Access to dataset

[Prekovic, S. (Stefan)]

Dear cBioPortal staff,

I am reaching out about a bladder cancer dataset (Cell Reports, 2022) that I am unable to access. I've been in contact with the lead author, and while they are trying to work on it from their end, they also suggested I should reach out to you, to see if you can share the dataset (both copy number and mutations) with me and my team. Thank you so much.

Cheers,

- -

Stefan Prekovic, PhD

Assistant Professor / Group Leader

Center for Molecular Medicine

University Medical Centre Utrecht

Utrecht

The Netherlands

---

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

---

This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.

Please consider the environment before printing this e-mail.

[Prekovic, S. (Stefan)]

Dear cBioPortal staff,

Could you please let me know if you can share the particular dataset referenced in my previous email (below).

Cheers,

Stefan

---

From: Prekovic, S. (Stefan)
Sent: Saturday, March 4, 2023 7:54:46 AM
To: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Access to dataset

 

[de Bruijn, Ino]

Hi Stefan,

 

Thanks for reaching out! Apologies for the delay in getting back to you – I’m forwarding your request to our data curation team

 

They should be able to assist you if we have received the data

 

Thanks so much!

Ino

 

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Prekovic, S. (Stefan) <S.Pre...@umcutrecht.nl>
Date: Wednesday, March 8, 2023 at 10:00 PM
To: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] Fwd: Access to dataset

Dear cBioPortal staff, Could you please let me know if you can share the particular dataset referenced in my previous email (below). Cheers, Stefan From: Prekovic, S. (Stefan) Sent: Saturday, March 4, 2023 7: 54: 46 AM To: cbioportal@ googlegroups. com

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/GV1PR10MB6634FAF7A5682174F1C74BB586B79%40GV1PR10MB6634.EURPRD10.PROD.OUTLOOK.COM.

=====================================================================

Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.

Disclaimer ID:MSKCC

[Prekovic, S. (Stefan)]

Dear all,

Have you had the chance to look at my request?

Thank you so much; i really appreciate the help.

Cheers,

- -

Stefan Prekovic, PhD

Assistant Professor / Group Leader

Center for Molecular Medicine

University Medical Centre Utrecht

Utrecht

The Netherlands

---

From: de Bruijn, Ino <debr...@mskcc.org>
Sent: Thursday, March 9, 2023 4:05 AM
To: Prekovic, S. (Stefan) <S.Pre...@umcutrecht.nl>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Cc: Kundra, Ritika <kun...@mskcc.org>; Satravada, Baby <Satr...@mskcc.org>; Madupuri, Ramyasree <madu...@mskcc.org>
Subject: Re: Access to dataset

 

[de Bruijn, Ino]

Hi Stefan,

 

Turns out the URL in the paper is incorrect. It should be:

 

https://www.cbioportal.org/study/summary?id=paired_bladder_2022

 

CC’ing authors to make them aware (URL in paper is pointing to our internal MSK instance)

 

Let us know if you have any further questions

 

Thanks!

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/GV1PR10MB6634E626803A0899167775ED86B99%40GV1PR10MB6634.EURPRD10.PROD.OUTLOOK.COM.

[Solit, David]

Stefan, I assume you can see it in the Public Version of cBioPortal.

[Prekovic, S. (Stefan)]

Dear all,

Indeed, i can access it through that link and download the patient’s information. However, i still dont have the access to mutation data for all genes etc.

As you can see below the download button is missing in the data set section of the portal:

Sorry for the inconvenience. And thank you so much for your assistance.

Cheers,

- -

Stefan Prekovic, PhD

Assistant Professor / Group Leader

Center for Molecular Medicine

University Medical Centre Utrecht

Utrecht

The Netherlands

---

From: Solit, David <sol...@MSKCC.ORG>
Sent: Monday, March 13, 2023 7:29:55 PM
To: de Bruijn, Ino <debr...@mskcc.org>; Prekovic, S. (Stefan) <S.Pre...@umcutrecht.nl>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>

[Ritika Kundra]

Hi Stefan,

The datasets will be made available today for download.

Thanks,

Ritika

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/GV1PR10MB6634C197D002D9EBB83F721186B99%40GV1PR10MB6634.EURPRD10.PROD.OUTLOOK.COM.

[Prekovic, S. (Stefan)]

Dear Ritika,

 

Thank you so much for the help.

 

Cheers,

Stefan