ScRNAseq of four syngeneic human melanoma cell lines (two replicate per cell line) to study mechanisms of resistance to the BRAF inhibitor vemurafenib
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER: Camille Stephan-Otto Attolini
PROVIDER: E-MTAB-12412 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. This neural stem cell potential is known to decline with age in the mouse. Here, we microdissected and dissociated into single cells the central canal region from the spinal cord of 4 young adult (3-to-4-month old) and 4 aged (18-to-19-month old) C57BL/6J mice to profile the transcriptomes of cells in and around the central canal using 10x Genomics technology.
2022-12-13 | E-MTAB-11561 | biostudies-arrayexpress
Project description:Human embryonic stem cell (hESC) line Man-13 was edited by CRISPR resulting in a hESC line carrying a heterozygous frameshift mutation with a premature stop codon in exon-1 of the HNF1B gene ([p.Val61Argfs*18]), functionally equivalent to a heterozygous whole-gene deletion. Kidney organoids were then created by differentiation (as per Takasato et al, 2015; Bantounas et al, 2018; Bantounas et al 2021) of this line and an isogenic non-mutant control line. Single-cell RNAseq (scRNAseq) was then performed on day-25 of differentiation to identify transcriptomic differences, as well as differences in identity and numbers of the cell populations comprising the organoids, with the aim of mechanistically explaining developmental aberrations observed in patients with mutations in this gene.
2024-04-30 | E-MTAB-13500 | biostudies-arrayexpress
Project description:The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus. To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray. Maximum differential gene expression was observed at 48 hpi in both genotypes with ZY821 responding more quickly than Westar. Specific sets of genes exhibited higher levels of expression at the earlier stages of the infection (6-12 hpi), including genes encoding defense-associated proteins such as chitinases, glucanases, osmotins and lectins and genes encoding transcription factors belonging to the zinc finger, WRKY, AP2, and MYB classes. Genes encoding enzymes involved in JA, ethylene, and auxin synthesis were induced in both genotypes, as were those for gibberellin degradation. Changes in metabolic pathways affecting carbohydrate and energy metabolism appeared to be directed toward shuttling carbon reserves to the TCA cycle. Genes involved in glucosinolate and phenylpropanoid biosynthesis were highly up-regulated suggesting that secondary metabolites are also important components of the response to S. sclerotiorum in B. napus. Keywords: Time course, infected vs mock infected Time course experiment (6hr, 12 hr, 24 hr, 48 hr, 72 hrs), sclerotinia infected vs mock-infected. Biological replicates: 3, independently harvested. Technical replicates: 2, dye swapped within each time for each biological replicate (total 6 slides per time point) time after innoculation: 6 hours: zy 6h inf vs control rep1, zy 6h control vs inf rep1, zy 6h inf vs control rep2, zy 6h control vs inf rep2, zy 6h inf vs control rep3, zy 6h control vs inf rep3 time after innoculation: 12 hours: zy 12h inf vs control rep1, zy 12h control vs inf rep1, zy 12h inf vs control rep2, zy 12h control vs inf rep2, zy 12h inf vs control rep3, zy 12h control vs inf rep3 time after innoculation: 24 hours: zy 24h inf vs control rep1, zy 24h control vs inf rep1, zy 24h inf vs control rep2, zy 24h control vs inf rep2, zy 24h inf vs control rep3, zy 24h control vs inf rep3 time after innoculation: 48 hours: zy 48h inf vs control rep1, zy 48h control vs inf rep1, zy 48h inf vs control rep2, zy 48h control vs inf rep2, zy 48h inf vs control rep3, zy 48h control vs inf rep3 time after innoculation: 72 hours: zy 72h inf vs control rep1, zy 72h control vs inf rep1, zy 72h inf vs control rep2, zy 72h control vs inf rep2, zy 72h inf vs control rep3, zy 72h control vs inf rep3 biological replicate: zy 6h inf vs control rep1, zy 6h inf vs control rep2, zy 6h inf vs control rep3 biological replicate: zy 6h control vs inf rep1, zy 6h control vs inf rep2, zy 6h control vs inf rep3 technical replicate - labeled-extract: zy 6h inf vs control rep1, zy 6h control vs inf rep1 technical replicate - labeled-extract: zy 6h inf vs control rep2, zy 6h control vs inf rep2 technical replicate - labeled-extract: zy 6h inf vs control rep3, zy 6h control vs inf rep3 biological replicate: zy 12h inf vs control rep1, zy 12h inf vs control rep2, zy 12h inf vs control rep3 biological replicate: zy 12h control vs inf rep1, zy 12h control vs inf rep2, zy 12h control vs inf rep3 technical replicate - labeled-extract: zy 12h inf vs control rep1, zy 12h control vs inf rep1 technical replicate - labeled-extract: zy 12h inf vs control rep2, zy 12h control vs inf rep2 technical replicate - labeled-extract: zy 12h inf vs control rep3, zy 12h control vs inf rep3 biological replicate: zy 24h inf vs control rep1, zy 24h inf vs control rep2, zy 24h inf vs control rep3 biological replicate: zy 24h control vs inf rep1, zy 24h control vs inf rep2, zy 24h control vs inf rep3 technical replicate - labeled-extract: zy 24h inf vs control rep1, zy 24h control vs inf rep1 technical replicate - labeled-extract: zy 24h inf vs control rep2, zy 24h control vs inf rep2 technical replicate - labeled-extract: zy 24h inf vs control rep3, zy 24h control vs inf rep3 biological replicate: zy 48h inf vs control rep1, zy 48h inf vs control rep2, zy 48h inf vs control rep3 biological replicate: zy 48h control vs inf rep1, zy 48h control vs inf rep2, zy 48h control vs inf rep3 technical replicate - labeled-extract: zy 48h inf vs control rep1, zy 48h control vs inf rep1 technical replicate - labeled-extract: zy 48h inf vs control rep2, zy 48h control vs inf rep2 technical replicate - labeled-extract: zy 48h inf vs control rep3, zy 48h control vs inf rep3 biological replicate: zy 72h inf vs control rep1, zy 72h inf vs control rep2, zy 72h inf vs control rep3 biological replicate: zy 72h control vs inf rep1, zy 72h control vs inf rep2, zy 72h control vs inf rep3 technical replicate - labeled-extract: zy 72h inf vs control rep1, zy 72h control vs inf rep1 technical replicate - labeled-extract: zy 72h inf vs control rep2, zy 72h control vs inf rep2 technical replicate - labeled-extract: zy 72h inf vs control rep3, zy 72h control vs inf rep3
2010-05-06 | E-GEOD-13256 | biostudies-arrayexpress
Project description:The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus. To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray. Maximum differential gene expression was observed at 48 hpi in both genotypes with ZY821 responding more quickly than Westar. Specific sets of genes exhibited higher levels of expression at the earlier stages of the infection (6-12 hpi), including genes encoding defense-associated proteins such as chitinases, glucanases, osmotins and lectins and genes encoding transcription factors belonging to the zinc finger, WRKY, AP2, and MYB classes. Genes encoding enzymes involved in JA, ethylene, and auxin synthesis were induced in both genotypes, as were those for gibberellin degradation. Changes in metabolic pathways affecting carbohydrate and energy metabolism appeared to be directed toward shuttling carbon reserves to the TCA cycle. Genes involved in glucosinolate and phenylpropanoid biosynthesis were highly up-regulated suggesting that secondary metabolites are also important components of the response to S. sclerotiorum in B. napus. Keywords: Time course, and infected vs mock infected Time course experiment (6hr, 12 hr, 24 hr, 48 hr, 72 hrs), sclerotinia infected vs mock-infected. Biological replicates: 3, independently harvested. Technical replicates: 2, dye swapped within each time for each biological replicate (total 6 slides per time point) time after innoculation: 6 hours: westar 6h inf vs control rep1, westar 6h control vs inf rep1, westar 6h inf vs control rep2, westar 6h control vs inf rep2, westar 6h inf vs control rep3, westar 6h control vs inf rep3 time after innoculation: 12 hours: westar 12h inf vs control rep1, westar 12h control vs inf rep1, westar 12h inf vs control rep2, westar 12h control vs inf rep2, westar 12h inf vs control rep3, westar 12h control vs inf rep3 time after innoculation: 24 hours: westar 24h inf vs control rep1, westar 24h control vs inf rep1, westar 24h inf vs control rep2, westar 24h control vs inf rep2, westar 24h inf vs control rep3, westar 24h control vs inf rep3 time after innoculation: 48 hours: westar 48h inf vs control rep1, westar 48h control vs inf rep1, westar 48h inf vs control rep2, westar 48h control vs inf rep2, westar 48h inf vs control rep3, westar 48h control vs inf rep3 time after innoculation: 72 hours: westar 72h inf vs control rep1, westar 72h control vs inf rep1, westar 72h inf vs control rep2, westar 72h control vs inf rep2, westar 72h inf vs control rep3, westar 72h control vs inf rep3 biological replicate: westar 6h inf vs control rep1, westar 6h inf vs control rep2, westar 6h inf vs control rep3 biological replicate: westar 6h control vs inf rep1, westar 6h control vs inf rep2, westar 6h control vs inf rep3 technical replicate - labeled-extract: westar 6h inf vs control rep1, westar 6h control vs inf rep1 technical replicate - labeled-extract: westar 6h inf vs control rep2, westar 6h control vs inf rep2 technical replicate - labeled-extract: westar 6h inf vs control rep3, westar 6h control vs inf rep3 biological replicate: westar 12h inf vs control rep1, westar 12h inf vs control rep2, westar 12h inf vs control rep3 biological replicate: westar 12h control vs inf rep1, westar 12h control vs inf rep2, westar 12h control vs inf rep3 technical replicate - labeled-extract: westar 12h inf vs control rep1, westar 12h control vs inf rep1 technical replicate - labeled-extract: westar 12h inf vs control rep2, westar 12h control vs inf rep2 technical replicate - labeled-extract: westar 12h inf vs control rep3, westar 12h control vs inf rep3 biological replicate: westar 24h inf vs control rep1, westar 24h inf vs control rep2, westar 24h inf vs control rep3 biological replicate: westar 24h control vs inf rep1, westar 24h control vs inf rep2, westar 24h control vs inf rep3 technical replicate - labeled-extract: westar 24h inf vs control rep1, westar 24h control vs inf rep1 technical replicate - labeled-extract: westar 24h inf vs control rep2, westar 24h control vs inf rep2 technical replicate - labeled-extract: westar 24h inf vs control rep3, westar 24h control vs inf rep3 biological replicate: westar 48h inf vs control rep1, westar 48h inf vs control rep2, westar 48h inf vs control rep3 biological replicate: westar 48h control vs inf rep1, westar 48h control vs inf rep2, westar 48h control vs inf rep3 technical replicate - labeled-extract: westar 48h inf vs control rep1, westar 48h control vs inf rep1 technical replicate - labeled-extract: westar 48h inf vs control rep2, westar 48h control vs inf rep2 technical replicate - labeled-extract: westar 48h inf vs control rep3, westar 48h control vs inf rep3 biological replicate: westar 72h inf vs control rep1, westar 72h inf vs control rep2, westar 72h inf vs control rep3 biological replicate: westar 72h control vs inf rep1, westar 72h control vs inf rep2, westar 72h control vs inf rep3 technical replicate - labeled-extract: westar 72h inf vs control rep1, westar 72h control vs inf rep1 technical replicate - labeled-extract: westar 72h inf vs control rep2, westar 72h control vs inf rep2 technical replicate - labeled-extract: westar 72h inf vs control rep3, westar 72h control vs inf rep3
2009-01-31 | E-GEOD-13254 | biostudies-arrayexpress
Project description:Human Umbilical Vein Endothelial Cells were treated with three newly synthesized compounds and DMSO as vehicle. Total RNA was isolated 6 and 24h after treatment and gene expression analysis was performed. Three independent experiments were performed, corresponding to rep1, rep2 and rep3. Experiment 1 (rep1) contained all substances at both time points tested. Experiment 2 (rep2) contained two of the compounds and control DMSO at both time points. Experiment 3 (rep3) contained the third compound and control DMSO at both time points.
2016-06-30 | GSE75588 | GEO
Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide (GO) on the (innate) immune system using zebrafish as a model. We previously performed single-cell RNA-sequencing of germ-free zebrafish embryos exposed to GO plus the microbial metabolite butyrate (BA). Here, we performed a follow up experiment using germ-free lck-GFP transgenic fish in which the zebrafish were exposed to GO plus BA at 5 dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single-cell RNA-sequencing using 10x Genomics.
2022-07-23 | E-MTAB-11991 | biostudies-arrayexpress
Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. We previously evaluated the impact of graphene oxide (GO) on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild-type versus AhR-deficient zebrafish. Here, we performed single-cell RNA-sequencing (10x Genomics) on whole (dissociated) germ-free (GF) zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.
2022-07-22 | E-MTAB-11984 | biostudies-arrayexpress
Project description:To identify genes transcriptionally regulated under energy/metabolic stress, we treated CCRF-CEM/HA-AMPKa2 cells with Glucose deprivation condition for 24 hours, and examined their RNA profile using RNA-Seq. More than 3000 genes was altered (Fold Change > 1.5 or < -1.5, q value < 0.05) under energy/metabolic stress (glucose deprivation) vs. control, with approximately 60-70% genes exhibiting downregulation, whereas the remainder show upregulation. Note: sample headers in data_matrix_ctrl_no_glucose.txt, CTRL_7: Ctrl rep1 sample count number; CTRL_8: Ctrl rep2 count number; ONG_9: No glucose rep1 count number; ONG_10: No glucose rep2 count number;
2023-12-06 | GSE210212 | GEO
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains CITE-seq data (surface protein and cytosolic RNA content) data from two biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11549 | biostudies-arrayexpress
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains fetal liver CITE-seq (surface protein and cytosolic RNA content) data from six biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11613 | biostudies-arrayexpress