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Sample GSM7913164 Query DataSets for GSM7913164
Status Public on Nov 24, 2023
Title dko LAP* transdifferentiated cells
Sample type SRA
 
Source name B cells
Organism Mus musculus
Characteristics cell type: B cells
genotype: mixed sample (Cebpa -/-, Cebpb -/-)
treatment: LAP* transdifferentiated
Treatment protocol pMSCV_LAP*_3x-FLAG_IRES_EGFP vector was transfected into Plat-E packaging cells to generate infectious retroviral supernatant. Retroviral supernatant was added to B cells in 1:1 (V:V) ratio in complete DMEM supplemented with 50 mM beta-mercaptoethanol and 8 ug/mL polybrene. Cells were centrifuged at 2000 rpm without break at 37°C for 1 hour, following by overnight incubation.
Growth protocol v-Abl-transformed pre-B cells were culture in completed DMEM medium (10% fetal bovine serum(FBS), 10 mM HEPES and penicillin/streptomycin) supplemented with 50 mM beta-mercaptoethanol.
Extracted molecule total RNA
Extraction protocol Cells at day 6 post-infection were subjected to EGFP sorting using AriaI/II/III (BD), EGFP positive cells were sorted directly into FACs buffer (HBSSwo, 2% FBS, 5mM EDTA) and further processed with single cell partitioning and scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description 10x Genomics
Data processing preprocessed by the Cellranger pipeline (version 2.1.0)
Analysis was done using Seurat 4 (Satija et al, 2015). Raw data was filtered, i.e.,cells with less than 400 features as well as more than 4000 features were removed. Additionally, cells containing a mitochondrial read percentage of more than 7 were removed as potentially dead cells. The WT and dKO samples were normalized using the 'LogNormalize' option, integrated and scaled. Dimension reduction by means of UMAP (McInnes et al, 2018) and clustering was performed by a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm with the resolution parameter set to 0.5.
Assembly: mm10
Supplementary files format and content: raw expression quantification in h5 format
 
Submission date Nov 21, 2023
Last update date Nov 24, 2023
Contact name Achim Leutz
E-mail(s) aleutz@mdc-berlin.de
Organization name Max Delbrück Center
Department Cell Differentiation and Tumorigenesis
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platform ID GPL21103
Series (1)
GSE248415 C/EBPβ-induced lymphoid-to-myeloid transdifferentiation emulates granulocyte-monocyte progenitor (GMP) biology
Relations
BioSample SAMN38351940
SRA SRX22601592

Supplementary file Size Download File type/resource
GSM7913164_B-dko_raw_data.h5 9.6 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA

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