|
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.
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|
|
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
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|
|
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 |