|
| Status |
Public on Apr 25, 2023 |
| Title |
RNA_kd_7d_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
RNA_kd_7d
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
tissue: planarian whole body
genotype: wtap knockdown
age: 7 dpa
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from planarain at different time points with TRIzol reagent and mRNA was further purified using Dynabeads mRNA purification kit (Ambion, 61006). Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA, K8401) according to the manufacturer’s protocol.
Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA, K8401) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA_kd_7d_rep2
all_rpkm.txt
|
| Data processing |
Adaptor sequences were trimmed off for all raw reads using the Cutadapt software (version 1.2.1). Reads that were less than 18 nt in length or contained an ambiguous nucleotide were discarded by Trimmomatic (version 0.30) .
The remaining reads were aligned to the Schmidtea mediterranea transcriptome smed_20140614 using Bowtie2 v2.2.9 default parameters.
Genome_build: Smed_20140614
Supplementary_files_format_and_content: rpkm for samples
|
| |
|
| Submission date |
Mar 31, 2021 |
| Last update date |
Apr 25, 2023 |
| Contact name |
Bao-Fa Sun |
| E-mail(s) |
sunbf@big.ac.cn
|
| Organization name |
Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)
|
| Street address |
Da-Tun Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL29967 |
| Series (2) |
| GSE171247 |
m6A Modification Regulates Planarian Regeneration [RNA-seq] |
| GSE171253 |
m6A Modification Promotes Planarian Regeneration |
|
| Relations |
| BioSample |
SAMN18577223 |
| SRA |
SRX10489589 |
