|
| Status |
Public on Jan 25, 2024 |
| Title |
RNAseq_Mac_180min_3 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell line: Hoxb8
cell type: Macrophages
treatment: +Apoptotic Jurkat cells (180min)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Mini Kit (Qiagen).
rRNAs were depleted using the NEBNext rRNA depletion kit, and libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Reads were aligned with STAR-2.7.9a. The output BAM files were sorted with samtools and raw read counts were generated with Htseq.
Assembly: mm39
Supplementary files format and content: raw_counts.txt: raw gene expression table (genes x samples) for RNA-seq data
|
| |
|
| Submission date |
Jan 18, 2024 |
| Last update date |
Mar 18, 2024 |
| Contact name |
Kodi S Ravichandran |
| E-mail(s) |
kodi@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Pathology and Immunology
|
| Street address |
660 Euclid Ave
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE253577 |
Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (RNA-Seq) |
| GSE253578 |
Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release |
|
| Relations |
| BioSample |
SAMN39487052 |
| SRA |
SRX23286334 |
