Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22163200_1.fastq.gz | Fastqsanger.gz | |||
| SRR22163200_2.fastq.gz | Fastqsanger.gz | |||
| SRR22163201_1.fastq.gz | Fastqsanger.gz | |||
| SRR22163201_2.fastq.gz | Fastqsanger.gz | |||
| SRR22163202_1.fastq.gz | Fastqsanger.gz |
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Project description:The three groups of MH-S cells were control group, 20 μg/ml CuO NPs group, and 20 μg/ml CuO NPs + 10 μM TTM group. Total RNA of the MH-S cells were extracted using cell RNA isolation kit (Vazyme Biotech Co., Ltd, China). The number of MH-S cell sample for each group were three (n = 3 cell samples/group). All samples were sent to Majorbio Biotech (Shanghai, China) for transcriptome sequencing.
2025-01-17 | GSE287049 | GEO
Project description:The C57BL/6J mice were randomly divided into three groups: control group (n=3), CuO NPs group (n=3), and CuO NPs + TTM group (n=3). A suspension of 2 mg/mL CuO NPs in 100 μl sterile saline was directly once administered by intratracheal instillation in CuO NPs treatment group. Mice in control group received 100 μl sterile saline. In the CuO NPs + TTM intervention group, 0.02 mg/mL TTM was added to the daily drinking water. All mice were sacrificed on day 7. Total RNA of the mouse lung tissues were extracted using tissue RNA isolation kit. All samples were sent to Majorbio Biotech (Shanghai, China) for transcriptome sequencing.
2025-01-13 | GSE286391 | GEO
Project description:To determine microbiota composition associated with loss of KDM5 in intestine, we carried out 16S rRNA seq analyses of dissected intestine from wildtype and kdm5 mutant. [GSM2628181-GSM2628190]. A total of 78 operational taxonomic units (OTUs) were identified in the sequence data. There were about 15 genera much less abundant in kdm5 mutant compared to wildtype. The kdm5 mutant were sensitive to pathogen. To confirm the microbiota associated with loss of KDM5 in intestine, 16S rRNA of new flies were sequenced and analyzed by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China) [GSM3243472-GSM3243481]. A total of 107 operational taxonomic units (OTUs) were identified in the sequence data. There were about 20 genera much less abundant in kdm5 mutant compared to wildtype. To confirm the microbiota associated with loss of KDM5 drosophila feeding with Lactobacillus plantarum, 16S rRNA of kdm5 mutant flies were sequenced and analyzed by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China) [GSM3263522-GSM3263527]. A total of 92 operational taxonomic units (OTUs) were identified in the sequence data. To confirm the microbiota associated with KDM5 knockdown in intestine, 16S rRNA of Myo1A-Gal4TS/+ and Myo1A-Gal4TS/+;+/kdm5RNAi flies were sequenced and analyzed by Biomarker Co. Ltd. (Beijing, China). [GSM3507915-GSM3507924]. A total of 50 operational taxonomic units (OTUs) were identified in the sequence data. There was a significant different based on the genus level between two groups.
2019-02-08 | GSE98944 | GEO
Project description:Protein quantification by iTRAQ was carried out according to the method of Lu et al. (2017). Equally mixed peptides were analyzed by Majorbio Biopharm Technology Co., Ltd. The mixed peptides were preseparated via a C18 reversed-phase column and analyzed via liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS).
2020-03-11 | PXD018004 |
Project description:Purpose: To reveal the global regulatory genes of clinical strain, we performed comparative transcriptomic analyses of the SC5314 and JL01.Methods: We isolated a clinical Candida albicans strain JL01 (Jinling Hospital in Nanjing, China) from a 21-year-old man who presented to our hospital with recurrent cervical lymphadenitis. Cells of the JL01 and SC5314 were inoculated from overnight cultures by 1% into liquid YPD plus 10% serum medium at 37°C for 3 h. Cells were collected and total RNA was extracted as described. RNA-Seq analysis was performed by the company Majorbio (Shanghai, China). mRNA was purified, fragmented and used to synthesize cDNA. The library products were sequenced on the HiSeq 4000 platform using the HisSeq 4000 PE Cluster Kit and HisSeq 4000 SBS Kit.Results: 421 genes were significantly differentially regulated (P≤0.05, |log2FC|≥1) in JL01 compared with SC5314. Of these 421 DEGs (differentially expressed genes), 216 were up-regulated, and 205 were down-regulated. Conclusions: Together the clinical, morphological and biological analyses, we suggest that azole drug resistance, invasive defect and hypo-virulence of the JL01 strain may correlate with its contribution in chronic fungal infection.
2019-06-07 | GSE110291 | GEO
Project description:Purpose: The goals of this study are to compare NGS-derived gingiva transcriptome profiling (RNA-seq) of rats with or without experimental periodontitis and to explore the effect of curcumin/ZNPs hydrogel on the transcription of gingiva in rats with periodontitis. Methods: Six-week-old male Sprague-Dawley rats weighing 250–300 g (Dashuo company, China) were randomly divided into five groups (n = 5 per group): i) healthy control (Sham); ii) experimental periodontitis (EP); iii) experimental periodontitis treated by curcumin hydrogel (EP+Cur); iv) experimental periodontitis treated by ZNPs hydrogel (EP+ZNPs); v) experimental periodontitis treated by curcumin/ZNPs hydrogel (EP+Cur/ZNPs). Animals were anesthetized with isoflurane (5% induction, 2% maintenance, sealed until euthanized) and intramuscularly administered 0.1 mL penicillin (40,000 U/mL) for 7 days. EP was established by ligature with 4–0 silk thread around the bilateral maxillary first molars. Three days after ligature, P. gingivalis ATCC 33277 (107 CFU/mL) was smeared onto silk twice. Rats in the EP+Cur group were treated by curcumin hydrogel (Dalian Meilun Biotech Co., Ltd), EP+ZNPs group were treated by ZNPs hydrogel (Shanghai aladdin Biochemical Technology Co., Ltd), and EP+Cur/ZNPs group were treated by curcumin/ZNPs hydrogel. Total RNA was extracted with TRIzol® reagent (Thermo Fisher Scientific, Inc.). The TruSeq Stranded total RNA with RiboZero Plus kit (IIlumina, San Diego, CA) was used to obtain a sequencing library from 1μg of total RNA. Eukaryotic mRNA sequencing was performed on Illumina Novaseq 6000 by Shanghai Majorbio Bio-pharm Technology Co., Ltd. Raw gene counts with a minimum of two counts per million in at least one sample were used for downstream analyses. Differentially expressed genes were determined by the DESeq2 Bioconductor/R package. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Transcriptome analysis of 25 samples was completed in this project, and a total of 184.45 Gb Clean Data was obtained. The Clean Data of each sample reached 5.92 Gb and above, and the Q30 base percentage was above 92.75%. The Clean Reads of each sample were compared with the designated reference genome, and the comparison rate ranged from 93.38% to 95.1%. A total of 26188 expressed genes were detected in this analysis, including 22736 known genes and 3452 new genes; 57,961 expressed transcripts, including 29332 known transcripts and 28629 new transcripts. Conclusions: Our study represents the first detailed analysis of gingival transcriptomes of rats treated by Cur/ZnO gel, with biologic replicates, generated by RNA-seq technology.
2022-01-01 | GSE185147 | GEO