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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 13, 2023 |
| Title |
Naïve MDP, bio rep 3 |
| Sample type |
SRA |
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| Source name |
BM progenitor cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: BM progenitor cells
sample group: Naïve MDP
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from sorted cells was extracted with an RNeasy Micro Kit (QIAGEN).
RNA-seq libraries were prepared using the NEBNext UltraII Directional RNA Library Prep Kit (NEW ENGLAND BioLabs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Adaptor sequences were removed from raw data using Trimmomatic (Galaxy Version 0.38.0).
Sequencing reads after trimming were aligned to a mouse reference genome sequence (GRCm38/mm10) in the RNA STAR (Galaxy Version 2.7.8).
Read counts per gene were calculated using featureCounts (Galaxy Version 2.0.1) based on GENCODE gene annotation version M25.
The fragments per kilobase of exon per million (FPKM) normalization was done account for gene length and read counts.
Assembly: GRCm38/mm10
Supplementary files format and content: EXCEL file includes FPKM values for all samples.
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| Submission date |
Jan 31, 2023 |
| Last update date |
Mar 13, 2023 |
| Contact name |
Kenichi Asano |
| E-mail(s) |
asanok@toyaku.ac.jp
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| Organization name |
Tokyo University of Pharmacy and Life Sciences
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| Department |
Life Sciences
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| Lab |
Immune Regulation
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| Street address |
1432-1 Horinouchi
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| City |
Hachioji |
| State/province |
Tokyo |
| ZIP/Postal code |
1920392 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE224102 |
GMP-MoPs display mixed gene expression profiles of both neutrophil and monocyte progenitors [RNAseq mouse] |
| GSE224702 |
mouse RNA-seq, human RNA-seq, ATAC-seq, and scRNA-seq analyses data |
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| Relations |
| BioSample |
SAMN32971950 |
| SRA |
SRX19226839 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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