GEO DataSets

(Submitter supplied) Investigation of annual transcriptome dynamics of Japanese cedar cuttings planted in three regions (Yamagata, Ibaraki and Kumamoto, Japan).

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL21366

78 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Microbiota

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL29674

20 Samples

Download data: TXT

(Submitter supplied) Microbiota dysbiosis has been reported to contribute to the pathogenesis of colitis, to demonstrate whether IL-17D protects against DSS-induced colitis through regulation of microflora, we performed 16S rRNA sequencing in feces from WT and Il17d-deficient mice. Our data indicate that Il17d deficiency results in microbiota dysibiosis in both steady state and DSS-induced colitis.

Organism:

Microbiota

Type:

Other

Platform:

GPL29674

16 Samples

Download data

(Submitter supplied) To investigate the mechanism of annual rhythms in Japanese cedar, annual time series samples were collected from the cuttings planted in natural condition. Also, to investigate the effects of photoperiod and temperature during transition to dormancy, the samples of cuttings grown in the controlled-environmental chamber were analyzed by a microarray.

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL21365

80 Samples

Download data: TXT

(Submitter supplied) Chinese fir (Cunninghamia lanceolata) is an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus (LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. more...

Organism:

Cunninghamia lanceolata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24913

2 Samples

Download data: FASTA, TXT

(Submitter supplied) Investigation of gene expression dynamics associated with male strobilus induction in Cryptomeria japonica in response to gibberellic acid (GA) treatment. [SUBMITTER_CITATION]: Transcriptome Analysis in Male Strobilus Induction by Gibberellin Treatment in Cryptomeria japonica D. Don Manabu Kurita 1,?, Kentaro Mishima 2,*,? , Miyoko Tsubomura 2, Yuya Takashima 2 , Mine Nose 2, Tomonori Hirao 2 and Makoto Takahashi 2 Forests 2020, 11(6), 633

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL25591

48 Samples

Download data: TXT

(Submitter supplied) In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families.

Organism:

Butyrivibrio fibrisolvens; Ruminococcus flavefaciens; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Segatella bryantii; Acetivibrio clariflavus; uncultured Neocallimastigales; Selenomonas ruminantium; Lactococcus lactis; Clostridioides difficile; Ruminiclostridium cellulolyticum; Limosilactobacillus fermentum; Cellulomonas flavigena; Neocallimastix patriciarum; Bifidobacterium animalis; Agathobacter rectalis; Enterobacter sp.; Orpinomyces joyonii; Piromyces rhizinflatus; Piromyces sp. 'equi'; Pseudobutyrivibrio xylanivorans; Bifidobacterium longum; Bacteroides fragilis; Xylanibacter ruminicola; Ruminococcus albus; Enterococcus faecium; Clostridium acetobutylicum; Acetivibrio thermocellus; Clostridium beijerinckii; Levilactobacillus brevis; Microbiota; Bacteroides ovatus; Fibrobacter intestinalis; Bacteroides sp.; Epidinium caudatum; Polyplastron multivesiculatum; Butyrivibrio hungatei; Epidinium ecaudatum; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Orpinomyces sp.; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; [Eubacterium] cellulosolvens; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Roseburia hominis

Type:

Genome variation profiling by array

Platform:

GPL25777

6 Samples

Download data: TXT

(Submitter supplied) To screen the genes related to nitrogen use efficiency, a Chinese fir clone named X6 was subjected to low nitrogen (LN) stress and was used along with control (CK) plants for de novo RNA sequencing of root transcriptomes. The differences in the expression of genes under both conditions were determined. A total of 4,300 significant differentially expressed genes (SDEGs) were obtained by comparing the transcriptomes of the plants in the LN and CK groups. more...

Organism:

Cunninghamia lanceolata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24913

2 Samples

Download data: TXT, XLSX

(Submitter supplied) Objective: In order to study the change law of Chinese fir gene expression caused by fertilization, it provides scientific basis for Chinese fir fertilization theory and practice. Method: Using Illumina HiSeq4000 high-throughput sequencing technology, sequencing sequences of four different fertilizer treatment materials (control CK1, nitrogen treatment N1, phosphorous treatment P1, and phosphorous and nitrogen mixture treatment NP1, each with three biological repeats) were obtained, and a series of comparative analysis of the differences were conducted. more...

Organism:

Cunninghamia lanceolata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24913

12 Samples

Download data: FASTA, TXT

(Submitter supplied) To reveal transcriptome dynamics during adventitious root formation in a coniferous tree, C. japonica, we conducted custom microarry experiments. Three parts from cuttings of easy-to-root clone of C. japonica were collected at eight time points during adventitious root formation. The results revealed major turning points on transcriptome toward adventitious root formation and the expression behavior of genes related to carbohydrate, plant hormone and others suggested the important biological changes for adventitious root formation.

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL21366

72 Samples

Download data: TXT

(Submitter supplied) We used transcriptomics to investigate how Mucispirillum schaedleri ASF 457 interferes with the gene expression of Salmonella Typhimurium in the cecum of gnotobiotic mice

Organism:

Microbiota

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25783

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Cryptomeria japonica

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL23104 GPL23106

951 Samples

Download data: CEL

(Submitter supplied) Japanese cedar (Cryptomeria japonica) is an allogamous coniferous species that relies on wind-mediated pollen and seed dispersal, and it is one of the most important forestry tree species in Japan. For accelerating breeding, we collected massive SNPs based on ESTs from several organs using NGS, and thus carried out QTL, GWAS and GS based on high-density linkage maps.

Organism:

Cryptomeria japonica

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL23106

478 Samples

Download data: CEL

(Submitter supplied) Japanese cedar (Cryptomeria japonica) is an allogamous coniferous species that relies on wind-mediated pollen and seed dispersal, and it is one of the most important forestry tree species in Japan. For accelerating breeding, we collected massive SNPs based on ESTs from several organs using NGS, and thus carried out QTL, GWAS and GS based on high-density linkage maps.

Organism:

Cryptomeria japonica

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL23104

473 Samples

Download data: CEL

(Submitter supplied) The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae we provide novel insights into the evolution of gbM and its underlying mechanism. The angiosperm- and eudicot-specific whole genome duplication events gave rise to what are now referred to as CMT1, 2 and 3 lineages. more...

Organism:

Lupinus angustifolius; Cyperus papyrus; Diplazium proliferum; Papuacedrus papuana; Encephalartos horridus; Thuja sutchuenensis; Psilotum; Equisetum; Synsepalum dulcificum; Araucaria; Juniperus virginiana; Pereskia grandiflora; Kalanchoe tomentosa; Aristolochia grandiflora; Gnetum gnemon; Urtica dioica; Cyathea; Aloe vera; Amentotaxus formosana; Cephalotaxus harringtonia; Selaginella kraussiana; Yucca brevifolia; Torreya taxifolia; Microsorum punctatum; Dacrycarpus compactus; Celtis occidentalis; Nepenthes bicalcarata; Amentotaxus argotaenia; Hypericum perforatum; Chamaecyparis hodginsii; Dacrydium balansae; Manoao colensoi; Cissus quadrangularis; Impatiens niamniamensis

Type:

Methylation profiling by high throughput sequencing

34 related Platforms

150 Samples

Download data: TXT

(Submitter supplied) A custom cDNA microarray analysis was designed based on a proprietary cDNA library and EST data to investigate seasonal gene expression in Japanese cedar cambial region.

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL18030

60 Samples

Download data: PAIR

(Submitter supplied) Investigation of gene expression changes among anther development in wild type and male sterile mutant.

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL19600

42 Samples

Download data: PAIR

(Submitter supplied) MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs in conifers because of the lack of reference sequences for these enormous genomes. In this study, Solexa sequencing of three small RNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese fir samples identified 76 known miRNAs from 27 miRNA families and 18 new potential miRNAs, of which 15 novel miRNA precursors were validated by RT-PCR and sequencing. more...

Organism:

Cunninghamia lanceolata

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18151

3 Samples

Download data: FA

(Submitter supplied) Investigation of transcriptome dynamics of Japanese cedar (Cryptomeria japonica) in winter (Dec. 22-23, 2011) and summer (July 30-31, 2012). We investigated seasonal and diurnal transcriptome dynamics of Japanese cedar (Cryptomeria japonica) by analyzing shoot samples collected at four-hour interval for two days in winter and summer, respectively. We first collected sequence data of expressed genes from shoots to designed microarray probes. more...

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL18152

44 Samples

Download data: PAIR

(Submitter supplied) We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer.

Organism:

Cunninghamia lanceolata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15423

3 Samples

Download data: TXT