From 48b9db22fbfe65d50ef0985f48349a0ad88b0513 Mon Sep 17 00:00:00 2001 From: Mateusz Date: Mon, 26 Aug 2019 15:42:49 -0400 Subject: [PATCH 01/12] Update 03.methods.md --- content/03.methods.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/content/03.methods.md b/content/03.methods.md index 240cae4f..4a439b64 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -1,6 +1,35 @@ ## Materials and Methods ### Children's Brain Tumor Tissue Consortium Data +The deidentified patient's blood and tumor tissue were prospectively collected by the Children's Brain Tumor Tissue Consortium (CBTTC). +The CBTTC [https://cbttc.org] is a collaborative, multi-institutional research program dedicated to the study of childhood brain tumors. +The consortium currently includes 16 institutions worldwide. +The CBTTC open source biorepository [https://eig.research.chop.edu/cbttc/] is available to member and non-member investigators through a submission request system [@doi:10.1186/s12864-016-2797-9]. +All CBTTC data is available for viewing and download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [https://kidsfirstdrc.org]. +Clinical reports can be downloaded as PDFs and Aperio SVS histology images. +Pre- and post-operative MRI images and reports are also available for a subset of the CBTTC subjects. + +The cell lines were generated by the CBTTC from either fresh tumor tissue obtained firectly from surgery performed at Children’s Hospital of Philadelphia (CHOP) or from prospectively collected tumor specimens stored in Recover Cell Culture Freezing media (Gibco, USA). +The tissue was dissociatiated using enzymatic method with papain( ***supplementary methods? or [https://www.biorxiv.org/content/10.1101/656587v1.full#ref-6]***). +Briefly, tissue was washed with HBSS (Thermo, USA), minced using sterile scalpels, and icubated with activated papin solution (SciQuest, USA) for up to 45 minutes. +The papain was inactivated using ovomucoid solution (SciQuest), tissue was briefly treated with DNase (Sigma, USA)and passed through the 100μm cell strainer (Greiner Bio-One, USA). +Two cell culture conditions were initiated based on the number of cells avialble. +For cultures utilizing the fetal bovine serum (FBS), a minimum density of 3×10^5 cells/ml were plated in DMEM/F-12 medium (Sigma) supplemented with 20% FBS (Hyclone, USA), 1% GlutaMAX (Gibco), Penicillin/Streptomycin-Amphotericin B Mixture (Lonza, USA) and 0.2% Normocin (Invitrogen, USA). +For the serum-free media conditions cells were plated at minimum density of 1×10^6 cells/ml in DMEM/F12 media supplemented with 1% GlutaMAX, 1x B-27 supplement minus vitamin A (Thermo), 1x N-2 supplement (Thermo), 20 ng/ml epidermal growth factor (Thermo), 20 ng/ml basic fibroblast growth factor (PeproTech, USA), 2.5μg/ml heparin (Sigma), Penicillin/Streptomycin-Amphotericin B Mixture and 0.2% Normocin. + +#### DNA/RNA extractions + +Blood, tissue and cell line DNA/RNA extraction was performed at Biorepository Core (BioRC) at CHOP. +Briefly, 10-20 mg frozen tissue, (***?x?***) blood or 2×10^6 cells pellet was used for extractions. +Specimens were lysed using a Qiagen TissueLyser II (Qiagen, USA) with 2×30 sec at 18Hz settings using 5 mm steel beads. +The AllPrep DNA/RNA/miRNA Universal kit (Qiagen, USA) including a CHCl3 extraction was utilized according to manufacturer’s protocol. +DNA and RNA quantity and quality was assessed by PerkinElmer DropletQuant UV-VIS spectrophotometer (PerkinElmer, USA) and an Agilent 4200 TapeStation (Agilent, USA) for RINe and DINe (RNA Integrity Number equivalent and DNA Integrity Number equivalent respectively). +Library preparation and sequencing was performed by the NantHealth sequencing center. +Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (Roche, USA); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit. +Whole genome sequencing (WGS) was performed at an average depth of coverage of 60X for tumor samples and 30X for germline. +RNA samples were sequenced to an average of 200M reads. +All samples were sequenced on the Illumina HiSeq platform (X/400) (Illumina, San Diego, USA) with 2 × 150bp read length. +For the cell line sequencing, samples labelled with “CL-adh” correspond to the adherent FBS cell lines and those labelled “CL-susp” are the serum-free lines. ### Pediatric Pacific Neuro-oncology Consortium Data From f9e1ebd7c2d780f562b295b07934851dd55760eb Mon Sep 17 00:00:00 2001 From: Mateusz Date: Wed, 28 Aug 2019 09:58:56 -0400 Subject: [PATCH 02/12] Update 03.methods.md --- content/03.methods.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/content/03.methods.md b/content/03.methods.md index 4a439b64..5fdc542e 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -10,7 +10,7 @@ Clinical reports can be downloaded as PDFs and Aperio SVS histology images. Pre- and post-operative MRI images and reports are also available for a subset of the CBTTC subjects. The cell lines were generated by the CBTTC from either fresh tumor tissue obtained firectly from surgery performed at Children’s Hospital of Philadelphia (CHOP) or from prospectively collected tumor specimens stored in Recover Cell Culture Freezing media (Gibco, USA). -The tissue was dissociatiated using enzymatic method with papain( ***supplementary methods? or [https://www.biorxiv.org/content/10.1101/656587v1.full#ref-6]***). +The tissue was dissociatiated using enzymatic method with papain as described [@doi:10.1101/656587]. Briefly, tissue was washed with HBSS (Thermo, USA), minced using sterile scalpels, and icubated with activated papin solution (SciQuest, USA) for up to 45 minutes. The papain was inactivated using ovomucoid solution (SciQuest), tissue was briefly treated with DNase (Sigma, USA)and passed through the 100μm cell strainer (Greiner Bio-One, USA). Two cell culture conditions were initiated based on the number of cells avialble. @@ -20,9 +20,11 @@ For the serum-free media conditions cells were plated at minimum density of 1×1 #### DNA/RNA extractions Blood, tissue and cell line DNA/RNA extraction was performed at Biorepository Core (BioRC) at CHOP. -Briefly, 10-20 mg frozen tissue, (***?x?***) blood or 2×10^6 cells pellet was used for extractions. -Specimens were lysed using a Qiagen TissueLyser II (Qiagen, USA) with 2×30 sec at 18Hz settings using 5 mm steel beads. -The AllPrep DNA/RNA/miRNA Universal kit (Qiagen, USA) including a CHCl3 extraction was utilized according to manufacturer’s protocol. +Briefly, 10-20 mg frozen tissue, 0.4-1ml of blood or 2×10^6 cells pellet was used for extractions. +Tissues were lysed using a Qiagen TissueLyser II (Qiagen, USA) with 2×30 sec at 18Hz settings using 5 mm steel beads. +Both tissue and cell pellets processes included a CHCl3 extraction and were run on the QiaCube automated platform using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen). +Blood was thawed and threated with RNase A (final concetration 2 mg/ml); 0.4-1ml was processed using the Qiagen QIAsymphony automated platform using the QIAsymphony DSP DNA Midi Kit (Qiagen). + DNA and RNA quantity and quality was assessed by PerkinElmer DropletQuant UV-VIS spectrophotometer (PerkinElmer, USA) and an Agilent 4200 TapeStation (Agilent, USA) for RINe and DINe (RNA Integrity Number equivalent and DNA Integrity Number equivalent respectively). Library preparation and sequencing was performed by the NantHealth sequencing center. Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (Roche, USA); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit. From 76df41fff83b7b5ca7aaa22901e28a5c91eba39c Mon Sep 17 00:00:00 2001 From: Mateusz Date: Wed, 28 Aug 2019 10:53:41 -0400 Subject: [PATCH 03/12] Update 03.methods.md --- content/03.methods.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/content/03.methods.md b/content/03.methods.md index 5fdc542e..28012396 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -9,28 +9,28 @@ All CBTTC data is available for viewing and download from the Gabriella Miller K Clinical reports can be downloaded as PDFs and Aperio SVS histology images. Pre- and post-operative MRI images and reports are also available for a subset of the CBTTC subjects. -The cell lines were generated by the CBTTC from either fresh tumor tissue obtained firectly from surgery performed at Children’s Hospital of Philadelphia (CHOP) or from prospectively collected tumor specimens stored in Recover Cell Culture Freezing media (Gibco, USA). +The cell lines were generated by the CBTTC from either fresh tumor tissue obtained firectly from surgery performed at Children’s Hospital of Philadelphia (CHOP) or from prospectively collected tumor specimens stored in Recover Cell Culture Freezing media (cat# 12648010, Gibco). The tissue was dissociatiated using enzymatic method with papain as described [@doi:10.1101/656587]. -Briefly, tissue was washed with HBSS (Thermo, USA), minced using sterile scalpels, and icubated with activated papin solution (SciQuest, USA) for up to 45 minutes. -The papain was inactivated using ovomucoid solution (SciQuest), tissue was briefly treated with DNase (Sigma, USA)and passed through the 100μm cell strainer (Greiner Bio-One, USA). +Briefly, tissue was washed with HBSS (cat# 14175095, Gibco), minced and icubated with activated papin solution (cat# LS003124, SciQuest) for up to 45 minutes. +The papain was inactivated using ovomucoid solution (cat# 542000, SciQuest), tissue was briefly treated with DNase (cat# 10104159001, Sigma) and passed through the 100μm cell strainer (cat# 542000, Greiner Bio-One). Two cell culture conditions were initiated based on the number of cells avialble. -For cultures utilizing the fetal bovine serum (FBS), a minimum density of 3×10^5 cells/ml were plated in DMEM/F-12 medium (Sigma) supplemented with 20% FBS (Hyclone, USA), 1% GlutaMAX (Gibco), Penicillin/Streptomycin-Amphotericin B Mixture (Lonza, USA) and 0.2% Normocin (Invitrogen, USA). -For the serum-free media conditions cells were plated at minimum density of 1×10^6 cells/ml in DMEM/F12 media supplemented with 1% GlutaMAX, 1x B-27 supplement minus vitamin A (Thermo), 1x N-2 supplement (Thermo), 20 ng/ml epidermal growth factor (Thermo), 20 ng/ml basic fibroblast growth factor (PeproTech, USA), 2.5μg/ml heparin (Sigma), Penicillin/Streptomycin-Amphotericin B Mixture and 0.2% Normocin. +For cultures utilizing the fetal bovine serum (FBS), a minimum density of 3×10^5 cells/ml were plated in DMEM/F-12 medium (cat# D8062, Sigma) supplemented with 20% FBS (cat# SH30910.03, Hyclone), 1% GlutaMAX (cat# 35050061, Gibco), Penicillin/Streptomycin-Amphotericin B Mixture (cat# 17-745E, Lonza) and 0.2% Normocin (cat# ant-nr-2, Invivogen). +For the serum-free media conditions cells were plated at minimum density of 1×10^6 cells/ml in DMEM/F12 media supplemented with 1% GlutaMAX, 1x B-27 supplement minus vitamin A (cat# 12587-010, Gibco), 1x N-2 supplement (cat# 17502001, Gibco), 20 ng/ml epidermal growth factor (cat# PHG0311L, Gibco), 20 ng/ml basic fibroblast growth factor (cat# 100-18B, PeproTech), 2.5μg/ml heparin (cat# H3149, Sigma), Penicillin/Streptomycin-Amphotericin B Mixture and 0.2% Normocin. #### DNA/RNA extractions Blood, tissue and cell line DNA/RNA extraction was performed at Biorepository Core (BioRC) at CHOP. Briefly, 10-20 mg frozen tissue, 0.4-1ml of blood or 2×10^6 cells pellet was used for extractions. -Tissues were lysed using a Qiagen TissueLyser II (Qiagen, USA) with 2×30 sec at 18Hz settings using 5 mm steel beads. -Both tissue and cell pellets processes included a CHCl3 extraction and were run on the QiaCube automated platform using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen). -Blood was thawed and threated with RNase A (final concetration 2 mg/ml); 0.4-1ml was processed using the Qiagen QIAsymphony automated platform using the QIAsymphony DSP DNA Midi Kit (Qiagen). +Tissues were lysed using a Qiagen TissueLyser II (Qiagen) with 2×30 sec at 18Hz settings using 5 mm steel beads (cat# 69989, Qiagen). +Both tissue and cell pellets processes included a CHCl3 extraction and were run on the QiaCube automated platform (Qiagen) using the AllPrep DNA/RNA/miRNA Universal kit (cat# 80224, Qiagen). +Blood was thawed and threated with RNase A (cat#, 19101, Qiagen); 0.4-1ml was processed using the Qiagen QIAsymphony automated platform (Qiagen) using the QIAsymphony DSP DNA Midi Kit (cat# 937255, Qiagen). -DNA and RNA quantity and quality was assessed by PerkinElmer DropletQuant UV-VIS spectrophotometer (PerkinElmer, USA) and an Agilent 4200 TapeStation (Agilent, USA) for RINe and DINe (RNA Integrity Number equivalent and DNA Integrity Number equivalent respectively). +DNA and RNA quantity and quality was assessed by PerkinElmer DropletQuant UV-VIS spectrophotometer (PerkinElmer) and an Agilent 4200 TapeStation (Agilent, USA) for RINe and DINe (RNA Integrity Number equivalent and DNA Integrity Number equivalent respectively). Library preparation and sequencing was performed by the NantHealth sequencing center. -Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (Roche, USA); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit. +Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (cat# KK8541, Roche); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit. Whole genome sequencing (WGS) was performed at an average depth of coverage of 60X for tumor samples and 30X for germline. RNA samples were sequenced to an average of 200M reads. -All samples were sequenced on the Illumina HiSeq platform (X/400) (Illumina, San Diego, USA) with 2 × 150bp read length. +All samples were sequenced on the Illumina HiSeq platform (X/400) (Illumina) with 2 × 150bp read length. For the cell line sequencing, samples labelled with “CL-adh” correspond to the adherent FBS cell lines and those labelled “CL-susp” are the serum-free lines. ### Pediatric Pacific Neuro-oncology Consortium Data From 1b8e003928dac921801dc2da95e83e987b47cd8d Mon Sep 17 00:00:00 2001 From: Mateusz Date: Wed, 28 Aug 2019 14:31:46 -0400 Subject: [PATCH 04/12] Update 03.methods.md --- content/03.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/03.methods.md b/content/03.methods.md index 28012396..c1793ea2 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -27,7 +27,7 @@ Blood was thawed and threated with RNase A (cat#, 19101, Qiagen); 0.4-1ml was pr DNA and RNA quantity and quality was assessed by PerkinElmer DropletQuant UV-VIS spectrophotometer (PerkinElmer) and an Agilent 4200 TapeStation (Agilent, USA) for RINe and DINe (RNA Integrity Number equivalent and DNA Integrity Number equivalent respectively). Library preparation and sequencing was performed by the NantHealth sequencing center. -Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (cat# KK8541, Roche); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit. +Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (cat# KK8541, Roche); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit(cat# KK8484, Roche). Whole genome sequencing (WGS) was performed at an average depth of coverage of 60X for tumor samples and 30X for germline. RNA samples were sequenced to an average of 200M reads. All samples were sequenced on the Illumina HiSeq platform (X/400) (Illumina) with 2 × 150bp read length. From 80815532a64e3ffcfa7e242c321ecaed21979d26 Mon Sep 17 00:00:00 2001 From: Mateusz Date: Thu, 29 Aug 2019 13:37:51 -0400 Subject: [PATCH 05/12] Update content/03.methods.md Co-Authored-By: Jaclyn Taroni --- content/03.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/03.methods.md b/content/03.methods.md index 6025d3f6..ffda279d 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -7,7 +7,7 @@ The Pediatric Brain Tumor Atlas specimens are comprised of samples from Children #### Children's Brain Tumor Tissue Consortium (CBTTC) The CBTTC [https://cbttc.org] is a collaborative, multi-institutional (16 institutions worldwide) research program dedicated to the study of childhood brain tumors. -The CBTTC open source biorepository [https://eig.research.chop.edu/cbttc/] is available to member and non-member investigators through a submission request system [@doi:10.1186/s12864-016-2797-9]. +The CBTTC open source biorepository [@url:https://eig.research.chop.edu/cbttc/] is available to member and non-member investigators through a submission request system [@doi:10.1186/s12864-016-2797-9]. All CBTTC data is available for viewing and download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [https://kidsfirstdrc.org]. Clinical reports can be downloaded as PDFs and Aperio SVS histology images. Pre- and post-operative MRI images and reports are also available for a subset of the CBTTC subjects. From 80c411139cab5ad096fc6a28166c31847287d1ae Mon Sep 17 00:00:00 2001 From: Mateusz Date: Thu, 29 Aug 2019 13:49:44 -0400 Subject: [PATCH 06/12] Update content/03.methods.md Co-Authored-By: Jaclyn Taroni --- content/03.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/03.methods.md b/content/03.methods.md index ffda279d..70a0ea19 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -15,7 +15,7 @@ Pre- and post-operative MRI images and reports are also available for a subset o The deidentified patient's blood and tumor tissue were prospectively collected by the consortium from patients enrolled within the CBTTC. The cell lines were generated by the CBTTC from either fresh tumor tissue obtained firectly from surgery performed at Children’s Hospital of Philadelphia (CHOP) or from prospectively collected tumor specimens stored in Recover Cell Culture Freezing media (cat# 12648010, Gibco). -The tissue was dissociatiated using enzymatic method with papain as described [@doi:10.1101/656587]. +The tissue was dissociated using enzymatic method with papain as described [@doi:10.1101/656587]. Briefly, tissue was washed with HBSS (cat# 14175095, Gibco), minced and icubated with activated papin solution (cat# LS003124, SciQuest) for up to 45 minutes. The papain was inactivated using ovomucoid solution (cat# 542000, SciQuest), tissue was briefly treated with DNase (cat# 10104159001, Sigma) and passed through the 100μm cell strainer (cat# 542000, Greiner Bio-One). Two cell culture conditions were initiated based on the number of cells avialble. From 3e66560ea096782f2f925fadb5335cbba453bc78 Mon Sep 17 00:00:00 2001 From: Mateusz Date: Thu, 29 Aug 2019 13:51:39 -0400 Subject: [PATCH 07/12] Update content/03.methods.md Co-Authored-By: Jaclyn Taroni --- content/03.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/03.methods.md b/content/03.methods.md index 70a0ea19..bd9376c5 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -6,7 +6,7 @@ The Pediatric Brain Tumor Atlas specimens are comprised of samples from Children #### Children's Brain Tumor Tissue Consortium (CBTTC) -The CBTTC [https://cbttc.org] is a collaborative, multi-institutional (16 institutions worldwide) research program dedicated to the study of childhood brain tumors. +The CBTTC [@url:https://cbttc.org] is a collaborative, multi-institutional (16 institutions worldwide) research program dedicated to the study of childhood brain tumors. The CBTTC open source biorepository [@url:https://eig.research.chop.edu/cbttc/] is available to member and non-member investigators through a submission request system [@doi:10.1186/s12864-016-2797-9]. All CBTTC data is available for viewing and download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [https://kidsfirstdrc.org]. Clinical reports can be downloaded as PDFs and Aperio SVS histology images. From 448088d34370eb5cd03035cfbb16eaf0776b2554 Mon Sep 17 00:00:00 2001 From: Mateusz Date: Thu, 29 Aug 2019 13:52:17 -0400 Subject: [PATCH 08/12] Update content/03.methods.md Co-Authored-By: Jaclyn Taroni --- content/03.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/03.methods.md b/content/03.methods.md index bd9376c5..2408e559 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -46,7 +46,7 @@ Both tissue and cell pellets processes included a CHCl3 extraction and were run Blood was thawed and threated with RNase A (cat#, 19101, Qiagen); 0.4-1ml was processed using the Qiagen QIAsymphony automated platform (Qiagen) using the QIAsymphony DSP DNA Midi Kit (cat# 937255, Qiagen). DNA and RNA quantity and quality was assessed by PerkinElmer DropletQuant UV-VIS spectrophotometer (PerkinElmer) and an Agilent 4200 TapeStation (Agilent, USA) for RINe and DINe (RNA Integrity Number equivalent and DNA Integrity Number equivalent respectively). Library preparation and sequencing was performed by the NantHealth sequencing center. -Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (cat# KK8541, Roche); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit(cat# KK8484, Roche). +Briefly, DNA sequencing libraries were prepared for tumor and matched-normal DNA using the KAPA Hyper prep kit (cat# KK8541, Roche); tumor RNA-Seq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase kit (cat# KK8484, Roche). Whole genome sequencing (WGS) was performed at an average depth of coverage of 60X for tumor samples and 30X for germline. RNA samples were sequenced to an average of 200M reads. All samples were sequenced on the Illumina HiSeq platform (X/400) (Illumina) with 2 × 150bp read length. From fa99bf19f9cf22889ece28390587ef04bf76a1df Mon Sep 17 00:00:00 2001 From: Mateusz Date: Thu, 29 Aug 2019 13:52:44 -0400 Subject: [PATCH 09/12] Update content/03.methods.md Co-Authored-By: Jaclyn Taroni --- content/03.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/03.methods.md b/content/03.methods.md index 2408e559..fb344379 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -8,7 +8,7 @@ The Pediatric Brain Tumor Atlas specimens are comprised of samples from Children The CBTTC [@url:https://cbttc.org] is a collaborative, multi-institutional (16 institutions worldwide) research program dedicated to the study of childhood brain tumors. The CBTTC open source biorepository [@url:https://eig.research.chop.edu/cbttc/] is available to member and non-member investigators through a submission request system [@doi:10.1186/s12864-016-2797-9]. -All CBTTC data is available for viewing and download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [https://kidsfirstdrc.org]. +All CBTTC data is available for viewing and download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [@url:https://kidsfirstdrc.org]. Clinical reports can be downloaded as PDFs and Aperio SVS histology images. Pre- and post-operative MRI images and reports are also available for a subset of the CBTTC subjects. From 81a2ad8c203212d454c8bc61fe0dea21ccb9949a Mon Sep 17 00:00:00 2001 From: Mateusz Date: Sat, 14 Sep 2019 16:53:56 -0400 Subject: [PATCH 10/12] Update 03.methods.md --- content/03.methods.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/content/03.methods.md b/content/03.methods.md index fb344379..69b7048b 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -7,8 +7,7 @@ The Pediatric Brain Tumor Atlas specimens are comprised of samples from Children #### Children's Brain Tumor Tissue Consortium (CBTTC) The CBTTC [@url:https://cbttc.org] is a collaborative, multi-institutional (16 institutions worldwide) research program dedicated to the study of childhood brain tumors. -The CBTTC open source biorepository [@url:https://eig.research.chop.edu/cbttc/] is available to member and non-member investigators through a submission request system [@doi:10.1186/s12864-016-2797-9]. -All CBTTC data is available for viewing and download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [@url:https://kidsfirstdrc.org]. +All CBTTC data can be download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [url@https://kidsfirstdrc.org]. Clinical reports can be downloaded as PDFs and Aperio SVS histology images. Pre- and post-operative MRI images and reports are also available for a subset of the CBTTC subjects. From eb3eea78f84555fe68d9cd134728559b0448814a Mon Sep 17 00:00:00 2001 From: Mateusz Date: Sat, 14 Sep 2019 17:07:07 -0400 Subject: [PATCH 11/12] Update 03.methods.md --- content/03.methods.md | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/content/03.methods.md b/content/03.methods.md index 69b7048b..6b149be5 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -7,10 +7,7 @@ The Pediatric Brain Tumor Atlas specimens are comprised of samples from Children #### Children's Brain Tumor Tissue Consortium (CBTTC) The CBTTC [@url:https://cbttc.org] is a collaborative, multi-institutional (16 institutions worldwide) research program dedicated to the study of childhood brain tumors. -All CBTTC data can be download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [url@https://kidsfirstdrc.org]. -Clinical reports can be downloaded as PDFs and Aperio SVS histology images. -Pre- and post-operative MRI images and reports are also available for a subset of the CBTTC subjects. - +All CBTTC data can be download from the Gabriella Miller Kids First Data Resource Center (KF-DRC), [@url:https://kidsfirstdrc.org]. The deidentified patient's blood and tumor tissue were prospectively collected by the consortium from patients enrolled within the CBTTC. The cell lines were generated by the CBTTC from either fresh tumor tissue obtained firectly from surgery performed at Children’s Hospital of Philadelphia (CHOP) or from prospectively collected tumor specimens stored in Recover Cell Culture Freezing media (cat# 12648010, Gibco). @@ -24,7 +21,7 @@ For the serum-free media conditions cells were plated at minimum density of 1×1 #### Pacific Pediatric Neuro Onclology Consortium (PNOC) The Pacific Pediatric Neuro-Oncology Consortium (PNOC) is an international consortium dedicated to bringing new therapies to children and young adults with brain tumors. -PNOC collected blood and tumor biospecimens from newly-diagnosed DIPG patients as part of the clinical trial [PNOC003/NCT02274987](https://clinicaltrials.gov/ct2/show/NCT02274987) [@doi:10.1002/ijc.32258]. +PNOC collected blood and tumor biospecimens from newly-diagnosed DIPG patients as part of the clinical trial [PNOC003/NCT02274987](@url:https://clinicaltrials.gov/ct2/show/NCT02274987) [@doi:10.1002/ijc.32258]. ### Nucleic acids extraction and library preparation From 421aacf05e9153423082976a88520ce71e5ba31f Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni Date: Sun, 15 Sep 2019 09:17:01 -0400 Subject: [PATCH 12/12] Update 03.methods.md --- content/03.methods.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/03.methods.md b/content/03.methods.md index 6b149be5..1269d093 100644 --- a/content/03.methods.md +++ b/content/03.methods.md @@ -21,7 +21,7 @@ For the serum-free media conditions cells were plated at minimum density of 1×1 #### Pacific Pediatric Neuro Onclology Consortium (PNOC) The Pacific Pediatric Neuro-Oncology Consortium (PNOC) is an international consortium dedicated to bringing new therapies to children and young adults with brain tumors. -PNOC collected blood and tumor biospecimens from newly-diagnosed DIPG patients as part of the clinical trial [PNOC003/NCT02274987](@url:https://clinicaltrials.gov/ct2/show/NCT02274987) [@doi:10.1002/ijc.32258]. +PNOC collected blood and tumor biospecimens from newly-diagnosed DIPG patients as part of the clinical trial [PNOC003/NCT02274987](https://clinicaltrials.gov/ct2/show/NCT02274987) [@doi:10.1002/ijc.32258]. ### Nucleic acids extraction and library preparation