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Sample GSM5341768 Query DataSets for GSM5341768
Status Public on Jun 28, 2021
Title mESC-3
Sample type SRA
Source name mouse embryonic stem cell
Organism Mus musculus
Characteristics strain background: 129/ola
cell type: embryonic stem cell
Treatment protocol using FACS to sort total cells from 3D+OP9 and3D+0.1%gelatin. In the 3D+OP9 hematopoietic differentiation system, we sorted D5-LSKCD201+ and D5-LSKCD201- cells, at the same time, we used PE-anti-mouse-SSEA-1 to sort mESC and sorted bone marrow derived D5-LSKCD201+ and fetal liver derived D5-LSKCD201+
Growth protocol 3D inducment derived hematopoietic like colonies were seeded on OP9 stromal and 0.1% gelatin
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from sorted cell samples using TRIzol Reagent (Life Technologies) following the manufacturer’s instructions.
cDNA libraries were constructed using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description mESC_3
Data processing Library sequencing was performed on an Illumina HiSeq X Ten platform (Illumina) to generate 150-bp paired-end reads.
The paired-end reads were processed and aligned to the reference genome (GRCm38) using HISAT2 (v.2.0.5).
Mapped reads for each sample were assembled into transcriptome data using StringTie (v.1.3.3) with a reference-based approach. The normalized expression value was represented by fragments per kilobase of transcript per million mapped reads (FPKMs).
Cuffdiff (v1.3.0) was used to calculate the differential expression genes for each sample. Only comparisons with q-values < 0.05 and absolute log2 (fold change) values ≥1 were considered as significantly differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Submission date May 26, 2021
Last update date Jun 28, 2021
Contact name Wei Shan
Phone 18768158120
Organization name Zhejiang University
Street address Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, Zhejiang, PR China.
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310000
Country China
Platform ID GPL21273
Series (1)
GSE175563 RNA-seq analysis of mouse pluripotent stem cells derived cells
BioSample SAMN19341802
SRA SRX10993493

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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