|
| Status |
Public on Dec 19, 2021 |
| Title |
D11 |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish kidney regeneration transcriptome
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
tissue: kidney
developmental stage: 6 months
treatment: 1 day after-injury (1 dpi ) sample 1
|
| Growth protocol |
Zebrafish were maintained in standard conditions under a 14-hours-light and 10-hours-dark cycle and fed three times daily
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After the zebrafish kidney was obtained by dissection, it was lysed in trizo, then extracted with PCI / CI, precipitated with isopropanol and eluted with 75% alcohol to obtain total RNA
After the total RNA sample is tested to be qualified, magnetic beads with oligo (DT) are selected for enrichment and purification. Fragment buffer is added to the purified mRNA to make its fragment into a short fragment. Then the second strand of cDNA is synthesized with the fragment mRNA as a template and purified by qiaquick PCR kit. The purified double stranded cDNA was then treated by terminal repair, base A and sequencing. Then the target fragment was recovered by agarose gel electrophoresis and PCR was amplified to complete the whole library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing data quality control, data comparison analysis and transcriptome in-depth analysis
The Seurat package was used to normalize data, dimensionality reduction, clustering, differential expression.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene
|
| |
|
| Submission date |
Dec 16, 2021 |
| Last update date |
Dec 19, 2021 |
| Contact name |
Xiaoliang Liu |
| E-mail(s) |
snliangovo@hotmail.com
|
| Organization name |
Xinqiao Hospital, Army Medical University (Third Military Medical University)
|
| Street address |
xinqiao street
|
| City |
chongqing |
| ZIP/Postal code |
400037 |
| Country |
China |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE191068 |
Zebrafish kidney regeneration transcriptome |
|
| Relations |
| BioSample |
SAMN24139336 |
| SRA |
SRX13427504 |
