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| Status |
Public on Oct 05, 2023 |
| Title |
JAK2V617F/V617F Rep1 |
| Sample type |
SRA |
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| Source name |
LSK cell from bone marrow
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| Organism |
Mus musculus |
| Characteristics |
cell type: LSK cells
strain: C57BL/6
genotype: JAK2V617F/V617F
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Mar 04, 2022 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Linda M.S. Resar |
| Organization name |
Johns Hopkins University
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| Department |
Department of Medicine / Division of Hematology
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| Street address |
720 Rutland Avenue
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| City |
BALTIMORE |
| State/province |
Maryland |
| ZIP/Postal code |
21210 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE189570 |
HMGA1 Chromatin Regulators Drive MPN Progression |
| GSE197942 |
HMGA1 Chromatin Regulators Drive MPN Progression [scRNA-Seq] |
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| Relations |
| BioSample |
SAMN26436358 |
| SRA |
SRX14368953 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5934251_BL-9_filtered_feature_bc_matrix.h5 |
10.9 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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