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| Status |
Public on Jan 25, 2024 |
| Title |
PROseq_Mac_90min_2 |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell line: Hoxb8
cell type: Macrophages
treatment: +Apoptotic Jurkat cells (90min)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were gently resuspended in wash buffer (10mM Tris-Cl, pH 8.0; 10mM KCl; 250mM Sucrose; 5mM MgCl2; 1mM EGTA; 0.5mM DTT; 10% Glycerol; SUPERase-IN RNase inhibitor) to obtain a single-cell suspension. Subsequently, cells were permeabilized by adding permeabilization buffer (10mM Tris-Cl, pH 8.0; 10mM KCl; 250mM Sucrose; 5mM MgCl2; 1mM EGTA; 0.1% Igepal CA-630; 0.5mM DTT; 0.05% Tween-20; 10% Glycerol; SUPERase-IN RNase inhibitor) and incubating on ice for 5 minutes. After centrifugation, cells were resuspended in wash buffer. Then, cells were resuspended in freezing buffer (50mM Tris-Cl, pH 8.0; 40% glycerol; 5mM MgCl2; 1.1mM EDTA; 0.5mM DTT; SUPERase-IN RNase inhibitor).
PRO-seq library preparation were conducted as previously described with slight modifications (PMID: 33440169).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Read pairs trimmed with cutadapt. Paired-end reads were mapped to a combined genome index, including both the spike (dm6) and primary (mm39) genomes using bowtie2. Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools, and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl).
Assembly: mm39
Supplementary files format and content: bw: BigWig genome browser track for PRO-seq data
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| Submission date |
Jan 18, 2024 |
| Last update date |
Mar 18, 2024 |
| Contact name |
Kodi S Ravichandran |
| E-mail(s) |
kodi@wustl.edu
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| Organization name |
Washington University School of Medicine
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| Department |
Pathology and Immunology
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| Street address |
660 Euclid Ave
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| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63108 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE253576 |
Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (PRO-Seq) |
| GSE253578 |
Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release |
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| Relations |
| BioSample |
SAMN39489426 |
| SRA |
SRX23307009 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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