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Sample GSM7903908 Query DataSets for GSM7903908
Status Public on Mar 14, 2024
Title Lin_neg_CD11b_Control_Rep2
Sample type SRA
 
Source name Mouse bone marrow
Organism Mus musculus
Characteristics tissue: Mouse bone marrow
genotype: Control
replicate: Rep2
Growth protocol Tet2 fl/fl mice (#017573, The Jackson Laboratory) were crossed to Mx1-Cre mice (#003556, The Jackson Laboratory). Mx1-Cre negative littermates were utilized as controls. 4 doses of 12.5 ug/g pI:pC (Amersham) were administered intraperitoneally to induce Cre activity.
Extracted molecule polyA RNA
Extraction protocol Cell sorting was performed on FACS Aria II (BD Biosciences). Single stained and Fluorescence Minus One stained cells were used as controls. Samples were incubated with the antibody cocktail in PBS 2% FBS for 30 minutes at 4 degrees before sorting. 7-AAD Viability Staining Solution (BioLegend) was included in the sample preparation for flow cytometry to exclude dead cells.
scRNA-seq was performed on a Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell Reagent Kit v2, Chromium Next GEM Chip A and Chromium i7 Multiplex Kit according to the manufacturer’s instructions. Briefly, single cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (according to the available cDNA quantity). scRNA-seq libraries were prepared according to the manufacturer’s instructions, checked and quantified on Tapestation 4200 (Agilent) and Qubit 4 fluorometer (Invitrogen).
Chromium Single Cell Reagent Kit v2, Chromium Next GEM Chip A and Chromium i7 Multiplex Kit
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Base call files were demultiplexed, for each flow cell directory, into FASTQ files using Cellranger v3.1.0 (https://github.com/10XGenomics/cellranger) mkfastq with default parameters. FASTQ files were then processed using Cellranger count with default parameters.
Gene-mapped counts were loaded into R as a Seurat object and used for downstream analysis. Genes with at least one UMI across cells were retained, and cells with a number of unique feature counts > 200 and total UMIs > 5000 and mitochondrial read percentage of < 5 % were initially retained. Normalization and scaling of RNA gene expression levels was then performed.
Assembly: mm10
Supplementary files format and content: Decomposed counts matrix. Counts data is indexed by gene (row), cell (column), and count where the geneNames file and cellMeta file provide annotations for rows and columns.
 
Submission date Nov 16, 2023
Last update date Mar 14, 2024
Contact name Fabiana Duarte
E-mail(s) fabiana_duarte@g.harvard.edu
Organization name Harvard University
Department HSCRB
Lab Buenrostro lab
Street address 7 Divinity Avenue
City Cambridge
State/province Massachusetts
ZIP/Postal code 02138
Country USA
 
Platform ID GPL24247
Series (2)
GSE247968 Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation [scRNA-seq]
GSE247970 Cell of origin epigenetic priming determines susceptibility to Tet2 oncogenic mutation
Relations
BioSample SAMN38283136
SRA SRX22547791

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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