Locating Geoduck single-cell RNAseq data

[sr320]

Somewhere there is single-cell geoduck RNAseq data
Any help finding this would be great

[kubu4]

Fairly certain Roberts Lab does not have this data.

[sr320]

A hint ... it is referred to here
https://github.com/sr320/paper-geoduck-gene-exp

top marker genes refer to single-cell data
https://htmlpreview.github.io/?https://github.com/sr320/paper-geoduck-gene-exp/blob/main/manuscript.html

[mgavery]

data: on gannet (/var/services/homes/charlie/geoduck_scRNASeq)

getting from the Cell Ranger -> clustering/top marker genes (using monocle) is attached.

geoduck_monocle.R.txt

[sr320]

@mgavery Thanks! and the four samples correspond to?

G1 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G1_introns/") 
G2 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G2_introns/") 
G3 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G3_introns/") 
G4 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G4_introns/") 

[mgavery]

They’re 4 separate samples of cells from geoduck gastrulae. Each sample (G1-4) targets a few thousand cells. Sent from my iPhoneOn Jun 17, 2026, at 8:07 PM, Steven Roberts ***@***.***> wrote:sr320 left a comment (RobertsLab/resources#2457) @mgavery Thanks! and the four samples correspond to? G1 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G1_introns/") G2 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G2_introns/") G3 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G3_introns/") G4 = load_cellranger_data(pipestance_path = "~/Documents/geoduck_scRNASeq/include_introns_outs/geoduck_G4_introns/") —Reply to this email directly, view it on GitHub, or unsubscribe.Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS and Android. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

[mgavery]

Protocol notes (in Mac's Gdrive folder and pasted below)

On 2/24/22 geoduck early embryos (17 hours post fertilization) were dissociated and cells prepared for single-cell RNA sequencing. We targeted 24,000 cells (6000 cells across 4 10x reactions)

Protocol: attached

Stage: early gastrula? - that is what we were aiming for. There is not good information for Pacific geoduck on developmental timing in early development.

Source: fertilized eggs (pooled parents) were brought back to UW lab from Taylor hatchery on 2/23/22. Embryos were kept at 16C during transit and placed in 16C incubator until time of sampling (images attached)

[Geoduck Embryo Cell Dissociation Protocol (1).pdf](https://github.com/user-attachments/files/29107517/Geoduck.Embryo.Cell.Dissociation.Protocol.1.pdf)

[sr320]

Curious if we have actual sequence data (pre Cell-Ranger processing)?

[mgavery]

sequence data is in same folder. Specific path:

~/geoduck_scRNASeq/geoduck_embryo_r1/outs/fastq_path/AAAM5KLHV

[mgavery]

I just added a "job_files" folder. Includes the mkref command for Cell Ranger as well as the Cell Ranger scripts for each batch of cells.