|
| Status |
Public on Sep 17, 2019 |
| Title |
RNA-seq st. 31 replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
pectoral fin bud at st. 31
|
| Organism |
Chiloscyllium punctatum |
| Characteristics |
tissue: pectoral fin bud
age: st. 31
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini plus kit
Described in the SAMPLES section
Using >100 μg of each of the RNA samples, strand-specific single-end RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Cat. No. RS-122-2101 and/or RS-122-2102 ). For purification, we applied 1.8x (after end repair) and 1.0x (after PCR) volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880). The optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be XXXX cycles for mouse limb buds and XXX cycles for bamboo shark fin buds. The quality of the libraries was checked by Agilent 4200 TapeStation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
replicate 3
bamboo_shark_fin_average_TPM_expression_data_with_gene_symbol.txt
bamboo_shark_fin_TPM_expression_data_with_gene_symbol.txt
|
| Data processing |
Basecalling with Illumina RTA 1.18.64
Short reads were aligned to curated, non-redundant genes in GCF_000001635.26_GRCm38.p6_rna.fna for mouse samples and a transcriptome assemble for bamboo shark samples using RSEM with bowtie2 (bowtie2 options: –no-mixed --no-discordant --gbar 1000 --end-to-end -k 200).
Transcripts per million (TPM) were calculated using RSEM and a perl script in Trinity software.
Genome_build: mm10 or a transcritopme assembly
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each species.
|
| |
|
| Submission date |
Aug 27, 2019 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Koh Onimaru |
| E-mail(s) |
koh.onimaru@gmail.com, koh.onimaru@riken.jp
|
| Phone |
484679398
|
| Organization name |
Center for Biosystems Dynamics Research
|
| Lab |
Laboratory for Bioinformatics Research
|
| Street address |
312 Information Science Building, 2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
| |
|
| Platform ID |
GPL27153 |
| Series (2) |
| GSE136437 |
A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [RNA-seq] |
| GSE136445 |
A comparison of evolutionary changes and constraints on gene regulation between fin and limb development |
|
| Relations |
| BioSample |
SAMN12643511 |
| SRA |
SRX6780666 |
