From fe5866ea76d0bdcf673e2885be7189fdc395e2c4 Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Fri, 11 Oct 2024 13:14:03 -0400 Subject: [PATCH 1/4] Adding phase 2 liaisons --- data_submission/Data_Liaisons.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/data_submission/Data_Liaisons.md b/data_submission/Data_Liaisons.md index aa332e5d..2d32da7a 100644 --- a/data_submission/Data_Liaisons.md +++ b/data_submission/Data_Liaisons.md @@ -6,7 +6,22 @@ order: 997 Upon joining HTAN, Centers are assigned a data liaison from the DCC. Trans-Network Projects (TNPs) are also assigned liaisons. The DCC liaisons assist each of the research centers in successfully uploading data and metadata files. -Here is the current list of centers, their atlases and DCC liaisons: +## Phase 2 Liaisons + +| Atlas | Academic Center | Atlas ID | Liaison | Email | +|-------|-----------------|----------|---------|-------| +| HTAN2_Gastric_PCA | MD Anderson | pending | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | +| HTAN2_Glioma_PCA | CalTech | pending | Ino de Bruijn | debruiji@mskcc.org | +| HTAN2_Myeloma_PCA | DFCI | pending | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | +| HTAN2_Pancreas_PCA | OHSU | pending | Adam Taylor | adam.taylor@sagebase.org | +| HTAN2_Skin_PCA | UCSF | pending | Adam Taylor | adam.taylor@sagebase.org | +| HTAN2_Colorectal_HTA | Vanderbilt | pending | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | +| HTAN2_Lymphoma_HTA | Yale | pending | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | +| HTAN2_Ovary_HTA | MD Anderson | pending | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | +| HTAN2_Pediatric_HTA | USC/CHLA | pending | Ino de Bruijn | debruiji@mskcc.org | +| HTAN2_Prostate_HTA | WUSTL | pending | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | + +## Phase 1 Liaisons | Atlas | Atlas ID | Liaison | Email | |-------|----------|---------|-------| From dabfb8c1a8a394378a4376fe3a8845a5c0d1d63a Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Tue, 15 Oct 2024 09:07:19 -0400 Subject: [PATCH 2/4] updated centers and data liaisons with center names proposed by ecerami. --- data_submission/Data_Liaisons.md | 23 ++++++++++++----------- overview/centers.md | 16 ++++++++++++++++ 2 files changed, 28 insertions(+), 11 deletions(-) diff --git a/data_submission/Data_Liaisons.md b/data_submission/Data_Liaisons.md index 2d32da7a..f464db6e 100644 --- a/data_submission/Data_Liaisons.md +++ b/data_submission/Data_Liaisons.md @@ -8,18 +8,19 @@ Upon joining HTAN, Centers are assigned a data liaison from the DCC. Trans-Netw ## Phase 2 Liaisons -| Atlas | Academic Center | Atlas ID | Liaison | Email | +| Atlas | Lead Institution | Atlas ID | Liaison | Email | |-------|-----------------|----------|---------|-------| -| HTAN2_Gastric_PCA | MD Anderson | pending | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | -| HTAN2_Glioma_PCA | CalTech | pending | Ino de Bruijn | debruiji@mskcc.org | -| HTAN2_Myeloma_PCA | DFCI | pending | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | -| HTAN2_Pancreas_PCA | OHSU | pending | Adam Taylor | adam.taylor@sagebase.org | -| HTAN2_Skin_PCA | UCSF | pending | Adam Taylor | adam.taylor@sagebase.org | -| HTAN2_Colorectal_HTA | Vanderbilt | pending | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | -| HTAN2_Lymphoma_HTA | Yale | pending | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | -| HTAN2_Ovary_HTA | MD Anderson | pending | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | -| HTAN2_Pediatric_HTA | USC/CHLA | pending | Ino de Bruijn | debruiji@mskcc.org | -| HTAN2_Prostate_HTA | WUSTL | pending | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | +| HTAN2_Skin_PCA | UCSF | HTA200 | Adam Taylor | adam.taylor@sagebase.org | +| HTAN2_Pancreas_PCA | OHSU | HTA201 | Adam Taylor | adam.taylor@sagebase.org | +| HTAN2_Glioma_PCA | CalTech | HTA202 | Ino de Bruijn | debruiji@mskcc.org | +| HTAN2_Gastric_PCA | MD Anderson | HTA203 | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | +| HTAN2_Myeloma_PCA | DFCI | HTA204 | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | +| HTAN2_Pediatric_HTA | USC/CHLA | HTA205 | Ino de Bruijn | debruiji@mskcc.org | +| HTAN2_Prostate_HTA | WUSTL | HTA206 | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | +| HTAN2_Colorectal_HTA | Vanderbilt | HTA207 | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | +| HTAN2_Ovary_HTA | MD Anderson | HTA208 | Jennifer Altreuter | jennifer@ds.dfci.harvard.edu | +| HTAN2_Lymphoma_HTA | Yale | HTA209 | Dar'ya Pozhidayeva | dpozhida@systemsbiology.org | + ## Phase 1 Liaisons diff --git a/overview/centers.md b/overview/centers.md index bbd5ddcf..05aab0db 100644 --- a/overview/centers.md +++ b/overview/centers.md @@ -6,6 +6,22 @@ order: 999 HTAN currently consists of ten research centers, and two pilot projects. There are also multiple trans-network projects, referred to as TNPs. Each research center or TNP Project is identified with a unique HTAN prefix. +## Phase 2 Centers +| Prefix | Contact Institution or Project Name | Atlas Type | Area of Focus | +| ------ | --------------------------------------- | ---------------- | --------------------------------- | +| HTA200 | University of California San Francisco | Pre-Cancer Atlas | Skin Cancer | +| HTA201 | Oregon Health & Science University (OHSU) | Pre-Cancer Atlas | Pancreatic Cancer | +| HTA202 | California Institute of Technology (CalTech) | Pre-Cancer Atlas | Low Grade Glioma | +| HTA203 | MD Anderson (MDA)| Pre-Cancer Atlas | Gastric Cancer | +| HTA204 | Dana-Farber Cancer Institute (DFCI) | Pre-Cancer Atlas | Myeloma | +| HTA205 | Children's Hosptital of Los Angeles | Tumor Atlas | Pediatric Cancers | +| HTA206 | Washington University in St. Louis | Tumor Atlas | Prostate Cancer | +| HTA207 | Vanderbilt University | Tumor Atlas | Colorectal Cancer | +| HTA208 | MD Anderson (MDA) | Tumor Atlas | Ovarian Cancer | +| HTA209 | Yale University | Tumor Atlas | Lymphoma | + +## Phase 1 Centers + | Prefix | Contact Institution or Project Name | Atlas Type | Area of Focus | | ------ | --------------------------------------- | ---------------- | --------------------------------- | | HTA1 | Human Tumor Atlas Pilot Project (HTAPP) | Tumor Atlas | Pilot Project | From 0675ece6eb68caed20b367b27f7e12024b76429e Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Tue, 15 Oct 2024 09:32:14 -0400 Subject: [PATCH 3/4] Minor change liaison column name --- data_submission/Data_Liaisons.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data_submission/Data_Liaisons.md b/data_submission/Data_Liaisons.md index f464db6e..2fe215d8 100644 --- a/data_submission/Data_Liaisons.md +++ b/data_submission/Data_Liaisons.md @@ -8,7 +8,7 @@ Upon joining HTAN, Centers are assigned a data liaison from the DCC. Trans-Netw ## Phase 2 Liaisons -| Atlas | Lead Institution | Atlas ID | Liaison | Email | +| Atlas | Awardee Organization | Atlas ID | Liaison | Email | |-------|-----------------|----------|---------|-------| | HTAN2_Skin_PCA | UCSF | HTA200 | Adam Taylor | adam.taylor@sagebase.org | | HTAN2_Pancreas_PCA | OHSU | HTA201 | Adam Taylor | adam.taylor@sagebase.org | From b5f15f762e7675bbe7773bbb982c445499933f6f Mon Sep 17 00:00:00 2001 From: Jennifer Altreuter Date: Tue, 15 Oct 2024 16:09:16 -0400 Subject: [PATCH 4/4] Adding Mass Spec specific details document link --- data_submission/specific_details.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/data_submission/specific_details.md b/data_submission/specific_details.md index 32853cc9..fa6a9fbf 100644 --- a/data_submission/specific_details.md +++ b/data_submission/specific_details.md @@ -14,6 +14,8 @@ Please see [Data Standards](https://data.humantumoratlas.org/standards) for an o [Imaging](https://docs.google.com/document/d/1iNicigsSytekEQLkmeNJd2NOJ9VTKzBDfYj3BmvGcro/edit#heading=h.b6j67xcu50c2) +[Mass Spectrometry](https://docs.google.com/document/d/1uW51P7b4Gl5PYnwbLKxbqjR5JEQ_J1yXyqaWCfsCTS8/edit?usp=sharing) + [RPPA](https://docs.google.com/document/d/1UznHRELT6TlPa7vtgCKKeDZ1jeAhAhdRjuBRmzu-Oss/edit?usp=sharing) [Sequencing Data](https://docs.google.com/document/d/1543YyAW_CwkrKFVzvS9Xwl_dpmruCzK6fA4sIRrZcLQ/edit?usp=sharing)