UCSF Brain Tumor Bioinformatics DAC

Contact Information

Aaron Diaz
aaron.diaz@ucsf.edu

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This DAC controls 54 datasets

Dataset ID	Description	Technology	Samples
EGAD00001002269	We expressed PDGFRAmut, wild-type PDGFRA and a GFP control from lentivirus, in two primary GBM patient-derived cell lines that we had cultured as monolayers.	Illumina HiSeq 4000	1
EGAD00001002270	We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001002271	We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001002272	We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001002273	We performed bulk exome-seq on a primary GBM and a blood sample from SF10345	Illumina HiSeq 2500	1
EGAD00001002274	We performed bulk exome-seq on a primary GBM and a blood sample from SF10360	Illumina HiSeq 2500	1
EGAD00001002275	We performed bulk exome-seq on a primary GBM and a blood sample from SF10282	Illumina HiSeq 2500	1
EGAD00001003107	We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.	Illumina HiSeq 2500	1
EGAD00001003108	We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.	Illumina HiSeq 2500	1
EGAD00001003109	We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.	Illumina HiSeq 2500	1
EGAD00001003110	We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.	Illumina HiSeq 2500	1
EGAD00001003111	We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.	Illumina HiSeq 2500	1
EGAD00001003112	We collected fresh tissue from an untreated GBM (SF10592) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001003113	We collected fresh tissue from an untreated GBM (SF10679) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001003114	We collected fresh tissue from an untreated GBM (SF10281) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001005391	SF11977 single cell RNA-seq IDHR132H Wild-type GBM Female, 61 Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	-
EGAD00001005392	SF11956 IDHR132H WT GBM. Male, 63. Single Cell RNA seq from high grade glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	-
EGAD00001005393	SF11644 Primary GBM Gender Male age 57. Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	-
EGAD00001005394	Single cell RNA-Seq Primary diffuse astrocytoma G2. IDH mutant, ATRX mutant. Gender Male Age 34. Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	-
EGAD00001005395	Single cell Primary astrocytoma G2. IDH mutant, ATRX negative. Male, 44. Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	-
EGAD00001005396	Single cell RNA-Seq Low Grade Astrocytoma IDHR132H mutant. Male, 64. Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	1
EGAD00001005397	SF11949 Primary oligodendroglioma G3 IDH1 Mutant. Male, 40 Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	-
EGAD00001005398	IDH1 mutant oligodendroglioma male, 40. Single Nuclei ATAC seq data from low grade human glioma sample. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005399	Single Nuclei RNA-Seq Primary High-grade Glioma. Gender Female Age 51. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference	Illumina NovaSeq 6000	1
EGAD00001005401	Single Nuclei RNA-Seq Primary High-grade Glioma. Gender Male Age 73. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	1
EGAD00001005402	Single Nuclei RNA-Seq Primary High-grade Glioma. Gender Female age 40. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	1
EGAD00001005403	Single Nuclei RNA Seq of primary GBM. Gender Female Age 44. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference	Illumina NovaSeq 6000	-
EGAD00001005405	IDH1 mutant GBM 55, Male. Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005406	IDHR132H Wildtype GBM. Male, 63 Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005407	High grade glioma sample, Gender Male Age 46. Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005408	SF11331 Primary GBM Male,55 Single Nuclei ATAC seq data from high grade human glioma sample. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005409	SF10022 single nuclei RNA-Seq Primary High-grade glioma. gender Male Age 65. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference	Illumina NovaSeq 6000	1
EGAD00001005410	Single Nuclei RNA-Seq Primary GBM. Gender Female Age 51. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	1
EGAD00001005411	Single Cell RNA seq from Recurrent oligodendroglioma sample. Gender Male Age 67. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)	Illumina NovaSeq 6000	-
EGAD00001005412	Single Nuclei RNA-Seq Primary IDHR132H Wild-type GBM. Male, 61. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	1
EGAD00001005413	SF11612 Recurrent oligodendroglioma. Gender Male Age 67. Single Nuclei ATAC seq data from low grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005414	Single Nuclei ATAC Seq IDHR132H mutant Astrocytoma . Male, 64. Single Nuclei ATAC seq data from low grade human glioma sample. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005415	Single Nuclei RNA-Seq Primary High-grade Glioma. Gender male age 39. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference	Illumina NovaSeq 6000	1
EGAD00001005418	SF11979 snATAC, IDHR132H WT GBM Female, 76 Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	1
EGAD00001005428	Single Nuceli Primary GBM 73 Male. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005429	Single Cell Prmary high grade glioma IDHR132H Wild-type Female 76 Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	-
EGAD00001005430	Single Nuclei Primary GBM IDHR132H Wildtype. Female 76. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.	Illumina NovaSeq 6000	1
EGAD00001006017	Single Cell RNA-Seq of Primary GBM. Gender Female, Age, 57.	Illumina NovaSeq 6000	1
EGAD00001006018	Mixed Sample of scRNA-Seq primary low grade glioma. Genders: Male, Age: 34, 44.	Illumina NovaSeq 6000	1
EGAD00001006019	Single Cell-RNA Seq of Wildtype Primary GBM for Female, Age 50.	Illumina NovaSeq 6000	1
EGAD00001006020	Primary diffuse astrocytoma G3 Male, 74	Illumina NovaSeq 6000	1
EGAD00001006830	RNA-exome	Illumina NovaSeq 6000	1
EGAD00001006831	RNA-exome	Illumina NovaSeq 6000	1
EGAD00001006832	RNA-exome	Illumina NovaSeq 6000	1
EGAD00001006833	RNA-exome	Illumina NovaSeq 6000	1
EGAD00001006834	RNA-exome	Illumina NovaSeq 6000	1
EGAD00001006835	RNA-exome	Illumina NovaSeq 6000	1
EGAD00001006836	RNA-exome	Illumina NovaSeq 6000	1
EGAD00001006837	RNA-exome	Illumina NovaSeq 6000	1