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Sample GSM3319155 Query DataSets for GSM3319155
Status Public on Jan 31, 2021
Title Brachial_Ganglion
Sample type SRA
 
Source name RNA extracted from whole tissue
Organism Octopus bimaculoides
Characteristics tissue: Brachial_Ganglion
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 NextSeq 500
 
Description 4_Ob_ArmCord-J13
O_bimaculoides_TPM_NextSeqRuns
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) [email protected]
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 GPL25425
Series (1)
GSE118128 Cephalopod Neurogenomics
Relations
BioSample SAMN09766152
SRA SRX4508628

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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