Update SRA to use the correct sample codes for Muday lab time course data

Check for SRA update:

• Visually checking one of the samples to see if it has been changed correctly
• "SRA record SRR25478288 should be re-annotated with sample code V.34.30.9"
• By using Run Selector I searched for the specific SRR name and found that it is still annotated as "F.34.30.9" and not the corrected version "V.34.30.9"
• The SRA has not been updated with the re-annotated names

Biosample data is all correct upon checking.

The metatable for SRA still contains the same 16 errors (V and F get switched in the labelling).
Attempting to alter the metatable to reflect this.
So in their records, the metatable has the error with 16 mislabelled samples.

In OUR file that was submitted
(https://docs.google.com/spreadsheets/d/1n4nsE4E8lykivizPtQyf17XJnL7FRELR/edit?usp=sharing&ouid=100714234126361751017&rtpof=true&sd=true )

it is all correct!

Pulling the table down from NCBI, these lines are the ones that get switched:

When we go from top down via the Bioproject:

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1017816

We see the 72 samples.
In the SRA table, I can see the errors as so:

I made changes and submitted to the SRA.
Changes now look like this:

! Can't seem to post the image!

SRR25478273
SRR25478277
SRR25478274
SRR25478276
SRR25478278
SRR25478272
SRR25478291
SRR25478260
SRR25478259
SRR25478262
SRR25478292
SRR25478289
SRR25478261
SRR25478288
SRR25478275
SRR25478279

We now wait.
Once we get word that SRA has made changes, we can retest the download.

SRA is now updated!
According to them.

I think we are ready to test once again if things are correct!
Assigning to Molly for testing which will act as the review.

After reviewing the changed names in run selector it seems that the "Library Names" were changed for the samples that needed to be re-annotated. But the other columns "replicate_code" and " Sample Name" were not changed. I put a picture of an example below. Each column will need to match before we can move forward with running it through nextflow again. Moving back to to do.

Uhoh, that will get trickier.
Those columns are not editable via the manage data tabs.

I will send an email to the SRA to get the Replicate code and library name columns to be in sync with Sample name column.

Rob

Apparently we do not contact the SRA people. The SRA data is correct.
We need to contact the Biosample people. biosamplehelp@ncbi.nlm.nih.gov

I will ping them and request the changes, as I cannot edit that metatable directly.

Rob

PRJNA1017816-changes2Biosample-reAssignSRR.xlsx

I have sent them what I think is a simple excel sheet highlighting these differences at the Biosample level.
We will see how they respond.
R

Changes made!
Time to review if all changes have truly been made.

For review:

Check the SRA and its various tables to see if there are any of the mislabels in there.

Review: I use the Run selector for SRP460750 on NCBI to check the newly re-annotated runs. I will review each of the 16 that needed to be re-annoted based on the check SRA markdown created.

• SRR25478288 was re-annotated with sample code V.34.30.9
• SRR25478289 was re-annotated with sample code V.28.30.9
• SRR25478291 was re-annotated with sample code V.34.15.9
• SRR25478292 was re-annotated with sample code V.28.15.9
• SRR25478276 was re-annotated with sample code V.34.75.9
• SRR25478277 was re-annotated with sample code V.28.75.9
• SRR25478278 was re-annotated with sample code V.34.45.9
• SRR25478279 was re-annotated with sample code V.28.45.9
• SRR25478272 was re-annotated with sample code F.34.30.9
• SRR25478273 was re-annotated with sample code F.28.30.9
• SRR25478274 was re-annotated with sample code F.34.15.9
• SRR25478275 was re-annotated with sample code F.28.15.9
• SRR25478259 was re-annotated with sample code F.34.75.9
• SRR25478260 was re-annotated with sample code F.28.75.9
• SRR25478261 was re-annotated with sample code F.34.45.9
• SRR25478262 was re-annotated with sample code F.28.45.9

After checking each of the samples that need to be re-annotated on SRA I see no problem with the data. Assigning ticket back to Dr. Reid to finalize and move to done! Then Once this ticket is closed new tickets can be made to rerun the new re-annotated data through the pipeline again.