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Sample GSM7663258 Query DataSets for GSM7663258
Status Public on Oct 02, 2023
Title Day3-YPPP, CD11c+I-AI-Ehigh cells day3_YPPP_2
Sample type SRA
 
Source name GM-CSF Bone marrow culture
Organism Mus musculus
Characteristics cell type: Bone marrrow derived dendritic cells
cell subset: CD11c+I-AI-Ehigh
treatment: YPPP for 3 days
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 Day3-YPPP, CD11c+I-AI-Ehigh cells
day3_YPPP_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 SAMN36716252
SRA SRX21164660

Supplementary file Size Download File type/resource
GSM7663258_day3_YPPP_2_gene_abundances.tsv.gz 611.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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