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SRX22526611: GSM7900395: Single cell multiome 10x from lineage-Sca1+ckit+ sorted marrow T58A cells replicate 2 ATAC; Mus musculus; OTHER
1 ILLUMINA (NextSeq 2000) run: 108M spots, 14.1G bases, 4.3Gb downloads

External Id: GSM7900395_r1
Submitted by: Basic Sciences, Fred Hutchinson Cancer Research Center
Study: RNASeq, multiome, and genomic profiling of hematopoietic progenitors and B cells from mice with a point mutation in MYC [Multiome]
show Abstracthide Abstract
We generated mice with a mutation at threonine 58 of MYC in the mouse germline (T58A mutant). These mice ultimately develop AML or B cell lymphomas. We profiled changes in gene expression and genomic occupation of MYC in single cells of sorted, immature bone marrow progenitor cells, mature (spleen derived) and immature (marrow derived) B cells. B cells were stimulated with LPS and IL7, respectively. Overall design: Lineage negative, ckit+, Sca1+ cells were sorted from marrow of WT or T58A littermate mice, and profiled for expression and DNA accessibility by single cell RNA-Seq and ATAC-Seq using the 10X genomic system. Bulk RNA-Seq was also performed on immature B cells isolated from bone marrow, and stimulated with IL7. RNA-Seq was also done on mature B cells isolated from spleens of these animals, and stimulated with lipopolysaccharide (LPS). Genomic profiling was done using CUT&RUN to determine MYC occupation, and histone modifications (H3K27Ac and H3K4Me2) were carried out in both the LPS and IL7 treated cells. For scRNA-Seq, 2 paired, biological replicate experiments (LSK_1 and LSK_2, comparing sorted cells from WT and T58A mutant mice) were done for each genotype. Each replicate consisted of LSK cells from 2 mice of each genotype, for a total of 4 mice per genotype for this experiment. For all genomic profiling experiments (CUT&RUN), 2 biological replicates per genoype (mice) were performed.
Sample: Single cell multiome 10x from lineage-Sca1+ckit+ sorted marrow T58A cells replicate 2 ATAC
SAMN38256730 • SRS19537812 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7900395
Instrument: NextSeq 2000
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Single celll multiome analysis ( scRNA-Seq and scATAC-Seq) was done using nuclei isolated according to the manufacturers specifications (10X Genomics). For this, cells were sorted on a flow cytometer (Lin-Sca1+ckit+), and nuclei were prepared in buffer containing digitonin. Cells were counted, barcoded, and extraction was carried out in the Fred Hutch Cancer Center genomics core as described for the 10X genomics system. After barcoding and extraction, single cell multiome libraries were constructed in the Fred Hutch Cancer Center genomics core using the 10X Genomics system. RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 kit. For CUT&RUN, cells were processed on a previously published, automated system at the Fred Hutch Cancer Center that uses KAPA DNA polymerase method for library preparation optimized for recovery of small DNA fragments.
Runs: 1 run, 108M spots, 14.1G bases, 4.3Gb
Run# of Spots# of BasesSizePublished
SRR26830643107,971,20614.1G4.3Gb2024-04-02

ID:
30517764

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