Project description:Acute megakaryoblastic leukemia of Down syndrome (DS-AMKL) is a model of clonal evolution from a preleukemic transient myeloproliferative disorder requiring both a trisomy 21 (T21) and a GATA1s mutation to a leukemia driven by additional driver mutations. We modelled this leukemic evolution through stepwise gene editing of GATA1s, SMC3+/- and MPLW515K providing 20 different trisomy or disomy 21 iPSC clones. Single cell analysis was performed on hematopoietic cells obtained from IPSC clones after 13 days of differentiation. Sample preparation was done at room temperature. Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. All samples were processed simultaneously with the Chromium Controller (10X Genomics) and the resulting libraries were prepared in parallel in a single batch. We pooled all of the libraries for sequencing in a single SP Illumina flow cell. All of the libraries were sequenced with an 8-base index read, a 28-base Read1 containing cell-identifying barcodes and unique molecular identifiers (UMIs), and a 91-base Read2 containing transcript sequences on an Illumina NovaSeq 6000.
Project description:To characterize the consequences of cytokine stimulation, we compared ET02-GLIS2 expressing cells from different origins by single cell transcriptomes (scRNAseq). We analysed FL and CB ET02-GLIS2-expressing CD34+ progeny after 7 days in vitro, human cells from diseased NSG (FL- and FBM-derived) and NSGS (CB- and FL-derived) recipients.
Project description:Single cell RNAseq from brain endothelial cells (BECs) isolated from wild-type and Iqgap2-/- (KO) mice to identify transcriptional changes in BECs caused by loss of Iqgap2. Mouse brains were dissociated to single cell suspension and labelled with CD31. CD31+ cells were flow sorted and processed for single cell RNAseq.
Project description:C56BL/6 mice (10 to 12-week-old) were immunized subcutaneously at the base of the tail with 100 μg of MOG (35–55) emulsified in complete Freund's adjuvant containing 500 μg of Mycobacterium tuberculosis. Pertussis toxin (200 ng; List Biological Laboratories) was injected intravenously at days 0 and 2 post-immunization. At day 17 post immunization, central nervous system CD45-positive immune cells were isolated and loaded onto a single channel of a 10x Chromium chip for each sample.
Project description:The experiment aims at characterizing the immune responses elicited by the BNT162b2 vaccine against SARS-CoV-2, initially administered in a two dose regimen (second dose after three weeks followinf the first dose) In particular the transcriptional landscape of circulating T and B lymphocytes has been profiled longitudinnaly by scRNA-seq coupleD with CITE-seq of 19 cell surface markers to better classify T cells subpopulations, LIBRA-seq to assess the Spike-specificity of BCRs and and V(D)J seq to also track T and B cell clones dynamics. Eeach sample was profiled before vaccination (T0), 21 days after the first dose (T1), 2 months after the first dose (1 month after the second dose) (T2). The immune responses were characterized using PBMC from 3 SARS-CoV-2 experienced donors (experiencing SARS-Cov-2 at least 4 months before the first vaccinatin) and 2 SARS-CoV-2 unexperienced donors.
Project description:Single cell RNAseq of Neural-derived haploid and diplod human embryonic stem cells, validating successful differentiation of haploid hESCs into neurons
Project description:These are the Visium spatial transcriptomic data (10x Genomics) from 9 patients with Head and Neck Squamous Cell Carcinoma (oral cavity) treated in Gustave Roussy. Patients are stratified by their tumoral density of multinucleated giant cells (MGC) : 6 patients have high MGC density (patients 1, 2, 3, 4, 5, 8) and 3 have low MGC density (patients 6, 7, 9). There is one data file for each patient, except for one patient that has 3 data files (patient 1). Accordingly, there are 9 patients but 11 samples. The source code of the is available on GitHub (https://github.com/AhmedAmineAnzali/MGC_Paper_Analysis). The results are published in the paper untitled : Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma (Gessain et al., 2024, Cancer Discovery). Please contact the corresponding author for more information.