Ontology highlight
ABSTRACT:
PROVIDER: PRJNA778960 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16930760_1.fastq.gz | Fastqsanger.gz | |||
| SRR16930760_2.fastq.gz | Fastqsanger.gz | |||
| SRR16930761_1.fastq.gz | Fastqsanger.gz | |||
| SRR16930761_2.fastq.gz | Fastqsanger.gz | |||
| SRR16930762_1.fastq.gz | Fastqsanger.gz |
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Project description:MICROBIOTA OF SLICED COOKED HAM PACKAGED IN MODIFIED ATMOSPHERE THROUGHOUT THE SHELF-LIFE
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Project description:modENCODE_submission_3152 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP102(official name : OP102 genotype : unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HAM-1::EGFP fusion protein is expressed in the correct ham-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HAM-1 transcription factor. made_by : R Waterston ); Developmental Stage: fed L1; Genotype: unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene ham-1; Strain OP102(official name : OP102 genotype : unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HAM-1::EGFP fusion protein is expressed in the correct ham-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HAM-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
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Project description:modENCODE_submission_3842 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP102(official name : OP102 genotype : unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HAM-1::EGFP fusion protein is expressed in the correct ham-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HAM-1 transcription factor. made_by : R Waterston ); Developmental Stage: L4; Genotype: unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene ham-1; Strain OP102(official name : OP102 genotype : unc-119 (ed3); wgIs102 (ham-1::TY1 EGFP FLAG; unc-119(+)) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HAM-1::EGFP fusion protein is expressed in the correct ham-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HAM-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
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Project description:Comparative genomics of 16 strains of Leuconostoc isolated from cooked ham
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Project description:We report the human homologous microRNA profiles in food-grade, bovine-sourced sirloin, heart and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts) Deep miRNA sequencing of sirloin (raw and cooked), heart tissue (raw, cooked, and pastuerized, freeze-dried extracts) and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts), 3 replicates each process group
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Project description:The destructured meat syndrome is clearly detrimental to cooked ham industry but still poorly understood. The affected muscles lose their fibrous aspect and give a soft whitened muscular mass without any organised structure. Normal (n=7) and destructured (n=7) groups of pigs were allotted 36 h post-mortem based on meat L* values. Transcriptome analysis of Semimembranosus muscles was conducted to identify genes potentially involved in this syndrome. Fifty nine genes were differentially expressed (p < 0.01) and 90% of them were upregulated in the affected muscles. Myofibrillar proteins involved in the contractile properties (TNNC2 and TNNT3) or in the integrity (TMOD4) of the sarcomere were increased in the affected muscle. Moreover, eight genes encoding enzymes of glycolysis (ALDOA, ENO3, GAPDH, LDHA, PGAM2, PKM2) or glycogenolysis (PGM1, PYGM) were upregulated in the destructured muscles. These results suggest that both myofibrillar and sarcoplasmic proteins might be involved in the etiology of this syndrom. Keywords: meat quality comparison
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Project description:Human T-lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is an inflammatory neurodegenerative disease that affects motor, urinary, intestinal, and sensory functions. Typically, HAM/TSP is slowly progressive, but it may vary from limited motor disability after decades (very slow progression) to loss of motor function in a few years from disease onset (rapid). In this study, we aimed to identify prognostic biomarkers for HAM/TSP to support patient management. Thus, proteomic analysis of the cerebrospinal fluid (CSF) was performed with samples from HTLV-1 asymptomatic carriers (AC) (n=13) and HAM/TSP patients (n=21) with rapid, typical, and very slow progression using quantitative label-free liquid chromatography/tandem mass spectrometry. Enrichment analyses were also carried out to identify key biological processes associated with distinct neurological conditions in HTLV-1 infection. Candidate biomarkers were validated by ELISA in paired CSF and serum samples, and samples from HTLV-1-seronegative individuals (n=9) were used as controls. CSF analysis identified 602 proteins. Leukocyte/cell activation, immune response processes and neurodegeneration pathways were enriched in rapid progressors. Conversely, HTLV-1 AC and HAM/TSP patients with typical and very slow progression had enriched processes for nervous system development. Differential expression analysis showed that soluble vascular cell adhesion molecule 1 (sVCAM-1), chitotriosidase 1 (CHIT1), and cathepsin C (CTSC) were upregulated in HAM/TSP. However, only CHIT1 was significantly elevated after validation, particularly in HAM/TSP rapid progressors. In contrast, none of these biomarkers were altered in serum. Additionally, CSF CHIT1 levels in HAM/TSP patients positively correlated with the speed of HAM/TSP progression, defined as points in the IPEC-2 HAM/TSP disability scale per year of disease, and with CSF levels of phosphorylated neurofilament heavy chain, neopterin, CXCL5, CXCL10, and CXCL11. In conclusion, higher CSF levels of CHIT1 were associated with HAM/TSP rapid progression and correlated with other biomarkers of neuroinflammation and neurodegeneration. Therefore, we propose CHIT1 as a surrogate CSF biomarker to identify HAM/TSP patients with a worse prognosis.
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