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Sample GSM7329753

Query DataSets for GSM7329753

Status

Public on May 15, 2023

Title

CMP, KO2

Sample type

SRA

Source name

Bone marrow

Organism

Mus musculus

Characteristics

tissue: Bone marrow
cell line: CMP
cell type: Hematopoietic stem/progenitor cells
genotype: Tet2 knockout

Extracted molecule

total RNA

Extraction protocol

Different populations of hematopoietic stem/progenitor cells (LT-HSC, ST-HSC, CMP, GMP, MEP, CLP) from bone marrow cells of different genotypes of mice (WT, Sting-KO, Tet2-KO, Tet2/Sting-dKO) were sorted by FACS with a number of 200 cells. The sorted cells were lysed with the lysis buffer obtained by SMART-seq construction Kit (Cat. N712, Vazyme) immediately and followed the library construction protocol from the Kit to generate cell full length mRNA library.
RNA libraries of pre-malignant cells were constructed by Smart-seq2 protocol, Nat. Methods 10, 1096–1098 (2013). RNA libraries of mouse hematopoietic cells were constructed by kit (Vazyme, NR611)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

T2KO2-CMP
TET2_project_counts.csv

Data processing

For RNA data, the raw data were trimmed by Trim Galore (v0.6.7) with default settings.
Then, the clean RNA-seq FASTQ data were mapped to mm10 using Hisat2 (v7.5.0) with default parameters.
DEG analysis was performed by using DESeq2 package with the raw count. Only genes with padj less than 0.05 and at least 2-fold-change were considered to be differentially expressed.
Assembly: mm9
Supplementary files format and content: raw count

Submission date

May 12, 2023

Last update date

May 15, 2023

Contact name

Shaoqin Rong

E-mail(s)

[email protected]

Organization name

Fudan University

Street address

138 Yi Xue Yuan Road