|
| Status |
Public on Dec 01, 2023 |
| Title |
G-CSF, rep2 [P2.G] |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
cell type: Stem Cell
|
| Treatment protocol |
Both mouse Ly6G+ neutrophils, and human CD34+, bone marrow cells were cultured with media and with cytokines IL-4 and/or G-CSF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using total RNA purifcation plus kit (Biotek Corp). 200 ng per sample was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared using NEBNext Ultra II directional RNA library prep kit following manufacturer's instruction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
human_featurecounts.txt
|
| Data processing |
genome build/assembly: grch38
Human data: Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0 [1]. Gene wise counts were generated with featureCounts from the subread package v1.5.1 [2] for genes annotated by ensembl Homo_sapiens.GRCh38.101, counting the primary alignment in the case of multimapped reads.
Mouse data: Individual FASTQ files were trimmed for adapter sequences and filtered using fastp v0.20.0. Mouse reference genome GRCm38.p6 and gene annotation described by Gene Transfer Format (GTF) were downloaded from Ensembl release 99 (January 2020). Reads alignment was performed against the reference genome using HISAT2 v2.1.0. Gene expression values for genes were quantified using the featureCounts tool of the Subread package v1.5.0-p2 in unstranded mode.
Supplementary files format and content: human_featurecounts.txt
Supplementary files format and content: mouse_counts.csv
|
| |
|
| Submission date |
Oct 09, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Amy Hite |
| Organization name |
The Ohio State University
|
| Department |
Biomedical Informatics
|
| Street address |
1800 Cannon Drive 250 Lincoln Tower
|
| City |
Columbus |
| State/province |
OH - Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE244934 |
Cytokine Polarized Bone Marrow Neutrophils Drive Axon Regeneration |
|
| Relations |
| BioSample |
SAMN37736910 |
| SRA |
SRX22037370 |
