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Sample GSM7663254 Query DataSets for GSM7663254
Status Public on Oct 02, 2023
Title Lineage (-) day0_2
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics cell type: Lineage negative cells
cell subset: CD3-CD19-NK1.1-CD11b-CD11c-FCeR1-Gr-1-
library type: NEB Next Ultra II Directional RNA Library Prep Kit
Treatment protocol DMSO or YPPP added to the dish of bone marrow culture at day 0.
Growth protocol Bone marrow cells from femur of C57BL/6 mice were cultured with 25 ng/ml GM-CSF and DMSO or YPPP.
Extracted molecule total RNA
Extraction protocol Total RNA of the dendritic cells were extracted with AllPrep DNA/RNA kit (QIAGEN) according to manufacturer instructions.
The libraries were constructed using NEB Next Ultra II Directional RNA Library Prep Kit according to manufacturer instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Lineage (-)
day0_2
Data processing The fastq fieles were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM) and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Jul 26, 2023
Last update date Oct 02, 2023
Contact name Hiroki Ura
E-mail(s) h-ura@kanazawa-med.ac.jp
Organization name Kanazawa Medical University Hospital
Lab Center for Clinical Genomics
Street address 1-1 Daigaku
City Uchinada
State/province Ishikawa
ZIP/Postal code 920-0293
Country Japan
 
Platform ID GPL19057
Series (1)
GSE239334 Transcriptome analysis of high potent DCs using small molecule compounds
Relations
BioSample SAMN36716256
SRA SRX21164656

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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