A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | AC | AD | |
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1 | Disease | Patient | Sample | Data Type | MGI work order | Status | MGH Data Location (filtered_feature_bc_matrix) | WashU Data location | Seurat Object (scrublet + CONICSmat) | Seurat Object (minimal QC) | ||||||||||||||||||||
2 | glioma, IDH mutant | B148 | scRNA-seq (10X 3') | /storage1/fs1/allegra.petti/Active/GBM/KimCollab2019/scrna/SAMPLES/GBM1_total_3p_GEX_CR3/outs/filtered_feature_bc_matrix | /rdcw/fs1/allegra.petti/Active/GBM/KimCollab2019/scrna/SAMPLES/GBM1_total_3p_GEX_CR3/seurat/B148.CONICS/B148.conics.rds | |||||||||||||||||||||||||
3 | GBM | B150 | scRNA-seq (10X 3') | /storage1/fs1/allegra.petti/Active/GBM/KimCollab2019/scrna/SAMPLES/GBM2_total_3p_GEX_CR3/outs/filtered_feature_bc_matrix | /rdcw/fs1/allegra.petti/Active/GBM/KimCollab2019/scrna/SAMPLES/GBM2_total_3p_GEX_CR3/seurat/B150.CONICS/B150.conics.rds | |||||||||||||||||||||||||
4 | GBM | B152 | scRNA-seq (10X 3') | /storage1/fs1/allegra.petti/Active/GBM/KimCollab2019/scrna/SAMPLES/GBM3_total_3p_GEX_CR3/outs/filtered_feature_bc_matrix" | /rdcw/fs1/allegra.petti/Active/GBM/KimCollab2019/scrna/SAMPLES/GBM3_total_3p_GEX_CR3/seurat/B152.CONICS/B152.conics.rds | |||||||||||||||||||||||||
5 | GBM | B172 | B172-01 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B172-01 | ||||||||||||||||||||||||
6 | GBM | B172 | B172-02 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B172-02 | ||||||||||||||||||||||||
7 | High-grade astrocytoma with piloid features | B174 | B174-01 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B174-01 | ||||||||||||||||||||||||
8 | glioma, IDH mutant | B175 | B175-01 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B175-01 | ||||||||||||||||||||||||
9 | GBM | B176 | B176-01-02 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B176-01-02 | ||||||||||||||||||||||||
10 | GBM | B176 | B176-02-01 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B176-02-01 | ||||||||||||||||||||||||
11 | GBM | B176 | B176-02-04 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B176-02-04 | ||||||||||||||||||||||||
12 | GBM | B178 | B178-02-01 | Spatial (Fresh Frozen) | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B178-02-01 | ||||||||||||||||||||||||
13 | GBM | B172 | B172-02 | snRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/snrnaseq/SAMPLES.B172-02_snRNA_seq | ||||||||||||||||||||||||
14 | GBM | B174 | B174-01 | snRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/snrnaseq/SAMPLES.B174-01_snRNA_seq | ||||||||||||||||||||||||
15 | GBM | B175 | B175-01 | snRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/snrnaseq/SAMPLES.B175_01_5p_snrna | ||||||||||||||||||||||||
16 | GBM | B176 | B176-01-02 | snRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/snrnaseq/SAMPLES.B176_01 | ||||||||||||||||||||||||
17 | GBM | B176 | B176-02-01 | snRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/snrnaseq/SAMPLES.B176_02 | ||||||||||||||||||||||||
18 | GBM | B178 | B178-02-01 | snRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/snrnaseq/SAMPLES.B178_02 | ||||||||||||||||||||||||
19 | GBM | B172 | B172-01 | Exome (100x) | Novogene | GMS processing profile: | /storage1/fs1/allegra.petti/Active/gmsroot/model_data/ab5c19d24ce443b6a14fb8f66e0f6e97/buildb10452a8ddfc4a61a07ac45b55f58c79/results/ | |||||||||||||||||||||||
20 | GBM | B174 | B174-01 | Exome (100x) | Novogene | GMS processing profile: | /storage1/fs1/allegra.petti/Active/gmsroot/model_data/a016e6d10d5348d4a47ce87ba97585ee/build50f992d4b16642b093b45d905ef70d4a/results/ | |||||||||||||||||||||||
21 | GBM | B175 | B175-01 | Exome (100x) | Novogene | GMS processing profile: | /storage1/fs1/allegra.petti/Active/gmsroot/model_data/8f5930942fc84218a1040490e6cf3c06/builde8b84fb7457c4f12a69a26cabd2967e9/results/ | |||||||||||||||||||||||
22 | GBM | B176 | B176-02-04 | Exome (100x) | Novogene | GMS processing profile: | /storage1/fs1/allegra.petti/Active/gmsroot/model_data/21f57639244542929fdd5cef856cc2b3/build1d5ff784f4ca4038a90252812f108fdc/results/ | |||||||||||||||||||||||
23 | GBM | B178 | B178-02-01 | Exome (100x) | Novogene | GMS processing profile: | /storage1/fs1/allegra.petti/Active/gmsroot/model_data/87d776be6ba14411bb18ccc8ffa6e415/build7ce0c5488de94ebe9ef0774c15aad8e6/results/ | |||||||||||||||||||||||
24 | GBM | B178 | B178-01 (fresh) | scRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Users/Desai/scRNA_Optimization_1/Cellranger5/B178_1_count_cellranger5 | /rdcw/fs1/allegra.petti/Active/Users/Desai/scRNA_Optimization_1/Cellranger5/B178_1_count_cellranger5/B178.CONICS/B178.conics.rds | |||||||||||||||||||||||
25 | GBM | B178 | B178-02 (DMSO) | scRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/scRNA_Optimization_1/Cellranger5/B178_2_count_cellranger5 | ||||||||||||||||||||||||
26 | GBM | B178 | B178-03 (Living Biopsy) | scRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/scRNA_Optimization_1/Cellranger5/B178_3_count_cellranger5 | ||||||||||||||||||||||||
27 | GBM | B183 | B183-01 (fresh) | scRNA-seq (10x 5' V1.1) | 2863953 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/scRNA_Optimization_1/Cellranger5/B183_1_count_cellranger5 | /rdcw/fs1/allegra.petti/Active/Users/Desai/scRNA_Optimization_1/Cellranger5/B183_1_count_cellranger5/B183.CONICS/B183.conics.rds | ||||||||||||||||||||||
28 | GBM | B183 | B183-02 (DMSO) | scRNA-seq (10x 5' V1.1) | 2863953 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/scRNA_Optimization_1/Cellranger5/B183_2_count_cellranger5 | |||||||||||||||||||||||
29 | GBM | B183 | B183-03 (Living Biopsy) | scRNA-seq (10x 5' V1.1) | 2863953 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/scRNA_Optimization_1/Cellranger5/B183_3_count_cellranger5 | |||||||||||||||||||||||
30 | GBM | B178 | B178-01 (fresh) | scRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B178_1 | ||||||||||||||||||||||||
31 | GBM | B178 | B178-02 (DMSO) | scRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B178_2/ | ||||||||||||||||||||||||
32 | GBM | B178 | B178-03 (Living Biopsy) | scRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B178_3/ | ||||||||||||||||||||||||
33 | GBM | B183 | B183-01 (fresh) | scRNA-seq (10x 5' V1.1) | 2863953 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B183_1 | |||||||||||||||||||||||
34 | GBM | B183 | B183-02 (DMSO) | scRNA-seq (10x 5' V1.1) | 2863953 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B183_2/ | |||||||||||||||||||||||
35 | GBM | B183 | B183-03 (Living Biopsy) | scRNA-seq (10x 5' V1.1) | 2863953 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B183_3/ | |||||||||||||||||||||||
36 | GBM | B185 | 185-01 tumor core area | Spatial (Fresh Frozen) | 2863929 | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B185-01 | |||||||||||||||||||||||
37 | GBM | B185 | 185-02 tumor intermediate area 1 | Spatial (Fresh Frozen) | 2863929 | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B185-02 | |||||||||||||||||||||||
38 | GBM | B185 | 185-03 tumor intermediate area 2 | Spatial (Fresh Frozen) | 2863929 | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B185-03 | |||||||||||||||||||||||
39 | GBM | B185 | 185-04 tumor edge area | Spatial (Fresh Frozen) | 2863929 | Processed (Spaceranger 1.0) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B185-04 | |||||||||||||||||||||||
40 | GBM | B185 | B185-01 (5ALA+) | scRNA-seq (10x 5' V1.1) | 2863952 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/B185_5ALA_sort/Cellranger5/B185_1_count/cellranger5 | |||||||||||||||||||||||
41 | GBM | B185 | B185-02 (5ALA-) | scRNA-seq (10x 5' V1.1) | 2863952 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/B185_5ALA_sort/Cellranger5/B185_2_count/cellranger5 | |||||||||||||||||||||||
42 | GBM | B185 | B185-03 (unsorted) | scRNA-seq (10x 5' V1.1) | 2863952 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Desai/B185_5ALA_sort/Cellranger5/B185_3_count_cellranger5/ | /rdcw/fs1/allegra.petti/Active/Users/Desai/B185_5ALA_sort/Cellranger5/B185_3_count_cellranger5/B185.CONICS/B185.conics.rds | ||||||||||||||||||||||
43 | GBM | B186 | 186-01 (B186 5ALA Core) | Spatial (Fresh Frozen) | 2864077 | Processed (Spaceranger 1.0) | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B186-01 | |||||||||||||||||||||||
44 | GBM | B186 | 186-02 (B186 5ALA intermediate 1) | Spatial (Fresh Frozen) | 2864077 | Processed (Spaceranger 1.0) | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B186-02 | |||||||||||||||||||||||
45 | GBM | B186 | 186-03 (B186 5ALA intermediate 2) | Spatial (Fresh Frozen) | 2864077 | Processed (Spaceranger 1.0) | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B186-03 | |||||||||||||||||||||||
46 | GBM | B186 | 186-04 (B186 5ALA Edge) | Spatial (Fresh Frozen) | 2864077 | Processed (Spaceranger 1.0) | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-B186-04 | |||||||||||||||||||||||
47 | GBM | B186 | B186 | scRNA-seq (10x 5' V1.1) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B186 | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/scrnaseq/SAMPLES/B186/B186.CONICS/B186.conics.rds | |||||||||||||||||||||||
48 | GBM | B189* | B189? called ST073021 since unclear | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/Users/Desai/Spatial/ST073021 | /rdcw/fs1/allegra.petti/Active/Users/Desai/ST073021/B189_count_cellranger5/B189.CONICS/B189.conics.rds | |||||||||||||||||||||||
49 | Grade 3 Oligodendroglioma | WU-1200 | Core_CD45pos (Grade 3 Oligodendroglioma) | scRNA-seq (10x 5' V2) | 2865037 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU-1200-Core_CD45pos | /rdcw/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU1200.Core.CONICS/WU1200.conics.rds | ||||||||||||||||||||||
50 | Grade 3 Oligodendroglioma | WU-1200 | Core_CD45neg (Grade 3 Oligodendroglioma) | scRNA-seq (10x 5' V2) | 2865037 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU-1200-Core_CD45neg | /rdcw/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU1200.Core.CONICS/WU1200.conics.rds | ||||||||||||||||||||||
51 | Grade 3 Oligodendroglioma | WU-1200 | Edge_CD45pos (Grade 3 Oligodendroglioma) | scRNA-seq (10x 5' V2) | 2865037 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU-1200-Edge_CD45pos | |||||||||||||||||||||||
52 | Grade 3 Oligodendroglioma | WU-1200 | Edge_CD45neg (Grade 3 Oligodendroglioma) | scRNA-seq (10x 5' V2) | 2865037 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU-1200-Edge_CD45neg | |||||||||||||||||||||||
53 | Grade 3 Oligodendroglioma | WU-1200 | Core_CD45pos (Grade 3 Oligodendroglioma) | 10x_SC_5'_V2_Enriched_Tcell | 2865037 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU-1200-Core_CD45pos_vdj | |||||||||||||||||||||||
54 | Grade 3 Oligodendroglioma | WU-1200 | Edge_CD45pos (Grade 3 Oligodendroglioma) | 10x_SC_5'_V2_Enriched_Tcell | 2865037 | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1200/WU-1200-Edge_CD45pos_vdj | |||||||||||||||||||||||
55 | GBM | TWBK-ST073021/B189 | TWBK-ST073021-2 (aka B189) Edge | Spatial (FFPE) | Processed (Spaceranger 1.3.0) | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-ST073021-2 | ||||||||||||||||||||||||
56 | GBM | TWBK-ST073021/B189 | TWBK-ST073021-4 (aka B189) Core | Spatial (FFPE) | Processed (Spaceranger 1.3.0) | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-ST073021-4 | ||||||||||||||||||||||||
57 | GBM | TWBK-ST073021/B189 | TWBK-ST073021-6 (aka B189) Core | Spatial (FFPE) | Processed (Spaceranger 1.3.0) | /rdcw/fs1/allegra.petti/Active/spatial_snRNAseq_gbm/spatial/SAMPLES/TWBK-ST073021-6 | ||||||||||||||||||||||||
58 | GBM with focal gliosarcocoma | ?? | ? | ? | ? | |||||||||||||||||||||||||
59 | GBM | WU-1225 | WU-1225 core | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1225/WU-1225-core | ||||||||||||||||||||||||
60 | GBM | WU-1225 | WU-1225 edge | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1225/WU-1225-edge | ||||||||||||||||||||||||
61 | GBM | WU-1226 | WU-1226 core CD45neg | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1226/WU-1226-coreCD45neg | ||||||||||||||||||||||||
62 | GBM | WU-1226 | WU-1226 edge CD45 neg | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /storage1/fs1/allegra.petti/Active/GBM/scEdgeCore/SAMPLES/WU-1226/WU-1226-edgeCD45neg | ||||||||||||||||||||||||
63 | GBM | GBM016 | GBM016_Core_CD45N | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /n/data1/mgh/neuro/petti/lab/data/human/scrna/SAMPLES/GBM016_Core_CD45N_cellranger | ||||||||||||||||||||||||
64 | GBM | GBM016 | GBM016_Core_CD45P | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /n/data1/mgh/neuro/petti/lab/data/human/scrna/SAMPLES/GBM016_Core_CD45P_cellranger | ||||||||||||||||||||||||
65 | GBM | GBM016 | GBM016_Edge | scRNA-seq (10x 5' V2) | Processed (Cellranger 5.0.1) | /n/data1/mgh/neuro/petti/lab/data/human/scrna/SAMPLES/GBM016_Edge_cellranger | ||||||||||||||||||||||||
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