|
| Status |
Public on Jan 30, 2023 |
| Title |
Smartseq2_cells_103_Bone_Marrow_AML |
| Sample type |
SRA |
| |
|
| Source name |
AML_BM_T3_Smartseq2
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
tissue type: AML
time point: T3
tissue: BM
strategy: Smartseq2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Preparation: Whole Bone Marrow (WBM) are isolated from mouse tibiae, femora and ilia leg bones by crushing in 2%FBS(PBS) buffer, add 1:1000 DNase1 and then translate into 15mL BD tube, centrifuge at 1200rpm, RT for 3min. Then discard the supernatant and add 3mL 1XACK lysis buffer to resuspend bone marrow pellet on ice for 3~5 min, and then add PBS (more than lysis buffer) to terminate lysis reaction, centrifuge at 1200rpm, RT for 3min. Discard the supernatant and then add 0.04% PBS-BSA buffer to resuspend cell pellet and then filtered through a 40μm cell strainer. More than 80% of the living cells in the sample and the density of living cells ranged from 600 to 1200 cells/μl was preferable. Sample quality is measured using Bio-rad TC20 automated cell counter.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform and modified SMART-seq2 protocol based on published previously (Fuchou Tang, 2010).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
WBH-AMLSC-2-WBH-AMLSC-2-P17_TKR180900407-18.out
processed data file:
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis.rds
mmu_smartseq2_scRNA_Landscape_of_leukemogenesis_unspliced.rds
|
| Data processing |
ScRNA-seq alignment process was completed by cellranger(version 2.1.0)
Seurat V3 workflow
Genome_build: mm10 mouse genome references for mouse and hg19 human genome references
Supplementary_files_format_and_content: txt files with gene counts, rds files with annotation and umap information
|
| |
|
| Submission date |
Dec 27, 2019 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Xaingyu Pan |
| E-mail(s) |
pangxueyu233@outlook.com
|
| Organization name |
Sichuan University
|
| Department |
State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.
|
| Lab |
Chen & Liu Lab
|
| Street address |
No.17 Renming road section3
|
| City |
Chengdu, Cihna |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE142645 |
Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression |
|
| Relations |
| BioSample |
SAMN13685001 |
| SRA |
SRX7445273 |
