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Upload Geoduck RNA-seq Raw data to SRA #630

Closed sr320 closed 5 years ago

sr320 commented 5 years ago

Particularly need accession numbers for

NR021_S8_L001_R1_001.fastq,NR021_S8_L002_R1_001.fastq \
NR021_S8_L001_R2_001.fastq,NR021_S8_L002_R2_001.fastq \

for Emmas paper.

kubu4 commented 5 years ago

What are these? Nightingales has these listed, but has no other information for them (other than species).

I found this notebook entry of yours: https://sr320.github.io/Illumina-Summary/

Seeing that, it seems fair to say these are "Larvae Day 5". However, I need more info for the SRA submission. What does day 5 represent - day 5 post-fertilization? Day 5 of some treatment? Day 5 of the larval stage?

Also, were there any treatments that I should be aware of?

Sorry for all the questions - don't have access to that Google Doc with the manuscript yet.

sr320 commented 5 years ago

What are these? Nightingales has these listed, but has no other information for them (other than species).

Should probably submit issue that Nightingales needs updating :)

Larvae are 5 days post fertilization, no treatment.

kubu4 commented 5 years ago

Adding Hollie's sample sheet for prosperity:

https://github.com/hputnam/project_larval_geoduck_OA/blob/master/Larval_Sample_Info.csv

And, sample submission to Illumina:

https://robertslab.github.io/sams-notebook/2016/12/21/sample-submission-geoduck-tissue-gdna-for-illumina-pilot-sequencing-project.html

kubu4 commented 5 years ago

PRJNA529226:

https://www.ncbi.nlm.nih.gov/bioproject/529226

SRA recommends using BioProject accession for publications (which is what's linked above), instead of the SRR/SRP accession