№ files_lp_3_process_7_096900
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Methodological description of sequencing data processing, genome alignment, peak identification, and differential expression analysis for ChIP-seq and RNA-seq experiments in Drosophila melanogaster.
Organism: Drosophila melanogaster
Data types: ChIP-seq and RNA-seq
Experimental conditions: wt and cuff homozygous mutant ovaries
Replicates: Three replicates per condition for RNA-seq and Pol2 ChIP-seq; two replicates for Cuff ChIP-seq
Reference genome version: FlyBase v5.41
Transposon dataset versions: FlyBase v9.41 and D_mel_transposon_sequence_set.fasta
Software and tools: cutadapt v1.2.1; bowtie2 v2.0.0-beta7; samtools v0.0.19; MACS2 v2.0.10.20130501; tophat2 v2.0.8; bedtools v2.17.0; DESeq v1.16.0
Statistical methods: IDR protocol with threshold 0.05; Benjamini-Hochberg multiple testing correction
Genomic features analyzed: protein-coding genes; rRNA; snRNA; snoRNA; piRNA clusters; canonical transposons
Number of Cuff peaks (genome-wide): 937 at IDR 0.05
Number of Cuff peaks (transposons): 149 at q-value < 0.05
Visualization platform: UCSC Genome Browser
Scope: Genome-wide alignment, peak detection, and differential expression analysis
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Drosophila melanogaster as a Substitute Model Organism for Autism Spectrum Disorder
Year: Not specified
Field: Neurodevelopmental Disorders Research
Topic: Use of animal models in Autism Spectrum Disorder studies
Document Type: Review Article
Subject: Drosophila melanogaster as a model organism for ASD research
Keywords: Animal model; Autism Spectrum Disorder; Drosophila melanogaster; Fruit fly; Neurodevelopmental disease
Scientific Focus: Genetics, neurodevelopment, and experimental disease modeling
Related Conditions: Autism Spectrum Disorder, Alzheimer’s disease, Parkinson’s disease
Historical References: Introduction of Drosophila into biomedical research in the early 1900s
Researchers Mentioned: Eugen Bleuler; Michele Markstein; Amos Abolaji; Charles Woodworth; Thomas Hunt Morgan
Institutions Referenced: Columbia University; Centers for Disease Control; World Health Organization
Research Context: Evaluation of limitations of established animal models and discussion of fruit flies in ASD-related studies
Statistical estimates of multiple transcription factors binding site clusters in the model plant genomes based on ChIP-seq data
Year: 2023
Region / City: Novosibirsk, Moscow
Topic: Transcription factor binding sites, ChIP-seq, plant genomes
Document type: Research article
Organization / Institution: Novosibirsk State University, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Moscow Witte Financial University, Financial Academy under the Government of the Russian Federation, Moscow State Technical University of Civil Aviation, Agrarian and Technological Institute, Peoples’ Friendship University of Russia, I.M. Sechenov First Moscow State Medical University
Author: A.I. Dergilev, N.G. Orlova, O.B. Dobrovolskaya, Y.L. Orlov
Target audience: Researchers, bioinformaticians, molecular biologists
Period of validity: N/A
Approval date: N/A
Modification date: N/A
Culture of mouse ES cells and histone modification analysis via LC-MS and ChIP-seq
Year: 2020
Region / City: Rockefeller University, McGill University
Subject: Mouse embryonic stem cell culture, histone modifications, chromatin immunoprecipitation sequencing
Document Type: Research Methodology
Organization / Institution: Rockefeller University, McGill University
Author: Not specified
Target Audience: Researchers in molecular biology and cell biology
Period of Action: Not specified
Approval Date: Not specified
Date of Changes: Not specified
Context: Methodology for culturing mouse ES cells, histone modification analysis, and chromatin immunoprecipitation sequencing techniques used in biological experiments.
Construction of RAD16-Deleted Yeast Strains and Genome-Wide Chromatin Analysis Using ChIP-seq and MNase-seq
Year: 2026
Organism: Saccharomyces cerevisiae
Gene Targeted: RAD16
Methods: Yeast strain construction, UV irradiation, chromatin preparation, ChIP-seq, MNase-seq, library preparation
Techniques: Lithium-acetate transformation, PCR, chromatin immunoprecipitation, micrococcal nuclease digestion, DNA sequencing library preparation
Authors: Reed et al., Yu, Teng, Kent, Powel
Sample Type: Yeast cells
Experimental Conditions: UV-C irradiation, formaldehyde crosslinking, MNase digestion
Storage: Glycerol stocks, snap-frozen cells
Sequencing Platforms: ChIP-seq libraries prepared according to Life Technologies protocol
Topics: Bioinformatic melanogaster ChIP-seq