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Sample GSM7211271 Query DataSets for GSM7211271
Status Public on May 15, 2024
Title old fasted
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
cell line: purified hematopoietic stem cells
cell type: hematopoietic stem cell
genotype: Gfp-Lc3
age: Old
treatment: 24 hr fast
Extracted molecule total RNA
Extraction protocol ~ 30,000 HSCs were sorted into 1.5 ml tubes containing 500 µl of HBSS/2% FBS and transferred to the Columbia Genome Center Single Cell Analysis Core Facility for microfluidic cell processing, library preparation and sequencing.
~10,000 HSCs were loaded for each sample and 1 sample was loaded per condition.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing QC was performed keeping cells with more than 500 genes detected, less than 100,000 total reads, and less than 20% mitochondrial reads.
Downstream analyses were done using Scanpy with cells normalized to 10,000 UMIs per cell and logarithmically transformed.
Highly variable genes (HVGs) were selected using the “FindVariableFeatures” method”. UMAP visualizations were obtained from 50 PCA components.
Cell clusters were defined using either Louvain or Leiden algorithms.
Assembly: mm10
Supplementary files format and content: CSV files containing differential gene expression by cluster
Supplementary files format and content: CSV files containing differential pathway analysis by cluster
 
Submission date Apr 21, 2023
Last update date May 15, 2024
Contact name Paul Vincent Dellorusso
E-mail(s) paul.dellorusso@gmail.com
Phone 5166552491
Organization name Columbia University Irving Medical Center
Department Genetics and Development
Lab Passegue Lab
Street address 701 West 168th Street, 724 Hammer Health Sciences Center
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL24247
Series (2)
GSE229137 Autophagy engaging and non-engaging hematopoietic stem cells
GSE230284 yHSC and oHSC 10X scRNAseq under ad lib, fasted, or fast refeed conditions to evaluate transcriptional impact of transient autophagy engagement in hematopoietic stem cells.
Relations
BioSample SAMN34286058

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

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