|
| Status |
Public on May 03, 2022 |
| Title |
Sample 5B Ubc-CreERT2; Csf1fl/fl, Ly6Chi monocytes |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell type: Sorted monocytes
genotype: Ubc-CreERT2; Csf1fl/fl
treatment: Tamoxyfen for 4 weeks
|
| Treatment protocol |
Single cell suspensions from bone marrows were obtained from pooled femurs, tibias and pelvises
Sorting was performed on an Aria Fusion cell sorter (BD Biosciences)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from sorted cells using PicoPure RNA Isolation Kit (Arcturus, cat #KIT0202)
Takara Smarter Stranded Total RNA-seq kit v2 pico Input Mammalian
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read mapping to the mouse reference genome (GRCm38) was done using hisat2 (v2.1.0)
SAM file to BAM file conversion and BAM file indexing was done using samtools (v1.9)
stringtie (v1.3.4d) was used for transcript assembly
Mapping quality control metrics were determined using picard (v2.10.9) and analyzed using multiqc (v1.6)
Gene-level read quantification was done using HTSeq (v0.10.0)
Assembly: GRCm38 (mm10)
Supplementary files format and content: Gene-level quantified raw reads from HTSeq (.tsv – tab separated) for each sample
|
| |
|
| Submission date |
Apr 20, 2022 |
| Last update date |
May 03, 2022 |
| Contact name |
Clinton S. Robbins |
| Organization name |
University Health Network
|
| Street address |
101 College Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE201162 |
Colony stimulating factor-1 producing endothelial cells and mesenchymal stromal cells maintain monocytes within a perivascular bone marrow niche |
|
| Relations |
| BioSample |
SAMN27673693 |
| SRA |
SRX14937715 |
