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| Status |
Public on Mar 01, 2023 |
| Title |
T-ALL |
| Sample type |
SRA |
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| Source name |
CD3+GFP+
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
age: 8-10 weeks
cell type: CD3+GFP+
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| Extracted molecule |
total RNA |
| Extraction protocol |
2x106 GFP+ leukemia cells were isolated from B-ALL, T-ALL, AML, and AUL mice. After staining with anti-B220-PerCP-Cyanine 5.5, anti-CD3e-PE-Cy7, anti-CD11b-APC-eFluor 780/anti-Gr1-APC-eFluor 780, and the 7 lineage cocktail antibodies, 2x106 B cells, T cells, myeloid cells, and lineage-negative cells were isolated from normal bone marrow as controls. Sorted cells were washed with 1 ml PBS, and re-suspended by 1ml Trizol reagent (Thermo Fisher). After total RNA extraction, mRNA was enriched by magnetic beads linked with Oligo (dT)
The first-strand cDNA was synthesized by random oligonucleotide primer, and the second cDNA was synthesized by DNA polymerase I. The double strand cDNA was modified by index primers, and sequenced by Illumina HiSeq 2000 at Novogene company (Tianjin Novogene Bioinformatics Technology Co., Ltd. Building B07, Venture Headquarter Base, Tianjin Wuqing Development Area, China). The sequenced strategy of Illumina PE150 (Pair end 150 bp) was taken in this project. Reads containing adaptors and uncertain bases were removed (quality control) before analysis. After filtration of unqualified reads, reads were compared with the public reference sequence of mouse UCSC mm10 (http://genome-asia.ucsc.edu/cgi-bin/hgGateway?redirect=manual&source=genome.ucsc.edu ). The expression level of RNA was quantified with fragments per kilo base of transcript per million mapped reads (FPKM).
Illumina PE150 (Pair end 150 bp) RNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using HTSeq (http://htseq.readthedocs.io/en/release_0.9.1; Anders S et al., 2015). Then DEGs was analyzed by edgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html; Robinson MD et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Mar 04, 2020 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Haitao Bai |
| E-mail(s) |
zhangqingyun@ihcams.ac.cn
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| Organization name |
Chinese Academy of Medical Sciences
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| Department |
Institute of Hematology & Blood Diseases Hospital
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| Street address |
288 Nanjing Road
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| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE146330 |
N-Myc overexpression leads to multiple types of acute leukemia in mice [RNA-Seq] |
| GSE146333 |
N-Myc overexpression leads to multiple types of acute leukemia in mice |
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| Relations |
| BioSample |
SAMN14278834 |
| SRA |
SRX7846390 |
| 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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