|
| Status |
Public on Apr 23, 2019 |
| Title |
3 mpf kidney-HSPC rep1 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
tissue: zebrafish kidney
cell type: hematopoietic stem and progenitor cells
Stage: 3 mpf
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit (Cat. No. 74104).
The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
BulkRNA_seq.FPKM.txt
|
| Data processing |
Reads quality were first checked by "Fastqc"
And then clean reads were mapped to the reference genome by HISAT
Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq
Reads counts matrix was then normalized to library size by DESeq2 with default parameters, and normalized reads were then used to calculate the FPKM
Genome_build: GRCz10
Supplementary_files_format_and_content: Contains the expression level of all samples, measured by FPKM
|
| |
|
| Submission date |
Sep 27, 2018 |
| Last update date |
Apr 23, 2019 |
| Contact name |
Denghui Liu |
| E-mail(s) |
[email protected]
|
| Phone |
+86-02154920572
|
| Organization name |
CAS-MPG Partner Institute for Computational Biology (PICB)
|
| Lab |
Jing-Dong Jackie Han's Lab
|
| Street address |
ShengLi Building, 320 Yueyang Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21741 |
| Series (2) |
| GSE120578 |
Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA-seq] |
| GSE120581 |
Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion |
|
| Relations |
| BioSample |
SAMN10138827 |
| SRA |
SRX4746036 |
