Project description:Transcriptional profiling with samples from BT549 cells that were infected with control or NFIL3 shRNA Two condition experiment: control (scr) shRNA (two replicates) and NFIL3 shRNA (two replicates)
Project description:This SuperSeries is composed of the following subset Series: GSE31425: BT549 cells with control or NFIL3 shRNA treatment GSE31426: HEK293 cells with control or NFIL3 shRNA treatment Refer to individual Series
Project description:The budding yeast Saccharomyces cerevisiae was used to study gene expression changes with step-wise reduction of nitrogen at a constant specific growth rate. Since nitrogen is critical for amino acid and nucleotide synthesis, reducing nitrogen content forces cells to reduce its proteome and transcriptome size.
Project description:Comparison of RNA levels between UACC-62 melanoma cell line and UACC-62 TRIB2 CRISPR/Cas9 knock-out cells. Three biological replicates of each cell line were analysed by bulk RNA-seq.
Project description:Vacuum-assisted biopsy (VAB) from normal breast tissue were obtained from women participating in the Breast Cancer - Anti-Progestin Prevention Study 1 (BC-APPS1). A baseline VAB was performed in the luteal phase of the menstrual cycle and a second VAB was performed after a 12-week anti-progestin (ulipristal acetate, daily 5mg oral tablet) treatment. For each VAB a small piece of breast tissue was snap frozen in theatre. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) and indexed PolyA libraries were prepared using 100ng of total RNA. Paired-end 75bp sequencing was carried out on a NextSeq 500 sequencer (Illumina Inc.).
Project description:Arginine-rich mixed charge domains (R-MCDs) contribute to and alter the properties of nuclear speckles. We are interested in how this affects the retention of poly-adenylated mRNAs in the nucleus. This experiment tests how the expression of the R-MCD of PPIG influences the nuclear-cytoplasmic distribution of mRNAs over time. Specifically, a HeLa cell line in which PPIG expression is driven by a doxycycline-inducible promoter was used, and doxycycline was added for 0, 4, 8 or 12 hours. This time course was performed in triplicates. Nuclear and cytoplasmic fractions were collected from the cells and RNA was extracted. 3' end sequencing libraries were produced by fragmenting the RNA and introducing Illumina adapters via a oligo-dT-primed reverse transcription and template switching oligo approach. The data indicate that mRNAs containing long, multivalent GA-rich regions in their coding sequences are more retained in the nucleus over time following expression of the R-MCD. The files provided in this accession have not been trimmed to remove adapters, 3' poly-A sequences, UMIs or G-stretches from TSOs. The data was analysed using nf-core/rna-seq using the following command: nextflow run nf-core/rnaseq \\ --input samplesheet.csv \\ --fasta '/camp/lab/ulej/home/users/farawar/genomes/hs/fasta/GRCh38.primary_assembly.genome.fa' \\ --gtf '/camp/lab/ulej/home/users/farawar/genomes/hs/annotation/gencode.v29.annotation.gtf' \\ --salmon_index '/camp/lab/ulej/home/users/farawar/genomes/hs/salmon_index/salmon_index' \\ --gencode \\ --pseudo_aligner salmon \\ --with_umi \\ --umitools_bc_pattern NNNNN \\ --clip_r1 5 \\ -resume \\ -profile crick \\ --outdir nf-core-results \\ -c extraconfig.config With the extra config file containing: withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' { ext.args = '--noLengthCorrection' } Therefore removing the first 5 nucleotides as UMI sequences and the following 5 nucleotides as they contain G-stretches from the template-switching oligo.
Project description:CLK kinases phosphorylate the SR domains of SR proteins. The phosphorylation state controls the localisation of SR proteins, with hypo-phosphorylated SR proteins being more enriched in nuclear speckles. We identified a set of mRNAs that are bound by SR proteins in the nucleus, and we wondered whether the activity of CLK kinases would alter the nuclear export of those mRNAs. We therefore treated HeLa cells with the CLK inhibitor CLK-IN-T3 or with DMSO for 8 hours and then collected nuclear and cytoplasmic fractions. We sequenced the 3' ends of poly-adenylated mRNAs in these fractions. The samples in this accession have been trimmed to remove Illumina adapters, 3' poly-A stretches, 5' G stretches from the TSO oligo and the UMIs have been moved to the header. The data was then processed using the following nf-core/rnaseq call: nextflow run nf-core/rnaseq \\ --input 'samplesheet.csv' \\ --fasta '/camp/lab/ulej/home/users/farawar/genomes/hs/fasta/GRCh38.primary_assembly.genome.fa' \\ --gtf '/camp/lab/ulej/home/users/farawar/genomes/hs/annotation/gencode.v29.annotation.gtf' \\ --salmon_index '/camp/lab/ulej/home/users/farawar/genomes/hs/salmon_index/salmon_index' \\ --gencode \\ --pseudo_aligner salmon \\ -resume \\ -profile crick \\ --outdir nf-core \\ -c extraconfig.config With the extra config file containing the following: withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' { ext.args = '--noLengthCorrection' }
Project description:Tumor-associated macrophages (TAMs) play important roles in cancer progression and resistance to therapy. Recent studies have shown that TAMs include both long-lived resident tissue macrophages (RTMs) and short-lived monocyte-derived macrophages (MDMs) with limited proliferative potential. RTMs and MDMs have been suggested to play divergent roles in tumorigenesis; RTMs are aligned with trophic functions, whereas MDMs are enriched for immune-regulatory pathways. Here we established a specific role for the AP-1 factor JUN in the differentiation and maintenance of MDMs and the specification of pro-tumoral trophic functions during tumor development. Alternatively, the immune-regulatory functions of TAMs remained JUN-independent. JUN was required for the specification and maintenance of pro-tumoral TAMs that support blood vessel maturation and tumor growth. Single-cell transcriptomics analysis uncovered the alternative fates for tumor-infiltrating monocytes and the development of distinct TAM states associated with trophic functions and immune-regulation. These studies demonstrate an important role for JUN in the specification of pro-tumoral monocyte-derived TAMs that could offer opportunities for selective TAM-targeted therapies for cancer.
Project description:Spodoptera frugiperda is a major crop pest worldwide. In its native are - the american continent- two mitochondrial strains have been described with different host-plant preferences: the corn strain (or SfC) and the rice strain (SfR). We have previously showed that constitutive differences existed between the strains at the transcriptomic level and were associated to mitochondrial differential expression. To determine whether maternal inheritance was impacting overall expression variations between the strains and eventually their physiological differences, we performed again RNA-seq experiment on the two strains and their F1 reciprocal hybrids (CR and RC) in triplicate, in laboratory conditions when fed on artificial diet and not on plant diet as to avoid the induced challenge by the plant diet on gene expression and focus only on the intrinsic differences.
Project description:To investigate whether ER stress underpins the secretion of mis-glycosylated glycoproteins by trophoblast, we treated trophoblast-like BeWo cells with the ER stress inducer thapsigargin (Tg), an inhibitor specific for sarco/endoplasmic reticulum Ca2+-ATPase.