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Sample GSM6042844 Query DataSets for GSM6042844
Status Public on Dec 02, 2022
Title mWT_Antibody_Capture
Sample type SRA
 
Source name mWT_Antibody_Capture
Organism Mus musculus
Characteristics tissue: Bone Marrow
sample type: Antibody_Capture
Extracted molecule other
Extraction protocol BM was extracted from femurs, pelvic bones, tibias and spines of TAM-treated Nfixflox/floxRosa26CreERT2+/+ and Nfixflox/floxRosa26CreERT2+/T mice via crushing
c-Kit+ cells were isolated via magnetic enrichment using anti-CD117 microbeads (Miltenyi Biotec, Carlsbad, CA) and an autoMACs magnetic cell separator (Miltenyi Biotec, Carlsbad, CA). For c-Kit+ cells, HSPC (Lineage-Sca-1+cKit+) and LT-HSC (Lineage-Sca-1+c-Kit+CD48-CD150+) isolation, cells were stained with anti-Lineage BV605 cocktail, anti-Sca-1-PerCPCy5.5 (E13-161.7), anti-c-Kit-APCe780 (2B8), anti-CD48-Alexa Fluor 700 (HM48-1), anti-CD150-PE-Cy7 (TC15-12F12.2). For CMP (Lineage-Sca-1-c-Kit+CD34+CD16/32med) isolation, cells were stained with anti-Lineage BV605 cocktail, anti-Sca-1-PerCP-Cy5.5 (E13-161.7), anti-c-Kit-APCe780 (2B8), anti-CD34-FITC (RAM34) and anti-CD16/32-Alexa Fluor 700 (2.4G2). In addition to FACS antibodies, cells were labeled with CITE-seq antibodies (see Supplementary Table S1). 4′,6-diamidino-2-phenylindole (DAPI) (Sigma-Aldrich, St. Louis, MO) was used for dead cell exclusion. All cell isolations were performed using cell sorting on FACSAria III (BD Biosciences, San Jose, CA). Post cell sorting, 7000 Lineage-cKit+ BM, 1000 HSPC, 1000 CMP, and 1000 LT-HSC were pooled together for 10x genomics
 
Library strategy RNA-Seq
Library source other
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description CITE-seq
manual_label.RData
Data processing Single cell data was analyzed using cellranger count. Transcriptome database was cellranger-mm10-3.0.0.
The weighted nearest-neighbor UMAP and cell clusters were generated using Seurat (v4.0.4) following the reference guide of “WNN analysis of CITE-seq, RNA+ADT”
Differential gene expression analysis was done using FindMarkers with “slot=data, logfc.threshold=0.2, test.used=wilcox, pseudocount.use=1”. Genes were further filtered by FDR<=0.01, which was calculated using the Benjamini-Hochberg method in R.
Genome_build: mm10
Supplementary_files_format_and_content:Rdata
 
Submission date Apr 13, 2022
Last update date Dec 02, 2022
Contact name Shannon McKinney-Freeman
E-mail(s) Shannon.McKinney-Freeman@STJUDE.ORG
Organization name St. Jude Children’s Research Hospital
Department Department of Hematology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38018
Country USA
 
Platform ID GPL24247
Series (1)
GSE166922 A Nuclear factor I-X mediated regulatory network governs the balance of hematopoietic stem and progenitor cells during hematopoiesis
Relations
BioSample SAMN27562384
SRA SRX14841653

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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