Posts in Core Rigor and Reproducibility (CoRRe)

Found quite a few have been given for a few at MSKCC … for example.



  *
SCR_017850<https://scicrunch.org/resources/Any/search?q=SCR_017850&l=SCR_017850>
- Molecular Cytogenetics Core Facility
  *
SCR_017691<https://scicrunch.org/resources/Any/search?q=SCR_017691&l=SCR_017691>
- Antibody & Bioresource Core Facility
  *
SCR_017853<https://scicrunch.org/resources/Any/search?q=SCR_017853&l=SCR_017853>
- Investigational Products Support Core Facility

From: Frances Weis-Garcia <email obscured>>
Date: Tuesday, June 2, 2020 at 11:48 AM
To: "Core Rigor and Reproducibility (CoRRe)" <email obscured>>
Subject: We have an RRID number

We have an RRID number
But cannot find other cores with RRID numbers (yet)

Only matters if we want to define the structure of the core RRID

[A screenshot of a cell phone  Description automatically generated]

image001.png 377.3kb

Sure!!

Laura Bover, PhD
Professor
Director Monoclonal Antibody Core Facility
University of Texas M.D.Anderson Cancer Center
Associate member of The University of Texas Graduate School of Biomedical
Sciences at Houston
Member of the Scientific Review Committee 2 (former CRC 2)
Member of the Steering Committee of the Immunology Program GSBS
Immunology Department/ Genomics Medicine Department
7455 Fannin St<x-apple-data-detectors://1/1> Room 1SCR4.2021
Houston- TX 77054<x-apple-data-detectors://2/0>
T  713-563-3301<tel:713-563-3301>
F 713-563-3276<tel:713-563-3276>
<email obscured><email obscured>>

On Jan 22, 2020, at 12:04 PM, Frances Weis-Garcia
<email obscured>> wrote:

I'm so glad you are attending.
We have to make time for a drink.

Frances

ZRC 1563
Office     646-888-2354
Mobile   516-967-0656


On 1/22/20, 1:01 PM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Bover,Laura" <email obscured> on behalf of <email obscured>> wrote:

   Thanks for the clarification! Obviously I was thinking in my type of
experiments, trying to identify new markers upon treatment with certain agents.
   We used to have a Core here for identification of cell lines, but I am not
sure of it is still operating.
   Thanks!
   And see you soon at ABRF meeting!
   Laura

   Laura Bover, PhD
   Professor
   Director Monoclonal Antibody Core Facility
   University of Texas M.D.Anderson Cancer Center
   Associate member of The University of Texas Graduate School of Biomedical
Sciences at Houston
   Member of the Scientific Review Committee 2 (former Clinical Research
Committee 2)
   Member of the Steering Committee of the Immunology Program GSBS
   Immunology Department/ Genomics Medicine Department
   7455 Fannin St Room 1SCR4.2021
   Houston- TX 77054
   T  713-563-3301 <tel:713-563-3301>
   F 713-563-3276 <tel:713-563-3276>
   <email obscured>


   On 1/21/20, 11:22 PM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Frances Weis-Garcia" <email obscured> on behalf of
<email obscured>> wrote:

       Thanks Laura and sorry for the confusion.

       What I am looking for is a way to tell cell line apart if they come from
the same parent.  For human lines that are from different people, STR profiles
are perfect ... but for lines derived from the same original (parent) line ...
there is currently no easy way to tell the difference between parent line A and
children lines A1, A2 much less grandchild A1.3.  Make sense ... If it was a
hybridoma, I would just sequence the CDRs.

       A colleague of mine and I were thinking of inserting a "DNA barcode" in
the lines, probably via CRISPR so we can put in as innocuous a site as
possible, but before developing a solving I was really hoping one already
existed ... so I thought I would poll this group ...

       All about cell line authentication ... one of the many building blocks
needed for RnR.

       Frances

       ZRC 1563
       Office     646-888-2354
       Mobile   516-967-0656


       On 1/21/20, 7:39 PM, "Core Rigor and Reproducibility (CoRRe) on behalf
of Bover,Laura" <email obscured> on behalf of <email obscured>> wrote:

           So, do you need to differentiate the parent cells from the ones
resulted from the division or proliferating?

           May be is not your question.
           What about staining with CFSE a bunch of cells and let them to
divide and sort the different peaks (usually 7, at least in normal cells such
as T cells proliferating) by FACS. The mean fluorescence as you know is going
lower with each division. Is that what you need?
           Depending on the proliferation time you will be able to separate the
last progeny, as well as the intermediate.

           In normal T cells after 5 days you can recover cells from each
division. Not sure if with a cell line you could do the same.

           Laura Bover, PhD
           Professor
           Director Monoclonal Antibody Core Facility
           University of Texas M.D.Anderson Cancer Center
           Associate member of The University of Texas Graduate School of
Biomedical Sciences at Houston
           Member of the Scientific Review Committee 2 (former CRC 2)
           Member of the Steering Committee of the Immunology Program GSBS
           Immunology Department/ Genomics Medicine Department
           7455 Fannin St Room 1SCR4.2021
           Houston- TX 77054
           T  713-563-3301 <tel:713-563-3301>
           F 713-563-3276 <tel:713-563-3276>
           <email obscured>

           In order to continue obtaining Core support in a challenging
environment, it is crucial that our users acknowledge the following grants in
all publications (see following text).  Thank you!
            “This work was supported in part by CCSG grant number P30
CA016672.”

           iLab-Solutions links:
https://mdanderson.ilabsolutions.com/service_center/show_external/3631
           or:  https://mdanderson.ilabsolutions.com/account/login
           If you do not already have an iLab account please create one prior
to sample submission


           On 1/21/20, 8:15 AM, "Core Rigor and Reproducibility (CoRRe) on
behalf of Frances Weis-Garcia" <email obscured> on behalf of
<email obscured>> wrote:

               WARNING: This email originated from outside of MD Anderson.
Please validate the sender's email address before clicking on links or
attachments as they may not be safe.

               Question ... Does anyone know of a way to reliably differentiate
between decedents / children of a cell line as well as the parent?

               One solution is to insert a plasmid to serve as an internal
barcode, but maybe there are other options ...
               ――
               View topic http://list.abrf.org/r/topic/34QaaQAFJeqW0i9xRxpxdF
               Leave group <email obscured>?Subject=Unsubscribe



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Thanks for the clarification! Obviously I was thinking in my type of
experiments, trying to identify new markers upon treatment with certain agents.
We used to have a Core here for identification of cell lines, but I am not sure
of it is still operating.
Thanks!
And see you soon at ABRF meeting!
Laura

Laura Bover, PhD
Professor
Director Monoclonal Antibody Core Facility
University of Texas M.D.Anderson Cancer Center
Associate member of The University of Texas Graduate School of Biomedical
Sciences at Houston
Member of the Scientific Review Committee 2 (former Clinical Research Committee
2)
Member of the Steering Committee of the Immunology Program GSBS
Immunology Department/ Genomics Medicine Department
7455 Fannin St Room 1SCR4.2021
Houston- TX 77054
T  713-563-3301 <tel:713-563-3301>
F 713-563-3276 <tel:713-563-3276>
<email obscured>


On 1/21/20, 11:22 PM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Frances Weis-Garcia" <email obscured> on behalf of
<email obscured>> wrote:

    Thanks Laura and sorry for the confusion.

    What I am looking for is a way to tell cell line apart if they come from
the same parent.  For human lines that are from different people, STR profiles
are perfect ... but for lines derived from the same original (parent) line ...
there is currently no easy way to tell the difference between parent line A and
children lines A1, A2 much less grandchild A1.3.  Make sense ... If it was a
hybridoma, I would just sequence the CDRs.

    A colleague of mine and I were thinking of inserting a "DNA barcode" in the
lines, probably via CRISPR so we can put in as innocuous a site as possible,
but before developing a solving I was really hoping one already existed ... so
I thought I would poll this group ...

    All about cell line authentication ... one of the many building blocks
needed for RnR.

    Frances

    ZRC 1563
    Office     646-888-2354
    Mobile   516-967-0656


    On 1/21/20, 7:39 PM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Bover,Laura" <email obscured> on behalf of <email obscured>> wrote:

        So, do you need to differentiate the parent cells from the ones
resulted from the division or proliferating?

        May be is not your question.
        What about staining with CFSE a bunch of cells and let them to divide
and sort the different peaks (usually 7, at least in normal cells such as T
cells proliferating) by FACS. The mean fluorescence as you know is going lower
with each division. Is that what you need?
        Depending on the proliferation time you will be able to separate the
last progeny, as well as the intermediate.

        In normal T cells after 5 days you can recover cells from each
division. Not sure if with a cell line you could do the same.

        Laura Bover, PhD
        Professor
        Director Monoclonal Antibody Core Facility
        University of Texas M.D.Anderson Cancer Center
        Associate member of The University of Texas Graduate School of
Biomedical Sciences at Houston
        Member of the Scientific Review Committee 2 (former CRC 2)
        Member of the Steering Committee of the Immunology Program GSBS
        Immunology Department/ Genomics Medicine Department
        7455 Fannin St Room 1SCR4.2021
        Houston- TX 77054
        T  713-563-3301 <tel:713-563-3301>
        F 713-563-3276 <tel:713-563-3276>
        <email obscured>

        In order to continue obtaining Core support in a challenging
environment, it is crucial that our users acknowledge the following grants in
all publications (see following text).  Thank you!
         “This work was supported in part by CCSG grant number P30 CA016672.”

        iLab-Solutions links:
        https://mdanderson.ilabsolutions.com/service_center/show_external/3631
        or:  https://mdanderson.ilabsolutions.com/account/login
        If you do not already have an iLab account please create one prior to
sample submission


        On 1/21/20, 8:15 AM, "Core Rigor and Reproducibility (CoRRe) on behalf
of Frances Weis-Garcia" <email obscured> on behalf of
<email obscured>> wrote:

            WARNING: This email originated from outside of MD Anderson. Please
validate the sender's email address before clicking on links or attachments as
they may not be safe.

            Question ... Does anyone know of a way to reliably differentiate
between decedents / children of a cell line as well as the parent?

            One solution is to insert a plasmid to serve as an internal
barcode, but maybe there are other options ...
            ――
            View topic http://list.abrf.org/r/topic/34QaaQAFJeqW0i9xRxpxdF
            Leave group <email obscured>?Subject=Unsubscribe



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The information contained in this e-mail message may be privileged,
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authorized representative of the intended recipient, any further review,
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So, do you need to differentiate the parent cells from the ones resulted from
the division or proliferating?

May be is not your question.
What about staining with CFSE a bunch of cells and let them to divide and sort
the different peaks (usually 7, at least in normal cells such as T cells
proliferating) by FACS. The mean fluorescence as you know is going lower with
each division. Is that what you need?
Depending on the proliferation time you will be able to separate the last
progeny, as well as the intermediate.

In normal T cells after 5 days you can recover cells from each division. Not
sure if with a cell line you could do the same.

Laura Bover, PhD
Professor
Director Monoclonal Antibody Core Facility
University of Texas M.D.Anderson Cancer Center
Associate member of The University of Texas Graduate School of Biomedical
Sciences at Houston
Member of the Scientific Review Committee 2 (former CRC 2)
Member of the Steering Committee of the Immunology Program GSBS
Immunology Department/ Genomics Medicine Department
7455 Fannin St Room 1SCR4.2021
Houston- TX 77054
T  713-563-3301 <tel:713-563-3301>
F 713-563-3276 <tel:713-563-3276>
<email obscured>

In order to continue obtaining Core support in a challenging environment, it is
crucial that our users acknowledge the following grants in all publications
(see following text).  Thank you!
 “This work was supported in part by CCSG grant number P30 CA016672.”

iLab-Solutions links:
https://mdanderson.ilabsolutions.com/service_center/show_external/3631
or:  https://mdanderson.ilabsolutions.com/account/login
If you do not already have an iLab account please create one prior to sample
submission


On 1/21/20, 8:15 AM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Frances Weis-Garcia" <email obscured> on behalf of
<email obscured>> wrote:

    WARNING: This email originated from outside of MD Anderson. Please validate
the sender's email address before clicking on links or attachments as they may
not be safe.

    Question ... Does anyone know of a way to reliably differentiate between
decedents / children of a cell line as well as the parent?

    One solution is to insert a plasmid to serve as an internal barcode, but
maybe there are other options ...
    ――
    View topic http://list.abrf.org/r/topic/34QaaQAFJeqW0i9xRxpxdF
    Leave group <email obscured>?Subject=Unsubscribe



The information contained in this e-mail message may be privileged,
confidential, and/or protected from disclosure. This e-mail message may contain
protected health information (PHI); dissemination of PHI should comply with
applicable federal and state laws. If you are not the intended recipient, or an
authorized representative of the intended recipient, any further review,
disclosure, use, dissemination, distribution, or copying of this message or any
attachment (or the information contained therein) is strictly prohibited. If
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the sender by return e-mail and delete all references to it and its contents
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Question ... Does anyone know of a way to reliably differentiate between
decedents / children of a cell line as well as the parent?

One solution is to insert a plasmid to serve as an internal barcode, but maybe
there are other options ...

Dear ABRF Core Rigor and Reproducibility Discussion Forum Members,

I just wanted to remind all of this that this is here for us to share
information, announce opportunities (e.g. the R2T game and the ABRF SW) focused
on RnR (and T), as well as ask questions, field ideas and even vent.

We are a pretty quite group ... but all share a common interest.

Hope everyone thinks about posting to this forum, shareing it with others and
by doing so, making each of us a bit wiser.

Frances

Dear Colleagues,

This may be of interest to many of you, a fun way to incorporate some R2T
training:

Kaizen is a gamified online training program for academic researchers developed
at UAB. The first game focuses on Rigor, Reproducibility, and Transparency.
The game begins February 17 and lasts one month; there will be teamwork and
prizes, all enabled by the Kaizen app.  And, its free!  More details and link
to registration (deadline is January 31) form
https://edgeforscholars.org/game-on-join-kaizen-to-score-rigor-reproducibility-training-points/

Susan Meyn | Director for Research Resources & Strategy
Vanderbilt University Medical Center | Office of Research
<http://www.vumc.org/oor/>
Twitter: @VUMCResearch | 615.322.0470 | <email obscured><email obscured>>

Wonderful!

On 10/28/19, 1:11 PM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Bover,Laura" <email obscured> on behalf of <email obscured>> wrote:

    I will probably go. This time I will not be in Argentina

    Sent from my iPhone

    > On Oct 28, 2019, at 12:05 PM, Frances Weis-Garcia
<email obscured>> wrote:
    >
    > Sure
    >
    > ABRF2020
    > Feb 29th - March 3rd
    > Palm Springs, CA
    >
    > https://conf.abrf.org/
    >
    > Registration should open soon.
    >
    >
    >
    > On 10/28/19, 10:33 AM, "Core Rigor and Reproducibility (CoRRe) on behalf
of Bover,Laura" <email obscured> on behalf of <email obscured>> wrote:
    >
    >    Frances please se d me the dates of ABRF 2020. I probably missed that
from previous emails because many of those mails fall in quarantine and after 7
dates deleted. And I was on vacations 21 days in September.
    >    MDAnderson’s rules on security are stricter   recently.
    >    Thanks!!
    >    Laura
    >
    >    Sent from my iPhone
    >
    >> On Oct 28, 2019, at 8:12 AM, Frances Weis-Garcia
<email obscured>> wrote:
    >>
    >> WARNING: This email originated from outside of MD Anderson. Please
validate the sender's email address before clicking on links or attachments as
they may not be safe.
    >>
    >> Happy Monday to those on this discussion forum because we do care about
Rigor and Reproducibility.
    >>
    >> We are a quite group of 65 members, but I wanted everyone to know that
those who know personally are passionate about the topic and encourage any
posts, be they for information purposes, discussions or questions. Speaking to
the later, the ABRF Committee on Core Rigor and Reproducibility has organized 2
things at ABRF2020 (https://conf.abrf.org/), specifically:
    >>
    >> 1.) A satellite workshop entitled " Essential Biostatistics Principles
for Core Scientists: Enabling rigorous experimental design, reproducible
results and effective data visualization."
    >>
    >> 2.) A 90 min panel discussion with journal editors entitled "Journals,
ABRF and You:  Partners Addressing Rigor and Reproducibility."
    >>
    >> Looking forward to seeing everyone there!
    >>
    >> Frances
    >>
    >> ――
    >> View topic http://list.abrf.org/r/topic/1Z8TPjT3nbmWWVIz7XILW
    >> Leave group <email obscured>?Subject=Unsubscribe
    >    The information contained in this e-mail message may be privileged,
confidential, and/or protected from disclosure. This e-mail message may contain
protected health information (PHI); dissemination of PHI should comply with
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    >
    >    ――
    >    View topic http://list.abrf.org/r/topic/1IWm8gFe4NLj4fqQR6OM6b
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    >
    >
    >
    > ――
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Sure

ABRF2020
Feb 29th - March 3rd
Palm Springs, CA

https://conf.abrf.org/

Registration should open soon.



On 10/28/19, 10:33 AM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Bover,Laura" <email obscured> on behalf of <email obscured>> wrote:

    Frances please se d me the dates of ABRF 2020. I probably missed that from
previous emails because many of those mails fall in quarantine and after 7
dates deleted. And I was on vacations 21 days in September.
    MDAnderson’s rules on security are stricter   recently.
    Thanks!!
    Laura

    Sent from my iPhone

    > On Oct 28, 2019, at 8:12 AM, Frances Weis-Garcia
<email obscured>> wrote:
    >
    > WARNING: This email originated from outside of MD Anderson. Please
validate the sender's email address before clicking on links or attachments as
they may not be safe.
    >
    > Happy Monday to those on this discussion forum because we do care about
Rigor and Reproducibility.
    >
    > We are a quite group of 65 members, but I wanted everyone to know that
those who know personally are passionate about the topic and encourage any
posts, be they for information purposes, discussions or questions. Speaking to
the later, the ABRF Committee on Core Rigor and Reproducibility has organized 2
things at ABRF2020 (https://conf.abrf.org/), specifically:
    >
    > 1.) A satellite workshop entitled " Essential Biostatistics Principles
for Core Scientists: Enabling rigorous experimental design, reproducible
results and effective data visualization."
    >
    > 2.) A 90 min panel discussion with journal editors entitled "Journals,
ABRF and You:  Partners Addressing Rigor and Reproducibility."
    >
    > Looking forward to seeing everyone there!
    >
    > Frances
    >
    > ――
    > View topic http://list.abrf.org/r/topic/1Z8TPjT3nbmWWVIz7XILW
    > Leave group <email obscured>?Subject=Unsubscribe
    The information contained in this e-mail message may be privileged,
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Reposting due to poor editing in the first post.
This is what I get for rushing.
Thank you for your patience ...

Happy Monday to those on this discussion forum because we do care about Rigor
and Reproducibility.

We are a quite group of 65 members, but I wanted everyone to know that those
who I know personally are passionate about the topic and I encourage everyone
that nothing is too insignificant to post ... be it for information purposes,
discussions or questions. Speaking to the firsrt one ... the ABRF Committee on
Core Rigor and Reproducibility has organized 2 things at ABRF2020
(https://conf.abrf.org/), specifically:

    1.) A satellite workshop entitled " Essential Biostatistics Principles for
Core Scientists: Enabling rigorous experimental design, reproducible results
and effective data visualization."

    2.) A 90 min panel discussion with journal editors entitled "Journals, ABRF
and You:  Partners Addressing Rigor and Reproducibility."

    Looking forward to seeing everyone there!

    Frances
__________________

On 10/28/19, 9:12 AM, "Core Rigor and Reproducibility (CoRRe) on behalf of
Frances Weis-Garcia" <email obscured> on behalf of
<email obscured>> wrote:

    Happy Monday to those on this discussion forum because we do care about
Rigor and Reproducibility.

    We are a quite group of 65 members, but I wanted everyone to know that
those who know personally are passionate about the topic and encourage any
posts, be they for information purposes, discussions or questions. Speaking to
the later, the ABRF Committee on Core Rigor and Reproducibility has organized 2
things at ABRF2020 (https://conf.abrf.org/), specifically:

    1.) A satellite workshop entitled " Essential Biostatistics Principles for
Core Scientists: Enabling rigorous experimental design, reproducible results
and effective data visualization."

    2.) A 90 min panel discussion with journal editors entitled "Journals, ABRF
and You:  Partners Addressing Rigor and Reproducibility."

    Looking forward to seeing everyone there!

    Frances

    ――
    View topic http://list.abrf.org/r/topic/1Z8TPjT3nbmWWVIz7XILW
    Leave group <email obscured>?Subject=Unsubscribe