|
| Status |
Public on Aug 11, 2023 |
| Title |
zebrafish, AR42_TFA_1, 3dpf |
| Sample type |
SRA |
| |
|
| Source name |
tail
|
| Organism |
Danio rerio |
| Characteristics |
tissue: tail
treatment: AR-42 treated larvae with TFA modeling
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co., Ltd.）
The de-duplicated consensus sequences were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCz10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 04, 2023 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Sijia Fan |
| Organization name |
Chongqing medical university
|
| Street address |
Chongqing Medical University, Medical College Road, Yuzhong District
|
| City |
Chongqing |
| ZIP/Postal code |
400016 |
| Country |
China |
| |
|
| Platform ID |
GPL30277 |
| Series (1) |
| GSE240080 |
Effects of AR-42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation (TFA) Model |
|
| Relations |
| BioSample |
SAMN36839084 |
| SRA |
SRX21249694 |
