Project description:Two fruit development stages of the wild chiltepin pepper (Capsicum annuum var. glabriusculum) were studied. RNA-Seq data was obtained from fruits at 20 and 68 days after anthesis with two biological replicates for a total of 4 samples. 260 million raw reads were sequenced and over 80% of them mapped back to the Capsicum annuum genome.
Project description:The parasite Plasmodium falciparum is responsible for severe malaria, which remains a major cause of death, particularly in sub-Saharan Africa. The reference strain NF54 (or its subclone 3D7) is commonly used for controlled human malaria infection (CHMI), but recently strains with a different geographic and genomic background have become available for CHMI, including 7G8, which was subcloned from the Brazilian isolate IMTM22 in 1984 (Burkot TR et al. 1984. Infectivity to mosquitoes of Plasmodium falciparum clones grown in vitro from the same isolate. Trans R Soc Trop Med Hyg 78 (3):339-41. doi: 10.1016/0035-9203(84)90114-7). In contrast to NF54, in which var gene expression resets after mosquito transmission, 7G8 shows a partial reset with retention of the C-type var gene PF7G8_040025600 in the human host. The three subclones A1G9 (almost exclusive var2csa expression, control), A2E10, and A2G2 (both predominantly expressing var gene PF7G8_040025600) recently obtained by limited dilution from the Sanaria 7G8 parasite working cell bank (Lot: SAN03-021214 dated 20. February 2014) were selected for gDNA sequencing to test whether parasite subclones expressing PF7G8_040025600 differ in their genomic background. 150 mL of P. falciparum cell culture with >10% parasitemia was harvested and gDNA isolation was performed using the MasterPure™ Complete DNA Purification Kit (Lucigen). The gDNA samples were tested for degradation and RNA contamination on an agarose gel and quantified using the Qubit™ dsDNA BR Assay Kit (ThermoFischer). DNA-seq was performed at BGI Genomics (Shenzhen, China) on the DNBseq platform to generate 150 bp paired-end sequencing reads.
Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.
Project description:Intent of the experiment: evaluate whether copy number gains and losses occur throughout the processing of passaging, i.e. test the genomic stability of the patient-derived xenograft models. DNA was extracted from frozen xenograft samples of different passages. KAPA DNA Library Preparation Kit was used to prepare DNA libraries, which were sequenced at low coverage on a HiSeq2000 (Illumina) with a V3 flowcell generating 50bp reads. Raw reads were aligned to the human reference genome version hg19 with Burrows-Wheeler Aligner software package and after duplicate removal further analyzed with QDNAseq to exclude known regions with low mapping quality, correct for the genomic wave and to count the reads per bin. Binned data were further segmented with the ASCAT (Allele-Specific Copy number Analysis of Tumours) algorithm.
Project description:SAGA member Ada2 is required for the majority of H3K9 acetylation in C. neoformans. To identify specific genomic loci that exhibit Ada2-dependent H3K9 acetylation, we performed ChIP-Seq against H3K9ac in wildtype and ada2Δ cells. ChIP-Seq was performed using antibodies for H3K9ac in KN99 wildtype cells and ada2Δ cells. Input and IPed DNA was collected in triplicate from each strain and sequenced on an Illumnina HiSeq 2000 flow cell producing 84 million reads. Due to the lack of quality scores, raw reads are omitted from the submission.
Project description:To identify more targets in soybean, particularly specific targets of Cd-stress-responsive miRNAs, high-throughput degradome sequencing was used. In total, we obtained 8913111 raw reads from the library which was constructed from a mixture of four samples (HX3-CK, HX3-Cd-treatment, ZH24-CK and ZH24-Cd-treatment). After removing the reads without the CAGAG adaptor, 5430126 unique raw-reads were obtained. The unique sequences were aligned to the G. max genome database, and 6516276 reads were mapped to the genome. The mapped reads from the libraries represented 51481 annotated G. max genes.
Project description:Antigenic variation in Plasmodium falciparum is achieved by transcriptional switching amongst polymorphic var genes, enforced by epigenetic modification of chromatin. Histone-modifying ‘sirtuin’ enzymes PfSir2a and PfSir2b have been implicated in this process. We examined the effect of genetic disruption of sirtuins on var gene expression. Comparative Genomic Hybridization profile indicate that loss of PfSir2a in 3D7 resulted in strikingly rearranged chromosomes.