Multi generation microbiome
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ABSTRACT:
PROVIDER: PRJNA940697 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Multi-site human microbiome Raw sequence reads
| PRJNA812896 | ENA
Project description:Purpose: to screen the candidate genes involved in the peanut drought stress response, we conducted global transcriptome analysis of peanut plants challenged with water deficit and ABA, using the Illumina HiSeq2000 sequencing platform. Methods: a sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA) were conducted based on above sequence library. For sequencing library construction, plants were grown under normal conditions, as described previously , Seeds were planted in soil and kep in the greenhouse at temperature of 25-30℃ and water well. Three tissues (leaves, roots, and stems) were collected at three development stages (four-leaf, flowering and podding stages), respectively. Then all of these tissues were mixed to extract the total RNA for sequence library construction. For DEGs study, two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 µmol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel. After treatments, Total RNA was extracted from 100 mg of plant material, and RNA integrity was checked by gel electrophoresis. Also RNA quality was checked and RNA was quantified using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA) and Nanodrop ND-1000 (Thermo Scientific, Waltham, USA). Results: we generated 4.96×107 raw sequence reads and assembled the high quality reads into 92,390 unique genes. Compared with the control, we found that 621 genes (≥1.5 fold change) responded rapidly to water deficit and 2665 genes (≥1.5 fold change) responded rapidly to ABA. We found 279 genes that overlapped between water deficit and ABA responses, 264 genes that showed the same trend in expression while 15 genes expression that showed opposite trend. Among the identified genes, 257 showed high induction by ABA (>5 fold), and 19 showed high induction by drought (>5 fold). In addition, we identified 100 transcription factor genes among the ABA-inducible genes but only 22 transcription factor genes among the water deficit-inducible genes. Conclusions: we identified genes differentially expressed in the early response to water deficit or ABA. These genes were annotated with GO functional categories for water deficit (33 categories) or ABA (31 categories). We found that only 19 genes were highly induced by water deficit, but 257 genes were highly induced by ABA. Our previous work has examined many of these genes and our future work will reveal their functions and relationships. These data will facilitate functional genomic studies and have established a biotechnological platform for examination of the early drought- and ABA-responsive transcriptome regulatory network in peanut.
2014-05-13 | GSE56439 | GEO
Project description:River water microbiome Raw sequence reads
| PRJNA751533 | ENA
Project description:We investigated the multi- and transgenerational impact of BaP on Xenopus females following F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1). 5 females from F1 and F2 generations by parentale xposure conditions (control vs BaP) were used for studying liver transcriptome by RNAseq. RNA-seq libraries were sequenced on an illumina GAIIx sequencer as 75bp single reads
2021-01-01 | GSE150911 | GEO
Project description:Purpose: to screen the candidate genes involved in the peanut drought stress response, we conducted global transcriptome analysis of peanut plants challenged with water deficit and ABA, using the Illumina HiSeq2000 sequencing platform. Methods: a sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA) were conducted based on above sequence library. For sequencing library construction, plants were grown under normal conditions, as described previously , Seeds were planted in soil and kep in the greenhouse at temperature of 25-30M-bM-^DM-^C and water well. Three tissues (leaves, roots, and stems) were collected at three development stages (four-leaf, flowering and podding stages), respectively. Then all of these tissues were mixed to extract the total RNA for sequence library construction. For DEGs study, two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 M-BM-5mol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel. After treatments, Total RNA was extracted from 100 mg of plant material, and RNA integrity was checked by gel electrophoresis. Also RNA quality was checked and RNA was quantified using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA) and Nanodrop ND-1000 (Thermo Scientific, Waltham, USA). Results: we generated 4.96M-CM-^W107 raw sequence reads and assembled the high quality reads into 92,390 unique genes. Compared with the control, we found that 621 genes (M-bM-^IM-%1.5 fold change) responded rapidly to water deficit and 2665 genes (M-bM-^IM-%1.5 fold change) responded rapidly to ABA. We found 279 genes that overlapped between water deficit and ABA responses, 264 genes that showed the same trend in expression while 15 genes expression that showed opposite trend. Among the identified genes, 257 showed high induction by ABA (>5 fold), and 19 showed high induction by drought (>5 fold). In addition, we identified 100 transcription factor genes among the ABA-inducible genes but only 22 transcription factor genes among the water deficit-inducible genes. Conclusions: we identified genes differentially expressed in the early response to water deficit or ABA. These genes were annotated with GO functional categories for water deficit (33 categories) or ABA (31 categories). We found that only 19 genes were highly induced by water deficit, but 257 genes were highly induced by ABA. Our previous work has examined many of these genes and our future work will reveal their functions and relationships. These data will facilitate functional genomic studies and have established a biotechnological platform for examination of the early drought- and ABA-responsive transcriptome regulatory network in peanut. Two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 M-BM-5mol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel.
2014-05-13 | E-GEOD-56439 | biostudies-arrayexpress
Project description:Systematic characterization of gut microbiome-secreted molecules by integrated multi-omics
2021-03-02 | MSV000086974 | MassIVE
Project description:In a prior report, we observed two distinct lung microbiomes in healthy subjects that we termed â??pneumotypesâ??: pneumotypeSPT, characterized by high bacterial load and supraglottic predominant taxa (SPT) such as the anaerobes Prevotella and Veillonella; and pneumotypeBPT, with low bacterial burden and background predominant taxa (BPT) found in the saline lavage and bronchoscope. Here, we determined the prevalence of these two contrasting lung microbiome types, in a multi-center study of healthy subjects. We confirmed that a lower airway microbiome enriched with upper airway microbes (pneumotypeSPT) was present in ~45% of healthy individuals. Cross-sectional Multicenter cohort. BAL of 49 healthy subjects from three cohort had their lower airway microbiome assessed by 16S rDNA sequencing and microbial gene content (metagenome) was computationally inferred from taxonomic assignments. The amplicons from total 100 samples are barcoded; the barcode and other clinical characteristics (e.g. inflammatory biomarkers and metabolome data) for each sample are provided in the 'Pneumotype.sep.Map.A1.txt' file.
2016-03-29 | E-GEOD-74395 | biostudies-arrayexpress
Project description:Environmental perturbations impact gene transcription. A subset of these transcriptional changes can be passed on to the next generation even in the absence of the initial stimulus. This phenomenon is known as transgenerational inheritance of environmental exposures (TIEE). Previous studies have mainly focused on what is transferred through the germ-line, i.e. DNA methylation, histone modifications, non-coding RNAs, etc. Nevertheless, the germ cells are not the only cells that are passed on from one generation to the next. The microbiota is also transmitted together with the host cells. In this study, we investigated the role of the gut microbiome in TIEE using Drosophila melanogaster as a model organism. We have reared flies in cold and control temperatures, 18 and 25 °C respectively, and looked at the transcriptional pattern in their offspring -grown in control condition- using RNA sequencing. To study the effect of the microbiome, we have carefully exchanged the parental feces introduced to the offspring. We observed genes responsive to thermal alteration, which have preserved their transcriptional status transgenerationally. A subset of these genes, mainly genes expressed in gut, were transcriptionally dependent on which microbiome they acquired. These findings show that the microbiota plays a previously unknown role in TIEE. Our study unveiled a new route for transmittance of environmental memories and thus represents an uncharted area to explore for researchers addressing non-genetic transgenerational inheritance.
2018-10-10 | GSE111116 | GEO
Project description:Environmental perturbations impact gene transcription. A subset of these transcriptional changes can be passed on to the next generation even in the absence of the initial stimulus. This phenomenon is known as transgenerational inheritance of environmental exposures (TIEE). Previous studies have mainly focused on what is transferred through the germ-line, i.e. DNA methylation, histone modifications, non-coding RNAs, etc. Nevertheless, the germ cells are not the only cells that are passed on from one generation to the next. The microbiota is also transmitted together with the host cells. In this study, we investigated the role of the gut microbiome in TIEE using Drosophila melanogaster as a model organism. We have reared flies in cold and control temperatures, 18 and 25 °C respectively, and looked at the transcriptional pattern in their offspring -grown in control condition- using RNA sequencing. To study the effect of the microbiome, we have carefully exchanged the parental feces introduced to the offspring. We observed genes responsive to thermal alteration, which have preserved their transcriptional status transgenerationally. A subset of these genes, mainly genes expressed in gut, were transcriptionally dependent on which microbiome they acquired. These findings show that the microbiota plays a previously unknown role in TIEE. Our study unveiled a new route for transmittance of environmental memories and thus represents an uncharted area to explore for researchers addressing non-genetic transgenerational inheritance.
2018-10-10 | GSE111048 | GEO
Project description:The transcriptome profiling of three samples in A. mongolicum Keng were studied using next-generation RNA sequencing under different drought stress conditions. This study aimed to identify genes of A. mongolicum Keng metabolism pathways that might be involved in this plant’s response to water deficit. 14.33 Gb high quality reads were assembled into 92,752 unigenes (unique transcripts), with a mean length of 1,303 bp. 76.26% had homologous genes in function databases.
2018-06-30 | GSE83457 | GEO