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| Status |
Public on Nov 02, 2022 |
| Title |
EO044: Old_IL1R1-/-_CentralMarrow |
| Sample type |
SRA |
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| Source name |
Central marrow stroma
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| Organism |
Mus musculus |
| Characteristics |
tissue: Central marrow stroma
cell type: Bone marrow stromal cells
age: 24 months
genotype: IL1R1-/-
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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 |
For stromal samples, 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, treated with red blood cell lysis buffer, and stained for surface protein expression. Live Ter119-/CD45- cells from each compartment were directly sorted into filter-sterilized alphaMEM supplemented with 10% FBS. For bone marrow samples, marrow was liberated by crushing bones, resuspended in ice-cold HBSS, filtered through 40 micron mesh, treated with red blood cell lysis buffer and stained for surface protein expression. Live Lineage-/cKit+ (LK) and Lineage-/cKit+/Sca-1+ (LSK) cells were sorted directly into HBSS supplemented with 2% FBS. For all samples, 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 v3 (10X Genomics). 5,000 cells were loaded for each sample and samples were sequenced in a NextSeq 550 sequencer (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
EO044
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| Data processing |
Raw fastq files were aligned and processed to count matrices using Cell Ranger v5.0.1.
We performed QC and kept: cells with number of detected genes > 150, cells with number of counts < 100,000, those genes where at least 1 UMI is detected in at least 1 cell, and only those cells with less than 20% of UMIs corresponding to mitochondrial genes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tar archives include barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and h5 files; contain a matrix of selected cellular barcodes, Ensembl IDs, official gene symbols and read counts.
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| Submission date |
Nov 19, 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 |
GPL19057 |
| Series (2) |
| GSE169162 |
Stromal niche inflammation mediated by IL-1 signaling is a targetable driver of hematopoietic aging |
| GSE189217 |
Stromal inflammation is a targetable driver of blood aging [droplet-based scRNAseq - Batch 2] |
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| Relations |
| BioSample |
SAMN23311541 |
| SRA |
SRX13179932 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5696264_EO044_cellranger_count_outs.tar.gz |
55.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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