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Sample GSM7832229 Query DataSets for GSM7832229
Status Public on Dec 01, 2023
Title IL-4, rep1 [P1.L4]
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 SAMN37736913
SRA SRX22037362

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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