SRX6940329 GSM4105833 SRP224016 SRS5468627 GSM4105833 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105833 GSM4105833 GEO Accession GSM4105833 SRX6940330 GSM4105834 SRP224016 SRS5468628 GSM4105834 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105834 GSM4105834 GEO Accession GSM4105834 SRX6940331 GSM4105824 SRP224016 SRS5468629 GSM4105824 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105824 GSM4105824 GEO Accession GSM4105824 SRX6940332 GSM4105825 SRP224016 SRS5468630 GSM4105825 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105825 GSM4105825 GEO Accession GSM4105825 SRX6940333 GSM4105826 SRP224016 SRS5468631 GSM4105826 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105826 GSM4105826 GEO Accession GSM4105826 SRX6940334 GSM4105827 SRP224016 SRS5468632 GSM4105827 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105827 GSM4105827 GEO Accession GSM4105827 SRX6940335 GSM4105828 SRP224016 SRS5468633 GSM4105828 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105828 GSM4105828 GEO Accession GSM4105828 SRX6940336 GSM4105829 SRP224016 SRS5468634 GSM4105829 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105829 GSM4105829 GEO Accession GSM4105829 SRX6940337 GSM4105830 SRP224016 SRS5468635 GSM4105830 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105830 GSM4105830 GEO Accession GSM4105830 SRX6940338 GSM4105831 SRP224016 SRS5468636 GSM4105831 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105831 GSM4105831 GEO Accession GSM4105831 SRX6940339 GSM4105832 SRP224016 SRS5468637 GSM4105832 RNA-Seq TRANSCRIPTOMIC cDNA Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer's instructions. Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer's recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. NextSeq 500 gds 304105832 GSM4105832 GEO Accession GSM4105832