Project description:E15.5 embryos were micro-disscted from Gata4 G295S mutant mice and littermate controls, RNA was isolated using Norgen total RNA isolation, and libraries were generated with the RNA TruSeq Stranded Total RNA kit. 50 base pair paired end reads were obtained on an illumina high seq 2500. Fastq files were aligned to the mouse genome using STAR aligner. QC was performed using RNASeQC and RSeQC. BAM files were processed using cufflinks pipeline.
Project description:Purpose: A method for mapping chromatin accessibility genome-wide, to reveal chromatin accessibility in Intestinal stem cells. Methods: Intestinal stem cells(Lgr5-high cells) were sorted by flow cytometry from wild type mice. The samples were prepared in duplicate. HISAT2 was used to align the sequences to the mouse genome and generate bam files. bamCoverage was used to generate bigwig files from bam files. MACS2 (v2.2.5) was used for peak calling and to generate bed files from aligned reads. Conclusions: ATAC-seq analysis confirmed that Fosb binding sites in Chip-seq assay were correlated with the chromatin accessibility .
Project description:Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align.
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
Project description:The goal of the study was to identify a gene expression signature capable of predicting a pathological complete response following neoadjuvant anthracycline-based chemotherapy of breast cancer. The samples were taken from the FEC arm (5-fluorouracil, epirubicin, cyclophosphamide) of the EORTC 10994 trial. EORTC 10994 is a phase III clinical trial comparing FEC with ET (epirubicin, docetaxel) in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). Frozen biopsies were taken at randomisation. RNA was extracted from 100um thickness of 14G core needle biopsies. Adjacent sections were tested by H&E to confirm >20% tumour cell content. 200 ng total RNA per chip was amplified using the Affymetrix small sample protocol (IVT then Enzo). 102 tumours were tested on Affymetrix X3P chips. Single biopsies were tested per tumour. The CEL files were quantile normalised using rma. The clinical response measure was pathological complete response (pCR, disappearance of the tumour after chemotherapy with at most scattered invasive cells detected by histology).
Project description:We investigated the biological features of FL and their relationship to patients’ outcome. Gene expression analysis was carried out on diagnosis biopsies from 148 follicular lymphoma patients enrolled in the PRIMA clinical trial. We developed a gene expression-based predictor of progression-free survival (PFS) in high-tumour burden FL patients and we analysed gene-expression signatures reflecting different aspects of tumour biology for their association with outcome. proposition SH: We investigated the biological features of FL and their relationship to patients’ outcome. Gene expression analysis was carried out on diagnosis biopsies from 148 follicular lymphoma patients enrolled in the PRIMA clinical trial. We developed a gene expression-based predictor of progression-free survival (PFS) in high-tumour burden FL patients and we analysed gene-expression signatures reflecting different aspects of tumour biology for their association with outcome.
Project description:EORTC 10994 is a phase III clinical trial comparing FEC with ET in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). Frozen biopsies were taken at randomisation. RNA was extracted from 100um thickness of 14G core needle biopsies. Adjacent sections were tested by H&E to confirm >20% tumour cell content. 100 ng total RNA per chip were amplified using the Affymetrix small sample protocol (IVT then Enzo). 49 tumours were tested on Affymetrix U133A chips. The CEL files were quantile normalised together using rma. Clinical response data are not available yet. Keywords = Apocrine carcinoma Keywords = breast cancer