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| Status |
Public on Nov 02, 2022 |
| Title |
EV004: Old_Endosteum |
| Sample type |
SRA |
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| Source name |
Endosteal stroma
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| Organism |
Mus musculus |
| Characteristics |
tissue: Endosteal stroma
cell type: Bone marrow stromal cells
age: 24 months
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| Growth protocol |
Mice were maintained in CUIMC animal facilities under SPF conditions.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bone chips (endosteum) were harvested by crushing bones and washing away marrow with ice-cold HBSS. Marrow plugs (central marrow) were harvested by flushing intact plugs with ice-cold HBSS. All samples were subjected to collagenase digestion as indicated in the manuscript to liberate stromal cells, filtered through 100 micron mesh, and stained for surface protein expression. Live Ter119-/CD45- cells from each compartment were directly sorted into filter-sterilized alphaMEM supplemented with 10% FBS and purity was confirmed to be >95% by running freshly sorted cells on the same sorter.
Libraries were constructed following manufacturer's instructions for Chromium Single Cell 3' Library & Bead Kit v2 (10X Genomics). 5,000 cells were loaded for each sample and samples were sequenced in a HiSeq4000 sequencer (Illumina) to obtain an average of ~286 million reads per sample
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw fastq files were aligned and processed to count matrices using CellRanger v2.1.1
Top 2,300 barcodes were selected for samples EV001, EV002, EV003 and top 2,858 were selected for EV004 using the "cellranger count" function with "force-cells=2300" for EV001, EV002 and EV003, or "force-cells=null" for EV004.
Genome_build: mm10
Supplementary_files_format_and_content: h5 files contain a matrix of selected cellular barcodes, Ensembl IDs, official gene symbols and read counts.
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| Submission date |
Mar 09, 2021 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Emmanuelle Passegue |
| E-mail(s) |
ep2828@cumc.columbia.edu
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| Organization name |
Columbia University Irving Medical Center
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| Department |
Columbia Stem Cell Initiative
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| Street address |
650 W 168th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE168586 |
Stromal inflammation is a targetable driver of hematopoietic aging [droplet-based scRNAseq] |
| GSE169162 |
Stromal niche inflammation mediated by IL-1 signaling is a targetable driver of hematopoietic aging |
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| Relations |
| BioSample |
SAMN18234322 |
| SRA |
SRX10297610 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5149493_EV004_filtered_gene_bc_matrices_h5.h5 |
7.9 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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