Project description:RNA-seq analysis was performed by BGI-Tech of China, and RNA-seq library preparation and sequencing were performed by BGI (Shenzhen, China).
Project description:We present the transcriptome analysis by RNA sequencing of endometrial B cells identifying potential B cell phenotypes and function in human endometrium during the mid-luteal phase. To achieve this, endometrial B cells were isolated from 15 endometrial biopsies, and cDNA library preparation was performed for RNA sequencing.
Project description:RNA-Seq technique was applied to investigate the effects of four cDNA amplification kits and two RNA-Seq library preparation kits to the deep sequencing results at different perspectives.
Project description:RNA-Seq technique was applied to investigate the effects of four cDNA amplification kits and two RNA-Seq library preparation kits to the deep sequencing results at different perspectives. The same set of semen samples were applied to investigate the qualitative and quantitative effect of four cDNA amplification methods and two RNA-Seq library preparation methods on sperm transcript profiling.
Project description:<p>Peripheral blood mononuclear cells (PBMC) from 82 T1D cases from the T1DGC study were fractionated by positive selection on magnetic beads into CD4+ T cells, CD8+ T cells and CD19+ B cells. RNA purification, library preparation and sequencing to an average of 50 million reads per sample were performed by the HudsonAlpha Genome Services Laboratory. The resulting dataset includes 82 subjects with data from at least one cell type; sequence data from all 3 cell types is available from 79 subjects. The individuals in this study can be linked to the <a href="./study.cgi?study_id=phs000911">phs000911 T1DGC ImmunoChip</a> study via subject ids to obtain both genotypic and phenotypic information, including genotypes used for expression quantitative trait locus analysis.</p>
Project description:RNA-sequencing analysis from whole heart ribosome depleted RNA from the 2-week old WT and Lmna-/- mice (N=5) . Strand specific RNA seq libraries where prepared form ribosome-depleted cardiac RNA samples using the Illumina TruSeq stranded total RNA library preparation kit. The samples weresequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate100 base paired end reads.
Project description:The goal of this study is to find the transcriptional targets downstream of PI3K signaling during lacrimal gland development. We performed laser capture microdissection of the lacrimal gland epithelial tissue at embryonic day E14.5 from control embryos and mutant embryos containing lacrimal gland-specific deletion of PI3K subunits. After tissue harvest, RNA was extracted, conversion to cDNA and amplification was performed by Clontech SMART-seq v4 Ultra low input RNA kit,and cDNA library construction was performed using Nextera XT DNA library preparation kit by core facility at Columbia university prior to RNA sequencing. After preparation of cDNA library, each sample was sequenced using Illumina platform
Project description:We evaluated the effect of the small RNA library preparation method on 5' tRNA-halves and miRNA abundance in libraries prepared from serum RNA using three commercially available small RNA library preparation kits (TruSeq small RNA library preparation kit v2 (Illumina), TailorMix miRNA sample preparation kit v2 (Seqmatic) and the NEBNext Multiplex Small RNA library prep kit (New England Biolabs)). RNA isolated from 100 µl of serum collected from healthy mice was used as input for the preparation of a small RNA library in duplicate and libraries were single end sequenced.
Project description:Studying medulloblastoma, the most common malignant paediatric brain tumour, requires simple yet realistic in vitro models. In this study, we optimised a robust, reliable, three-dimensional (3D) culture method for medulloblastoma able to recapitulate the spatial conformation, cell-cell and cellmatrix interactions that exist in vivo and in patient tumours. We investigated the initial stages of metastatic dissemination using brain-specific hyaluronan hydrogel matrices. In order to perform NGS of SHH medulloblastoma metastasis models, it was essential to extract high quality RNA for library preparation and sequencing. However, RNA isolation from hydrogels proved particularly difficult due to the low yields of RNA obtained. To efficiently utilise our samples, we chose to adopt two NGS technologies: traditional mRNA sequencing, which required at least 100 ng of RNA per sample, and 3' UPX sequencing, a method used for low input samples that sequenced the 3' end of RNA near the poly-A tail. Firstly, RNA was extracted from samples using the NucleoSpin RNA Plus kit (Macherey-Nagel). Following extraction, samples were shipped to QIAGEN Genomic Services (Hilden, Germany) where the subsequent steps of NGS were performed. Quality control of the RNA was performed using the Qubit RNA high sensitivity assay (Invitrogen) which quantified the amount of RNA in each sample. Samples with 100 ng or more of RNA in total were suitable for mRNA NGS. Samples with lower RNA yields were lyophilised and resuspended in a smaller volume of RNase-free water. Another quality control step was performed to quantify the RNA. Samples with an RNA concentration above 1.4 ng/mL were appropriate for 3' UPX NGS. However, samples with a lower RNA concentration were unsuitable for either method of NGS. Following RNA extraction and quantification, libraries were prepared and sequenced. For mRNA NGS, library preparation was carried out using the TruSeq Stranded mRNA library preparation kit. All prepared libraries successfully passed QIAGEN’s internal quality control checks and were subsequently sequenced on a NextSeq 500 Illumina sequencer. Following sequencing, quality control of the sequencing data was performed using FastQC analysis. All samples had high quality scores, indicating good technical performance of the sequencing. For 3' UPX NGS, library preparation was performed using the QIAseq UPX 3' Transcriptome kit. All prepared libraries successfully passed QIAGEN’s internal quality control checks and were sequenced on a NextSeq 500 Illumina sequencer. Following sequencing, FastQC analysis of the sequencing data was performed and all samples were considered suitable for downstream primary and secondary data analysis.