|
| Status |
Public on Jun 28, 2021 |
| Title |
3D+0.1%gel_3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse pluripotent stem cells derived total cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129/ola
cell type: pluripotent stem cells derived total cells
|
| 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 |
BGISEQ-500 |
| |
|
| Description |
D5_ gel_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 |
| E-mail(s) |
shanwei0616@126.com
|
| 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 |
GPL23479 |
| Series (1) |
| GSE175563 |
RNA-seq analysis of mouse pluripotent stem cells derived cells |
|
| Relations |
| BioSample |
SAMN19341807 |
| SRA |
SRX10993490 |
