|
| Status |
Public on Jan 31, 2021 |
| Title |
Optic_Lobe_Periphery-Plexiform_1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA extracted from whole tissue
|
| Organism |
Octopus bimaculoides |
| Characteristics |
tissue: Optic_Lobe_Periphery-Plexiform
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For tissue transcriptomes, RNA was extracted from whole tissues and subsequently converted to cDNA. Single neurons were processed without RNA extraction to cDNA.
cDNA was constructed with reverse transcriptase, sequencing library was made using NEBNEXT Ultra I or II Library Construction for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
10C_3879_8_L_OLPeriph_A_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate
|
| Data processing |
Base calling and initial adapter trimming performed by Illumina Real Time Analysis v2
Additional adapter trimming and alignment to annotated genome performed using Trimmomatic (v0.32) and STAR (v2.3).
Quantification to produce transcripts per million mapped reads (TPMs) was produced by Rsubread (v1.22.3) and edgeR (v3.14.0)
Genome_build: Reference Genome: PRJNA270931, Reference assembly: GCA_001194135.1
Supplementary_files_format_and_content: TPMs for all samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using reference assembly gene models. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
|
| |
|
| Submission date |
Aug 04, 2018 |
| Last update date |
Jan 31, 2021 |
| Contact name |
Leonid L Moroz |
| E-mail(s) |
moroz@whitney.ufl.edu
|
| Organization name |
University of Florida
|
| Street address |
9505 Ocean Shore Blvd
|
| City |
St Augustine |
| State/province |
FL |
| ZIP/Postal code |
32080 |
| Country |
USA |
| |
|
| Platform ID |
GPL25424 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN09766106 |
| SRA |
SRX4508538 |
