txid4550[Organism:noexp] - GEO DataSets

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Select item 2002284071.

ChIP-seq of holocentric Chionographis japonica to determine the centromere distribution and genome organization

(Submitter supplied) To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2

Organism:: Chionographis japonica; Secale cereale

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL33287 GPL33288
8 Samples

Download data: BIGWIG

Series

Accession:: GSE228407

ID:: 200228407

PubMed Full text in PMC Similar studies

Select item 2001084052.

Transcriptomics study of three Blumeria graminis formae speciales

(Submitter supplied) We analyzed the gene expression and especially the expression of effector candidate genes in wheat and rye powdery mildews.

Organism:: Secale cereale; Blumeria graminis f. sp. tritici; Triticum aestivum; x Triticosecale; Blumeria graminis f. sp. secalis; Blumeria graminis f. sp. triticale

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24426 GPL24424 GPL24425
21 Samples

Download data: TXT

Series

Accession:: GSE108405

ID:: 200108405

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000586783.

Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

(Submitter supplied) To distinguish transcripts expressed from each of the three wheat genomes and those from the rye chromatins, genomic probes generated from diploid progenitors of wheat and rye were synthesized

Organism:: Triticum aestivum; Triticum urartu; Aegilops speltoides; Aegilops tauschii; Secale cereale

Type:: Expression profiling by array

Platform:: GPL18847
12 Samples

Download data: PAIR, TXT

Series

Accession:: GSE58678

ID:: 200058678

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000478824.

Differential gene expression during cold-acclimation in barley, wheat and rye

(Submitter supplied) The present transcript profiling compares the gene expression during cold-acclimation in different genotypes of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.) and rye (Secale cereale L.) in order to determine factors influencing frost tolerance. Because of its outstanding robustness against adverse environmental conditions rye is considered to be a model species for abiotic stress tolerance. more...

Organism:: Triticum aestivum; Secale cereale; Hordeum vulgare

Type:: Expression profiling by array

Platform:: GPL17286
72 Samples

Download data: TXT, XLS

Series

Accession:: GSE47882

ID:: 200047882

Analyze with GEO2R

Select item 1000332885.

Illumina NovaSeq 6000 (Chionographis japonica; Secale cereale)

Organism:: Secale cereale; Chionographis japonica

1 Series
4 Samples

Download data

Platform

Accession:: GPL33288

ID:: 100033288

Select item 1000244256.

Illumina HiSeq 2000 (Blumeria graminis f. sp. secalis; Secale cereale)

Organism:: Secale cereale; Blumeria graminis f. sp. secalis

1 Series
6 Samples

Download data

Platform

Accession:: GPL24425

ID:: 100024425

Select item 1000220667.

Affymetrix Axiom® Rye600k Genotyping Array

(Submitter supplied) We generated comprehensive whole-genome shotgun (WGS) sequence data from rye inbred line Lo7 to generate the first rye genome assembly (Lo7_v2) and resequenced a panel of ten diverse rye inbred lines and Secale vavilovii for exploring genome diversity. We discovered more than 90 million single nucleotide variants (SNVs) in the rye genome and developed a high-density genotyping array to experimentally validate more than 600k SNVs (SNPs and short indels). more...