Project description:T cell receptor (TCR) signaling in Jurkat cells was investigated using the CROP-seq method for CRISPR single-cell sequencing. In CROP-seq, genetic perturbations are introduced into single cells in a pooled fashion, and single-cell RNA-seq is used to determine the transcriptional response to the CRISPR-induced perturbation in a large number of single cells in parallel. Importantly, the CROP-seq vector makes individual guide-RNAs detectable using standard single-cell RNA-seq technology. The dataset presented here is based on CROP-seq in combination with single-cell RNA-seq using the 10x Genomics v2 chemistry. It recapitulates a previously published CROP-seq dataset (Datlinger et al. 2017 Nature Methods; GEO: GSE92872) that used the Drop-seq protocol as the single-cell RNA-seq readout. Additional information on CROP-seq are available from the following website: http://crop-seq.computational-epigenetics.org/ .
Project description:A total of 9 primary gastric cancers (1 pair of primary-metastasis, GC6) analyzed using Visium 10X platform-based spatial transcriptomics.
Project description:Isogenic population of yeast cells was grown in a maltose-glucose-maltose media shift schema. Time point samples were taken throughout the experiment, and were analyzed for single-cell gene expression using 10x Genomics platform.
Project description:By performing 10x 3’ scRNA-seq on Jurkat cells post TCR acivation in CRISPR/Cas9 screening, we want to investigate the compatibility of the A/G mixed capture sequence on multiple single cell RNA-seq platforms. By mimicking the adenylated endogenous mRNA, gRNA transcripts could be directly captured by poly(dT) primer during the reverse transcription, and serve as perturbation index in high identification rate.
Project description:Sheep testes undergo a dramatic rate of development with structural changes during sexual maturity, including the proliferation and maturation of somatic niche cells and the initiation of spermatogenesis. To explore this complex process, 12,843 testicular cells from three sexual maturity (3 month-old) rams were sequenced using 10x Genomic platform single-cell sequencing (scRNA-seq).Nine testicular somatic cell types and five male germ cell types were observed.The study revealed significant changes in germline stem cells during sexual maturation. Candidate factors and pathways for the regulation of germ and somatic cell development were identified that represent the scientific basis for the development of a livestock stem cell breeding program.
Project description:Hair follicles of the yak are in anagen and catagen , the hair follicles of healthy female yaks around 2 years old are collected for the preparation of single-cell suspension, the cells were sequenced by scRNA-seq on the 10x genome platform. A total of about 12000 single-cell transcriptome information were obtained. According to the reported marker genes, the main cell groups in anagen and catagen of yak were identified. Based on the analysis of pseudotime trajectory, the differentiation trajectory of epidermal cell lineage and dermal cell lineage during hair follicle development and the dynamic changes of genes during differentiation were described.
Project description:Single-cell RNA-seq and TCR-seq were conducted using coding RNA of single cells isolated from mouse lung MNCs with or without 7DW8-5 according to the manufacturer’s instructions. In brief, single cells from the mouse lung MNCs were incubated with mouse Fc block and then stained by anti-mouse CD45+ antibody and DAPI. Sorted viable CD45+DAPI- single cells were loaded into 10x genomics ChromiumTM controller (samples were split into 4 lanes, Saline1 and Saline2 without 7DW8-5 treatment, and 7DW1 and 7DW2 with 7DW8-5 treatment) to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library and TCR library were sequenced with Illumina Novaseq. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of the samples Saline1, Saline2, 7DW1, and 7DW2.