Single-cell RNA sequencing of ovarian, colorectal and breast cancer
ABSTRACT: We profile single cells from patients with colorectum, ovary and breast cancer using various single-cell technologies, including Chromium 3’ and 5’ single-cell RNA-sequencing. Note: Raw data files have been removed upon submitter's request.
Project description:We profile single cells from patients with colorectum, ovary and breast cancer using various single-cell technologies, including Chromium 3’ and 5’ single-cell RNA-sequencing. <br>Note: Raw data files have been removed upon submitter's request.
Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (firstname.lastname@example.org) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format. Resting mature peripheral primary B cells were enriched from the spleens of B1-8i (anti-NP gene targeted) mice. We sought to compare the genome-binding landscape of Irf4 and PU.1 prior to differentiation yet after B cell activation (Day 1) and after B cell differentiation (Day 3) of activated B cells into plasma cells (see Molecular Systems Biology 7:495 for description of cellular system). To this end, we used ChIP-seq (using the Illumina GA2 system) to obtain millions of unbiased, genome-wide, binding events. Sequences were mapped to the reference genome (mm9) and enrichment was calculated, relative to an Input sample, using QuEST algorithms.
Project description:Gene expression changes in MLL leukaemia following I-BET151 treatment. Note: Additional archives available (E-MTAB-774.additional.1.zip and E-MTAB-774.additional.2.zip) containing individual raw files. Select 'Browse all available files' to view.
Project description:The Polycomb group gene BMI1 is essential for efficient muscle regeneration in a mouse model of Duchenne Muscular Dystrophy and its enhanced expression in adult skeletal muscle satellite cells ameliorates the muscle strength in this model. In this experiment, we investigated the impact of mild BMI1 overexpression in human cells. We showed translation between observed mouse and human phenotypes. In human myoblasts, BMI1 overexpression increases mitochondrial activity leading to an enhanced energetic state with increased ATP production and concomitant protection against DNA damage both in vitro and upon xenografting in a severe dystrophic mouse model. These preclinical data in mouse models and in human cells provide a strong rationale for the development of pharmacological approaches to target BMI1-mediated mitochondrial regulation and protection from DNA damage to sustain the regenerative potential of the skeletal muscle in conditions of chronic muscle wasting. <br<</br>This ArrayExpress record is for the RNA-seq data from three independently prepared normal and DMD myoblasts cell cultures infected with GFP and BMI1Over lentiviral particles and induced to differentiate for 2 days.<br></br>Please note that each biological sample has one library, and each library is sequenced with two NextSeq runs, each run on identical 4 lane configurations. Hence for each biological sample, there are 16 raw fastq files. The run and lane information has been captured in the “run batch” and “lane batch” attributes respectively in the samples table, and should be used for bath corrections during analysis.
Project description:Gene expression array analysis on a series of ten different histological special types of invasive breast carcinomas (tubular, micropapillary, mucinous A, mucinous B, endocrine, apocrine, metaplastic, medullary, adenoid cystic, invasive ductal carcinoma with osteoclastic giant cells) and invasive lobular carcinoma.<br><br>Note: this experiment was reloaded into ArrayExpress in August 2010 to include mappings between raw and processed data files. It now includes additional dye-swap combined normalized data files.
Project description:MOTIVATION:High-throughput next-generation sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resources. This is a significant issue, especially for machines with limited hardware capabilities. As the redundancy of the sequences typically increases with coverage, collapsing such files into compact sets of non-redundant reads has the 2-fold advantage of reducing file size and speeding-up the alignment, avoiding to map the same sequence multiple times. METHOD:BioSeqZip generates compact and sorted lists of alignment-ready non-redundant sequences, keeping track of their occurrences in the raw files as well as of their quality score information. By exploiting a memory-constrained external sorting algorithm, it can be executed on either single- or multi-sample datasets even on computers with medium computational capabilities. On request, it can even re-expand the compacted files to their original state. RESULTS:Our extensive experiments on RNA-Seq data show that BioSeqZip considerably brings down the computational costs of a standard sequence analysis pipeline, with particular benefits for the alignment procedures that typically have the highest requirements in terms of memory and execution time. In our tests, BioSeqZip was able to compact 2.7 billion of reads into 963 million of unique tags reducing the size of sequence files up to 70% and speeding-up the alignment by 50% at least. AVAILABILITY AND IMPLEMENTATION:BioSeqZip is available at https://github.com/bioinformatics-polito/BioSeqZip. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
Project description:We used RNA-sequencing to deeply characterize the cellular factors and pathways modulated by CCL2 blocking in MDMs and involved in HIV-1 replication restriction. Gene differential expression analysis was performed and then Functional annotation was done to up-regulated genes Reads that failed mapping to human genome was mapped to HIV-1 reference genome. Note that some samples in this experiment have no raw files as the data has been lost.
Project description:<b>Background: </b>Generic drugs are heavily promoted in Japan. The aim of this retrospective single-center study was to clarify whether the frequency and reason that patients request a switch from a generic drug to the original drug differ according to therapeutic category and dosage form.<br><br><b>Methods: </b>This study was performed at Chiba University Hospital. Prescription inquiries about 121 generic drugs from community pharmacies over a 3-year period (from July 2014 to June 2017) were analyzed.<br><br><b>Results: </b>Approximately 30% of the requests were related to the efficacy, safety, and comfort of the generic drug. The most cited motive was "patient's desire with no reason given" at 44.5%. According to multiple logistic regression analysis, therapeutic categories and dosage forms were associated with the requests. The median request frequency differed according to therapeutic category and dosage form. The frequency was highest for "agents affecting the central nervous system" and "tablets and capsules", respectively. Among the therapeutic categories, "agents affecting the central nervous system" had the highest median number of requests related to "decreased effectiveness"; "cardiovascular agents" had the highest median number of requests related to "physician's instruction"; and "agents for the epidermis" had the highest median number of requests related to "uncomfortable to use". Among dosage forms, the odds ratio for patients' original drug request for "liniment and patch" was about 1.5 times that for "tablets and capsules". "Liniment and patch" had the highest median frequency of requests related to "decreased effectiveness", "uncomfortable to use", and "patient's desire with no reason given".<br><br><b>Conclusions: </b>The request frequency and reason differed according to therapeutic category and dosage form. Pharmacists should advise each patient properly about the choice and switching of drug brands, taking into account the therapeutic category and dosage form, especially liniments and patches.
Project description:The distinction between metastasis from a colorectal adenocarcinoma into the ovary and an ovarian adenocarcinoma is vital, but challenging at times, due to overlapping morphological features. Similarly, a distinction between an ovarian metastasis into the colorectum and a colorectal adenocarcinoma, although rare; is important and can be daunting. We report an analysis of 20 cases of ovarian involvement by metastatic colorectal adenocarcinomas and colorectal involvement by metastatic ovarian adenocarcinomas, including the value of differential expression of cytokeratins 7 & 20 by immunohistochemistry (IHC), in these cases. Nine cases (45%) were identified as colorectal adenocarcinomas metastatic to the ovary. On biopsy, all these cases showed a 'garland-like' tumor necrosis, with desmoplasia and predominantly exhibited a tubuloalveolar pattern (67% cases). On IHC, all 8 of 9 such cases, where staining for cytokeratin 20 was performed, displayed strong positivity and 7 cases, where staining for carcinoembryogenic antigen (CEA) was performed, revealed positivity for this marker (100%). Other 11 cases (55%) were ovarian adenocarcinomas, metastatic to the colorectum. These showed metachronous presentations, with the ovarian tumor preceding the colorectal tumor deposits. Morphologically, psammomatous calcification was noted in 73% of these cases, whereas 'garland-like' necrosis was absent in all. The chief morphological subtype was serous papillary cystadenocarcinoma (55% cases). On IHC, CK7 and CA 125 were positive in all 6 of 11 such cases, whereas CK 20 was negative in all these cases.In cases of complex presentations like an ovarian involvement by a metastatic colorectal adenocarcinoma and vice-versa, certain clinicopathological features are useful. Differential expression of CK 7 and CK20 is vital in resolving these dilemmas. CK20 positivity and CK7 negativity is associated with a colorectal adenocarcinoma. Markers like CEA and CA-125 have an added value.
Project description:Glioblastoma multiforme is the most common and aggressive type of brain cancer. Little is known about the complex relationship between genomic and epigenomic as tumour progresses. We present the following base resolution whole genome maps of matched tumour/margin and blood samples from a glioblastoma multiforme patient:<br>* Single nucleotide variations (SNVs), copy number variations (CNVs) and structural variations (SVs) as revealed by DNA sequencing. </br> <br>* 5-methylcytosine and 5-hydroxymethylcytosine levels obtained using (oxidative)bisulfite sequencing. </br> <br>* Transcript levels produced using RNA sequencing.</br> <br>For the three samples with very large bam raw data files ('Blood DNA-seq', 'Margin DNA-seq' and 'Tumour DNA-seq'), bai index files are available from https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5171/E-MTAB-5171.additional.1.zip