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Sample GSM5934253 Query DataSets for GSM5934253
Status Public on Oct 05, 2023
Title JAK2V617F/V617F - Hmga1+/- Rep1
Sample type SRA
 
Source name LSK cell from bone marrow
Organism Mus musculus
Characteristics cell type: LSK cells
strain: C57BL/6
genotype: JAK2V617F/V617F-Hmga1+/-
Extracted molecule total RNA
Extraction protocol Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) and Chromium instrument (10X Genomics) were used following the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 1.2 (10X Genomics).
Additional quality control (QC) was performed by visual inspection of QC plots using Seurat.
Count matrix files from Cellranger alignments/counting of cells from male and female animals with JAK2V617F/V617F and JAK2V617F/V617F-Hmga1+/-, were imported into Seurat.
Cells with <700 or >7000 detectable genes were removed as outliers, as were genes found in fewer than 50 cells. Individual samples were combined into a single object using the ‘merge’ function in Seurat with default parameters.
Counts for individual cells were scaled and logged using the ‘NormalizeData’ function with default parameters, followed by ‘FindVariableFeatures’ with loess correction to stabilize variables and identify the 3000 most variable features for input into clustering and dimension reduction algorithms. Finally, the ‘ScaleData’ function was used with default parameters to scale count levels of individual features. Single cells were clustered over the top 20 components of a PCA, using ‘FindNeighbors’ function followed by ‘FindClusters’ with resolution set to 0.5.
Genome_build: mm10
Supplementary_files_format_and_content: a .h5 file containing cellranger filtered cell barcodes and gene expression counts
 
Submission date Mar 04, 2022
Last update date Oct 05, 2023
Contact name Linda M.S. Resar
Organization name Johns Hopkins University
Department Department of Medicine / Division of Hematology
Street address 720 Rutland Avenue
City BALTIMORE
State/province Maryland
ZIP/Postal code 21210
Country USA
 
Platform ID GPL24247
Series (2)
GSE189570 HMGA1 Chromatin Regulators Drive MPN Progression
GSE197942 HMGA1 Chromatin Regulators Drive MPN Progression [scRNA-Seq]
Relations
BioSample SAMN26436356
SRA SRX14368955

Supplementary file Size Download File type/resource
GSM5934253_BL-11_filtered_feature_bc_matrix.h5 13.2 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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