Lbraz_isoseq_replicates
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB60504 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11004829.fastq.gz | Fastqsanger.gz | |||
| ERR11004830.fastq.gz | Fastqsanger.gz | |||
| ERR11004831.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:The main objective of this study is to identify the list of genes differentially expressed between infected with Leishmania braziliensis and non-infected macrophage cultures based on gene expression microarray profiling The dataset is comprised by the expression profile of 6 samples from three independent experiments and each experiment had three technical replicates. 3 of the 6 samples were U937 derived macrophages infected by Leishmania braziliensis and the other 3 were U937 derived macrophages without infection with Leishmania braziliensis. A total of 18 microarrays analysis were performed.
2015-06-10 | E-GEOD-61211 | biostudies-arrayexpress
Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.
2013-10-30 | E-GEOD-51861 | biostudies-arrayexpress
Project description:We evaluated the trancriptome of primary cutaneous leisions caused by infection with Leishmania braziliensis. mRNA-seq technique was used to study the trancriptome of both host and parasite. A total of 10 samples was obtained from primary skin ulcers of two extreme clinical forms of American tegumentary leishmaniasis: (i) individuals that after antimonial treatment cured completely (localized cutaneous leishmaniasis - LCL, n=5) and (ii) individuals that developed mucosal lesions in naso and oropharynx areas long after initial healing of the cutaneous lesion (mucosal leishmaniasis - ML, n=5). The sequencing generated an average of 13+ 5 million reads per samples. The reads were aligned to Homo sapiens (USCS - hg19) and to Leishmania braziliensis (Wellcome Trust Sanger Institute - V2_29072008) genomes. Approximately, 15,000 human genes could be detected in the samples. Low amount of L. braziliensis reads did not allow the evaluation of parasite gene expression. LCL and ML samples showed different patterns of gene expression, indicating a more robust immune response in LCL individuals. In summary, this study demonstrated that next-generation sequencing can be used for identification of potentially important biological pathways and drug targets in the host-response to L. braziliensis infection and for characterization of a gene expression signature that could be used to predict the disease outcome. Moreover, we also showed the ability of this technique in, simultaneously, sequence host and pathogen mRNA.
2012-10-24 | GSE33601 | GEO
Project description:The main objective of this study is to identify the list of genes differentially expressed between infected with Leishmania braziliensis and non-infected macrophage cultures based on gene expression microarray profiling
2015-06-10 | GSE61211 | GEO
Project description:Throughout their life cycle, Leishmania parasites, causative agents of the life-threatening leishmaniasis, alternate between the phlebotomine vector and the mammalian host, encountering significant environmental changes that require rapid adaptation in gene expression for survival. In the absence of conventional promoters for RNA polymerase II and given the polycistronic nature of transcription, gene expression regulation in Leishmania occurs primarily at the post-transcriptional level. Although putative regulatory non-coding RNAs (ncRNAs) have been detected in the transcriptomes of L. braziliensis and other trypanosomatids, their functional role remains poorly understood. Recognizing the critical role of RNA structure in cellular systems, we sought to identify evolutionarily conserved RNA structures. We performed a genome-wide alignment of L. braziliensis genome with closely related genomes, predicting 142 conserved RNA structures, among which 38 overlap with previously identified ncRNA transcripts. One of the putative ncRNAs with a conserved structure, a 407-nucleotide long ncRNA (lncRNA45), was previously shown to be differentially expressed across the lifecycle stages of L. braziliensis. Here, we conducted a functional characterization of lncRNA45 using a knockout line, demonstrating that the transcript is crucial for parasite fitness. Reintroduction of the original lncRNA45 sequence restored the fitness of the knockout cell line to parental levels, whereas a sequence carrying a single nucleotide substitution in the structured locus did not. In vitro pull-down assays with both the original and modified versions of lncRNA45 revealed differences in the profile of lncRNA-binding proteins. Our results indicate that lncRNA45 is enrolled cellular processes of L. braziliensis promastigotes, and this activity, along with its interaction with proteins, depends on its secondary structure. This study underscores the importance of structured lncRNAs in Leishmania and advocates for further research into their regulatory roles and therapeutic potential.
2025-08-18 | GSE287035 | GEO
Project description:We evaluated the trancriptome of primary cutaneous leisions caused by infection with Leishmania braziliensis. mRNA-seq technique was used to study the trancriptome of both host and parasite. A total of 10 samples was obtained from primary skin ulcers of two extreme clinical forms of American tegumentary leishmaniasis: (i) individuals that after antimonial treatment cured completely (localized cutaneous leishmaniasis - LCL, n=5) and (ii) individuals that developed mucosal lesions in naso and oropharynx areas long after initial healing of the cutaneous lesion (mucosal leishmaniasis - ML, n=5). The sequencing generated an average of 13+ 5 million reads per samples. The reads were aligned to Homo sapiens (USCS - hg19) and to Leishmania braziliensis (Wellcome Trust Sanger Institute - V2_29072008) genomes. Approximately, 15,000 human genes could be detected in the samples. Low amount of L. braziliensis reads did not allow the evaluation of parasite gene expression. LCL and ML samples showed different patterns of gene expression, indicating a more robust immune response in LCL individuals. In summary, this study demonstrated that next-generation sequencing can be used for identification of potentially important biological pathways and drug targets in the host-response to L. braziliensis infection and for characterization of a gene expression signature that could be used to predict the disease outcome. Moreover, we also showed the ability of this technique in, simultaneously, sequence host and pathogen mRNA. Examination of 10 fragments of cutaneous lesions: 5 from localized cutaneous leishmaniasis patients and 5 from mucosal leishmaniasis patients.
2012-10-24 | E-GEOD-33601 | biostudies-arrayexpress
Project description:Leishmania braziliensis infection results in inflammation and skin injury, with highly variable and unpredictable clinical outcomes. Here, we investigated the potential impact of microbiota on infection-induced inflammatory responses and disease resolution by conducting an integrated analysis of the skin microbiome and host transcriptome on a cohort of 62 L. braziliensis-infected patients. We found that overall bacterial burden and microbiome configurations dominated with Staphylococcus spp. were associated with delayed healing and enhanced inflammatory responses, especially by IL-1 family members. Dual RNA-seq of human lesions revealed that high lesional S. aureus transcript abundance was associated with delayed healing and increased expression of IL-1β. This cytokine was critical for modulating disease outcome in L. braziliensis-infected mice colonized with S. aureus, as its neutralization reduced pathology and inflammation. These results implicate the microbiome in cutaneous leishmaniasis disease outcomes in humans and suggest host-directed therapies to mitigate the inflammatory consequences.
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