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| Status |
Public on Jan 30, 2023 |
| Title |
AML_Patients_1 |
| Sample type |
SRA |
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| Source name |
WBC
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| Organism |
Homo sapiens |
| Characteristics |
tissue type: AML patient
tissue: WBC
strategy: Smartseq2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
WBC Preparation: Blood samples of newly diagnosed patients with a higher leukemia cells number and normal samples are collected in tubes containing EDTA, Collect 4 ml of each person. Centrifuge samples at 800 g for 5 min at room temperature, remove the upper plasma layer with a transfer pipet, being careful not to disturb the cells layer, and add 10mL 1XACK lysis buffer to resuspend cells on ice for 5 min, and then centrifuge at 400g at room temperature for 3min. Discard the supernatant and wash cells twice with PBS then centrifuge at 400g at RT for 3min, add 2%FBS(PBS) buffer to resuspend WBCs ,and count with a manual counter. 2 million WBCs was used to extract RNA with 1ml Trizol.
RNA-seq libraries were constructed by Illumina Stranded mRNA Sample Preparation Kit (NEB, Cat#E7770) according to the manufacturer’s protocol,
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
P-1_FRAS202431932-1r
processed data file:
AML_VS_Normal_count_and_DESeq2Normalised_anno.csv,AML_VS_Normal_rMATS_results.csv
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| Data processing |
Sequenced reads were mapped to hg19 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM) and differentially expressed genes identified by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: txt files with gene TPM
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| Submission date |
Jun 09, 2021 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Xaingyu Pan |
| E-mail(s) |
pangxueyu233@outlook.com
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| Organization name |
Sichuan University
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| Department |
State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.
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| Lab |
Chen & Liu Lab
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| Street address |
No.17 Renming road section3
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| City |
Chengdu, Cihna |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE142645 |
Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression |
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| Relations |
| BioSample |
SAMN19644753 |
| SRA |
SRX11101879 |
| 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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