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| Status |
Public on Dec 15, 2022 |
| Title |
3mix-random, 3mix-random-plate1_7 |
| Sample type |
SRA |
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| Source name |
Cell line mixture of murine T cell, murine leukemia cell, and murine hematopoietic progenitor cell
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| Organism |
Mus musculus |
| Characteristics |
strain: NA
cell type: random selection
isolation method: ALPS
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| Treatment protocol |
Murine T cells, leukemia cells, hematopoietic progenitor cells, and PBMCs were isolated by ALPS or FACS
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
3mix-random-plate1_7
3mix_RNA_expression.txt
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| Data processing |
Basecalls performed by Illumina MiSeq or Hiseq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq or using bcl2fastq for Illumina Hiseq resultes
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA molecules per cell for each gene is listed (cells which were not filtered out are shown).
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| Submission date |
Jul 12, 2021 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Katsuyuki Shiroguchi |
| E-mail(s) |
katsuyuki.shiroguchi@riken.jp
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| Organization name |
RIKEN
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| Department |
Center for Biosystems Dynamics Research (BDR)
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| Lab |
Laboratory for Prediction of Cell Systems Dynamics
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| Street address |
6-2-3 Furuedai
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| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0874 |
| Country |
Japan |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE179943 |
Single cell gene expression profiling of cell lines and murine peripheral blood mononuclear cells (PBMCs) |
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| Relations |
| BioSample |
SAMN20173046 |
| SRA |
SRX11412846 |
| 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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