Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Summer 7, Fall 1
Description
IGBF-3838 and IGBF-3863, investigates PBMC bam file that was published in 2016. Find single cell RNA seq datasets and provide links that someone can use to open up in IGB. Provide a description for the dataset including genome assembly, data creation date, species, publications associated. Find up to 5 datasets.
10XGenomics Datasets: https://www.10xgenomics.com/datasets?query=&page=1&configure%5BhitsPerPage%5D=50&configure%5BmaxValuesPerFacet%5D=1000
Attachments
Issue Links
Activity
Datasets that uses Cell Ranger v8.0.0
| Dataset Link | Genome Version | Species | Publication | Published Date | Quickload Link | Bulk Download |
|---|---|---|---|---|---|---|
| 10k Human PBMCs Stained with TotalSeq™-B Human TBNK Cocktail, Chromium GEM-X Single Cell 3' | GRCh38.p14 | Human | NA | 2024-03-13 | Quickload | bam , bai |
| 5k Mouse Splenocytes, Chromium NextGEM Single Cell 5' | GRCm39-2024-A | Mouse | NA | 2024-04-15 | Quickload | bam , bai |
| 10k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells, Chromium NextGEM Single Cell 3' | GRCm39-2024-A | Mouse | NA | 2024-04-15 | Quickload | bam , bai |
| 1k A375 Cells Transduced with Non-Target and Target sgRNA, Chromium GEM-X Single Cell 5' | GRCh38-2024-A | Human | NA | 2024-04-15 | Quickload | bam , bai |
| 10k Human DTC Melanoma, Chromium GEM-X Single Cell 3' | GRCh38-2024-A | Human | NA | 2024-03-13 | Quickload | bam , bai |
The Dataset URL goes to a page with a link to "Output and Supplemental files". On that page, there is an option "bulk download." Clicking "bulk download" shows the URL of the bam alignment file and its index:
I am still trying to find publications that uses these datasets or similar datasets for their research so that we can observe genes of interest mentioned in those publications in IGB. If I can find the GEO accession numbers of these datasets it would be easier to find related publications. I could not find any indication if these datasets have been uploaded to NCBI GEO/SRA. 10xGenomics does however have instructions on how to submit the data there. Looking for any information there to help with the publication search.
https://kb.10xgenomics.com/hc/en-us/articles/360024716391-What-format-of-10x-Genomics-data-should-I-submit-to-NCBI-GEO-SRA
Dataset from different Cell Ranger versions to find if the samtags are consistent across pipeline version.
| Dataset Link | Genome Version | Species | CR version | Publication | Published Date | Quickload Link | Bulk Download |
|---|---|---|---|---|---|---|---|
| 5k Human PBMCs | GRCh38-2020-A | Human | 7.0.1 | NA | 2022-10-18 | Quickload | bam , bai |
| 10k Human PBMCs | GRCh38-2020-A | Human | 6.1.2 | NA | 2022-03-29 | Quickload | bam , bai |
| PBMCs from a Healthy Donor | GRCh38-2020-A | Human | 4.0.0 | NA | 2020-07-07 | Quickload | bam , bai |
| 10k PBMCs from a Healthy Donor | GRCh38 | Human | 3.0.0 | NA | 2018-11-19 | Quickload | bam , bai |
The Dataset URL goes to a page with a link to "Output and Supplemental files". On that page, there is an option "bulk download." Clicking "bulk download" shows the URL of the bam alignment file and its index
*CR Version => Cell Ranger Version
After discussing with Dr. Nowlan Freese, the immediate purpose of the datasets is to see if the samtool tags is consistent across cell ranger pipeline versions. Finding relevant publications and observing the genes of interest in those publications in IGB can be put off until the samtool tags' consistency has been verified and the possibility of adding them to the IGB filter function is considered and possibly implemented. The datasets mentioned above should be enough to do that.
Moving this ticket to first level review.
Closing ticket
I would like to see:
One newer bam file (2022-2024) that was created with something other than 10X genomics.This will be addressed in a separate ticket.Searchable datasets at 10X genomics: https://www.10xgenomics.com/datasets?query=&page=2&configure%5BhitsPerPage%5D=50&configure%5BmaxValuesPerFacet%5D=1000