Quentmeier et al: The LL-100 panel: 100 cell lines for blood cancer studies. Sci Rep 2019.

[mcnaircm]

Link to paper on pubmed (PMID=PMC6547646): PubMedLink
Link to files associated with WES: EBI_WES_Data
Link to files associated with RNASeq: EBI_RNASeq_Data

Please keep this checklist for curation of a new study.

• create a issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
• List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
• Document the curation process, e.g. how and by whom the data was transformed
• Follow the data checklist
• Create a pull request to datahub once the data is curated
• Push to triage portal
• Import into msk and public portal database
• Update the default quick select study list see options for selecting tcga + non-tcga studies cbioportal#5831 (only for studies that are not overlapping with existing ones; only for human tumors, not cell lines)
• Update cBioPortal news

[yichaoS]

Data Issue:

• Under the ENA data links seems like there are are only separated FASTQ files for each sample.
• In the paper’s supplemental section, seems like there’s no data we can use either.

[mcnaircm]

What data types are needed for RNASeq and WES experiments in order to be curated and used?

…

________________________________ From: Yichao Sun <notifications@github.com> Sent: Thursday, January 30, 2020 3:38 PM To: cBioPortal/datahub <datahub@noreply.github.com> Cc: Christopher McNair <Christopher.McNair@jefferson.edu>; Author <author@noreply.github.com> Subject: Re: [cBioPortal/datahub] Quentmeier et al: The LL-100 panel: 100 cell lines for blood cancer studies. Sci Rep 2019. (#850) WARNING: External Email - This email originated outside of Jefferson. DO NOT CLICK links or attachments unless you recognize the sender and are expecting the email. Data Issue: * Under the ENA data links seems like there are are only separated FASTQ files for each sample. * In the paper’s supplemental section, seems like there’s no data we can use either. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FcBioPortal%2Fdatahub%2Fissues%2F850%3Femail_source%3Dnotifications%26email_token%3DAEY7EEQCLPL2KVT43XRICEDRAM3FJA5CNFSM4I73DGPKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKMPI4A%23issuecomment-580449392&data=02%7C01%7Cchristopher.mcnair%40jefferson.edu%7C79d8f84ba3d946b01fc608d7a5c4677a%7C55a89906c710436bbc444c590cb67c4a%7C0%7C1%7C637160135282863373&sdata=QJsV%2FOFn1PC8CDicZVAUnpdgRAX%2Bm5EW%2FzSo4jfNndo%3D&reserved=0>, or unsubscribe<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAEY7EESONNXOC2RGD5XZHI3RAM3FJANCNFSM4I73DGPA&data=02%7C01%7Cchristopher.mcnair%40jefferson.edu%7C79d8f84ba3d946b01fc608d7a5c4677a%7C55a89906c710436bbc444c590cb67c4a%7C0%7C1%7C637160135282873367&sdata=VOKAt83%2BByqP3sMt0zwx4nYc7kxiUgd17qcaiMFAJV0%3D&reserved=0>. The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

[yichaoS]

Hi @mcnaircm We defined our file format here: https://github.com/cbioportal/cbioportal/blob/master/docs/File-Formats.md

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[jjgao]

Since we could not find the data, let's close it for now.