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Sample GSM4233521 Query DataSets for GSM4233521
Status Public on Jan 30, 2023
Title Smartseq2_cells_7_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-1-WBH-AMLSC-1-P16_TKR180900408-16.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 SAMN13684986
SRA SRX7445257

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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