Galliformes sp.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA324492 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3630010_1.fastq.gz | Fastqsanger.gz | |||
| SRR3630010_2.fastq.gz | Fastqsanger.gz | |||
| SRR3630011_1.fastq.gz | Fastqsanger.gz | |||
| SRR3630011_2.fastq.gz | Fastqsanger.gz | |||
| SRR3630012_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 22 |
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Project description:The transcript profiles of Nesterenkonia sp. AN1 grown at 5 ºC (Cold) and 21 ºC (Topt) were acccessed to evaluate the cold reposnse of this Antarctic Nesterenkonia strain. The strain was grown in triplicates at the optimum growth temperature of 21 ºC and a test temperature of 5 ºC. Total RNA was extracted from two replicate samples for each treatment condition and the total RNA was enriched for mRNA. RNA-seq was done using Illumina Miseq platform at Inqaba Biotech, South Africa. The reads were mapped against the genome sequence of Nesterenkonia sp. AN1 (obtained from NCBI database) and assesed for differeential gene expression using CLC Genomics Workbench 7.5. Evaluation of RNA-seq data for Nesterenkonia sp. AN1 at 5 ºC (Cold) and 21 ºC (Topt) in two biological replicates
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Project description:By applying Illumina Novaseq 6000, Chlorella sp. TLD6B cells of the control group on day zero and 18, as well as under low salt stress (NaCl1) and under high salt stress (NaCl2) on day 18 were selected for transcriptome sequencing analysis. Meanwhile, 0.05 g/mL ( PEG1) and 0.1 g/mL PEG-6000 (medium for drought stress, PEG2 ) were used to prepare the drought-stressed Chlorella sp. TLD6B cells. Each treatment had two replicates. Clean data were filtered after the removal of adapters, poly-N strands, and low-quality reads. There were no reference genomes for Chlorella sp. TLD6B, and de novo assembly for clean reads was performed by using Trinity. The sequences were compared with databases such as NR, NT, Swiss-Pro, GO, KEGG, PFAM, and KOG using Blast X (e-value ≤ 10-5). The GO annotation of unigenes was obtained using BLAST2GO. FPKM method was used for the analysis of gene expression levels (Trapnell et al., 2010). Out of six samples, a total of 963,078,184 raw reads were generated. A total of 947,225,244 clean reads were obtained based on the base quality score and read length. Meanwhile, the GC percentage in clean reads reached nearly 66.0%, with Q20 being above 96%. A total of 219,577 transcripts with an average length of 1,394 bp were obtained. In total, 155,503 non-redundant unigenes were assembled for the following analyses. The length of the unigenes ranged from 200 bp to 23,825 bp, with an average length of 1,842 bp. Under different salt stress, verification had been conducted with qRT-PCR on nine unigenes of different pathways, which were related to lipid metabolism. The detection results by qRT-PCR were highly correlated with RNA-Seq results (r = 0.890, r2 = 0.791), which indicated that the RNA-Seq data of Chlorella sp. TLD6B under salt stress were accurate and reliable. Our study represents the first detailed analysis of Chlorella sp. TLD6B under salt stress transcriptomes. Hierarchical clustering of differentially expressed genes uncovered several currently uncharacterized genes that may contribute to the function about lipid accumulation of Chlorella sp. TLD6B under salt stress.
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Project description:In humans there are two surfactant protein A (SP-A) functional genes SFTPA1 and SFTPA2 encoding innate immune molecules, SP-A1 and SP-A2, respectively, with numerous genetic variants each. SP-A interacts and regulates many of the functions of alveolar macrophages (AM). It is shown that SP-A variants differ in their ability to regulate the AM miRNome in response to oxidative stress (OxS). Because humans have both SP-A gene products, we were interested to determine the combined effect of co-expressed SP-A1/SP-A2 (co-ex) in response to ozone (O3) induced OxS on AM miRNome. Human transgenic (hTG) mice, carrying both SP-A1/SP-A2 (6A2/1A0, co-ex) and SP-A- KO were utilized. The hTG and KO mice were exposed to filtered air (FA) or O3 and miRNA levels were measured after AM isolation with or without normalization to KO. We found: (i) The AM miRNome of co-ex males and females in response to OxS to be largely downregulated after normalization to KO, but after Bonferroni multiple comparison analysis only in females the AM miRNome remained significantly different compared to control (FA); (ii) The targets of the significantly changed miRNAs were downregulated in females and upregulated in males; (iii) Several of the validated mRNA targets were involved in pro-inflammatory response, anti-apoptosis, cell cycle, cellular growth and proliferation; (iv) The AM of SP-A2 male, shown, previously to have major effect on the male AM miRNome in response to OxS, shared similarities with the co-ex, namely in pathways involved in the pro-inflammatory response and anti-apoptosis but also exhibited differences with the cell-cycle, growth, and proliferation pathway being involved in co-ex and ROS homeostasis in SP-A2 male. We speculate that the presence of both gene products versus single gene products differentially impact the AM responses in males and females in response to OxS.
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Project description:BACKGROUND: Human SP-A1 and SP-A2, encoded by SFTPA1 and SFTPA2 and their genetic variants differentially impact alveolar macrophage (AM) functions and regulation, including the miRNome. We investigated whether miRNome differences previously observed between AM from SP-A2 and SP-A1/SP-A2 mice are due to continued qualitative differences or a delayed response of mice carrying a single gene. METHODS: Human transgenic (hTG) mice, carrying SP-A2 or both SP-A genes and SP-A-KO mice were exposed to filtered air (FA) or O3. AM miRNA levels, target gene expression and pathways determined 18 h after O3 exposure. RESULTS: We found: (a) Differences in miRNome due to sex, SP-A genotype, and exposure; (b) miRNome of both sexes was largely downregulated by O3 ; co-ex had fewer changed (≥2X) miRNAs than either group. (c) the number and direction of expression of genes with significant changes in males and females in co-ex is almost the opposite of those in SP-A2; (iv) The same pathways were found in the studied groups; (e) O3 exposure attenuated sex differences; a higher number of genotype-dependent and genotype-independent miRNAs was common in both sexes after O3 exposure. CONCLUSION: Qualitative differences between SP-A2 and co-ex persist 18 h post-O3, and O3 attenuates sex differences.
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