--- title: "Datasets" canonical: "https://help.biobam.com/space/BTP/3309076481/Datasets" format: markdown --- ## Profiling of CD34+ cells from human bone marrow to understand hematopoiesis ### Code Name: Healthy Bone Marrow **Technology: ****[10x Chromium 3' v2](https://support.10xgenomics.com/permalink/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v2-chemistry)** ### Article: [Characterization of cell fate probabilities in single-cell data with Palantir](https://www.nature.com/articles/s41587-019-0068-4) ***Description: ***Differentiation is among the most fundamental processes in cell biology. Single-cell RNA-seq studies have demonstrated that differentiation is a continuous process, and in particular, cell states are observed to reside in large continuous spaces. We have developed Palantir, a graph-based algorithm that models continuities in cell state transitions and fate choices. Modeling differentiation as a Markov chain, Palantir determines probabilities of reaching terminal states from cells in each intermediate state. The entropy of these probabilities represents the differentiation potential of the cell in the corresponding state. Applied to a single-cell RNA-seq dataset of CD34+ hematopoietic cells from human bone marrows, Palantir accurately identified key events leading up to cell fate commitment. Integration with ATAC-seq data from bulk-sorted populations helped identify key regulators that correlate with cell fate specification and commitment. ***Experimental Design/Set-up*** 1. Cryopreserved bone marrow stem/progenitor CD34+ cells from healthy donors were purchased from AllCells, LLC. (catalog no. ABM022F) and stored in vapor phase nitrogen until use. 2. scRNA-seq was performed with a 10x genomics system using Chromium Single Cell 3’ Library and Gel Bead Kit V2 (catalog no. 120234). 3. Briefly, 8,700 cells (viability 90–97%) were loaded per reaction, targeting the recovery of 5,000 cells with a 3.9% multiplet rate. After reverse transcription reaction emulsions were broken, barcoded complementary DNA was purified with DynaBeads, followed by 12 cycles of PCR amplification. 4. The resulting amplified cDNA was sufficient to construct next-generation sequencing libraries sequenced on an Illumina HiSeq 2500 system (HiSeq SBS V4 chemistry kit). ***Download Links*** 1. European Nucleotide Archive: [PRJEB37166](https://www.ebi.ac.uk/ena/browser/view/PRJEB37166): Contains raw FastQ-files 2. Human Cell Atlas: [Data Portal](https://data.humancellatlas.org/explore/projects/091cf39b-01bc-42e5-9437-f419a66c8a45): Processed files and FastQ-files. ***Code for Analysis: ******[Github](https://github.com/spriyansh/re_analysis_scRNA/tree/main/setty_et_al/scripts)*** ---