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  1. IGB
  2. IGBF-3864

Find more single cell RNA seq datasets in10XGenomics

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          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

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              relates to

              Task - A task that needs to be done. IGBF-3880 Investigate samtools tags consistency across datasets from Cell Ranger

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3838 Obtain and view sequence read alignments for PBMC dataset from Seurat vignette

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3863 Investigate Seurat marker gene alignments in IGB

              • Major - Major loss of function.
              • Closed

                Activity

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                karthik Karthik Raveendran created issue -
                karthik Karthik Raveendran made changes -
                Field Original Value New Value
                Epic Link IGBF-3765 [ 22984 ]
                karthik Karthik Raveendran made changes -
                Link This issue blocks IGBF-3863 [ IGBF-3863 ]
                karthik Karthik Raveendran made changes -
                Link This issue blocks IGBF-3838 [ IGBF-3838 ]
                karthik Karthik Raveendran made changes -
                Link This issue relates to IGBF-3863 [ IGBF-3863 ]
                karthik Karthik Raveendran made changes -
                Link This issue blocks IGBF-3838 [ IGBF-3838 ]
                karthik Karthik Raveendran made changes -
                Link This issue blocks IGBF-3863 [ IGBF-3863 ]
                karthik Karthik Raveendran made changes -
                Link This issue relates to IGBF-3838 [ IGBF-3838 ]
                ann.loraine Ann Loraine made changes -
                Description IGBF-3838 and IGBF-3863, investigates PMBC bam file that was published in 2016. Find and view single cell datasets that are more recently published. IGBF-3838 and IGBF-3863, investigates PMBC bam file that was published in 2016. Find and view single cell datasets that are more recently published.
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                nfreese Nowlan Freese added a comment - - edited

                I would like to see:

                • One newer bam file (2022-2024) that was created with a more up to date version of CellRanger.
                • 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

                Show
                nfreese Nowlan Freese added a comment - - edited I would like to see: One newer bam file (2022-2024) that was created with a more up to date version of CellRanger. 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
                karthik Karthik Raveendran made changes -
                Description IGBF-3838 and IGBF-3863, investigates PMBC bam file that was published in 2016. Find and view single cell datasets that are more recently published. IGBF-3838 and IGBF-3863, investigates PBMC bam file that was published in 2016. Find and view single cell datasets that are more recently published.
                karthik Karthik Raveendran made changes -
                Description IGBF-3838 and IGBF-3863, investigates PBMC bam file that was published in 2016. Find and view single cell datasets that are more recently published. 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.
                karthik Karthik Raveendran made changes -
                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. 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 upto 5 datasets.
                karthik Karthik Raveendran made changes -
                Summary Find more single cell datasets and view in IGB Find more single cell RNA seq datasets in 10XGenomics
                karthik Karthik Raveendran made changes -
                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 upto 5 datasets. 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.
                karthik Karthik Raveendran made changes -
                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. 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
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                karthik Karthik Raveendran added a comment - - edited

                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:

                Show
                karthik Karthik Raveendran added a comment - - edited 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:
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                karthik Karthik Raveendran added a comment - - edited

                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

                Show
                karthik Karthik Raveendran added a comment - - edited 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
                ann.loraine Ann Loraine made changes -
                Sprint Summer 7 [ 201 ] Summer 7, Fall 1 [ 201, 202 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                karthik Karthik Raveendran added a comment - - edited

                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

                Show
                karthik Karthik Raveendran added a comment - - edited 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
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                karthik Karthik Raveendran added a comment - - edited

                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.

                Show
                karthik Karthik Raveendran added a comment - - edited 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.
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Summary Find more single cell RNA seq datasets in 10XGenomics Find more single cell RNA seq datasets in10XGenomics
                karthik Karthik Raveendran made changes -
                Link This issue relates to IGBF-3880 [ IGBF-3880 ]
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                nfreese Nowlan Freese added a comment -

                Closing ticket

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                nfreese Nowlan Freese added a comment - Closing ticket
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Assignee Karthik Raveendran [ karthik ]

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                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    karthik Karthik Raveendran
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                      Updated:
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