal and to 4X milking. Therefore, the milk yield response to 4X milking may be mediated by genes that are acutely regulated by removal of milk from the mammary gland. 8 samples from 4 cows in experiment 1; 6 samples from 3 cows in experiment 2

2012-02-27 | E-GEOD-27380 | 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