title: Wilms tumor [203271750144_R07C01]


title: atypical teratoid/rhabdoid tumor [203496240008_R01C01]

status: Public on Oct 10 2024

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

hyb_protocol: We analyzed the 950 independent test samples using Illumina Methylation BeadChip (EPIC) arrays according to the manufacturer's instructions. In summary, DNA was isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue using the Maxwell® Clinical Sample Concentrator system (Promega, Madison, WI). Following extraction, DNA was quantified using a Qubit fluorometer and quantitation reagents (Thermo Fisher Scientific, Waltham, MA), and bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA). The overall DNA input amount was approximately 250 ng. All methylation dta were analyzed in R (http://www.r-project.org, version 3.5.3), using a number of packages from Bioconductor and other repositories. Specifically, array data were preprocessed using the minfi package (v.1.28.4) (13). Background correction with dye-bias normalization was performed for all samples using noob (normal-exponential out-of-band) with “single” dye method (14). Filtering was performed to remove probes located on sex chromosomes, probes containing nucleotide polymorphisms (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, or probes mapping to multiple sites on hg19 (allowing for one mismatch), and cross-reactive probes.

scan_protocol: DNA methylation profiling was carried out with the Infinium HumanMethylationEPIC BeadChip (850K) array (Illumina Inc., San Diego, CA) on the Illumina iScan platform.

data_processing:
All methylation data were analyzed in R (http://www.r-project.org, version 3.5.3), using a number of packages from Bioconductor and other repositories. Specifically, array data were preprocessed using the minfi package (v.1.28.4) (13). Background correction with dye-bias normalization was performed for all samples using noob (normal-exponential out-of-band) with “single” dye method (14). Filtering was performed to remove probes located on sex chromosomes, probes containing nucleotide polymorphisms (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, or probes mapping to multiple sites on hg19 (allowing for one mismatch), and cross-reactive probes.
Average beta values that were normalized by functional normalization from minfi R package

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE

label_protocol: Illumina

growth_protocol: FFPE or frozen tumor samples representing pediatric patient samples encountered on the typical pathology service were evaluated.  The samples represented 650 samples expected to be present in the reference series and 300, true negative samples representative of non-brain solid tumors known to be absent from the reference series

treatment_protocol: Standard Illumina protocol

tag: tissue

value: FFPE

tag: Sex

value: Male


title: Medulloblastoma, non-WNT/non-SHH [203496240008_R08C01]

extract_protocol: We analyzed the 950 independent test samples using Illumina Methylation BeadChip (EPIC) arrays according to the manufacturer's instructions. In summary, DNA was isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue using the Maxwell® Clinical Sample Concentrator system (Promega, Madison, WI).


title: myoepithelial tumor [203496240011_R03C01]

value: Female


title: Diffuse astrocytoma, MYBL1-altered [203271750144_R03C01]


title: pediatric type diffuse glioma, IDH-wildtype/H3 wildtype [203496240008_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [203496240008_R04C01]


title: CIC-rearranged sarcoma [203271750144_R06C01]


title: rhabdomyosarcoma [203271750144_R05C01]


title: Posterior fossa group A (PFA) ependyoma [203496240108_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [203271750144_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [203271750143_R03C01]


title: atypical teratoid/rhabdoid tumor [203496240063_R06C01]


title: Posterior fossa group A (PFA) ependyoma [203271750143_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [203271750110_R07C01]


title: myoepithelial tumor [203271750105_R04C01]


title: myxopapillary ependymoma [203271750110_R01C01]


title: Neuroblastoma [203259760141_R03C01]


title: Neuroblastoma [203259760058_R07C01]


title: myoepithelial tumor [203271750105_R03C01]


title: Neuroblastoma [203259760141_R01C01]


title: Medulloblastoma, WNT-activated [203496240008_R05C01]


title: Neuroblastoma [203259760058_R05C01]


title: Neuroblastoma [203259760058_R06C01]


title: Neuroblastoma [203259760058_R02C01]


title: Neuroblastoma [203259060125_R03C01]


title: Neuroblastoma [203259060109_R07C01]


title: Neuroblastoma [203259060109_R05C01]


title: Neuroblastoma [203259060109_R04C01]


title: Neuroblastoma [203259060109_R02C01]


title: Neuroblastoma [203259060109_R01C01]


title: Neuroblastoma [203257030086_R06C01]


title: Posterior fossa group A (PFA) ependyoma [203271750143_R05C01]


title: Neuroblastoma [203257030114_R08C01]


title: Neuroblastoma [203257030086_R01C01]


title: posterior fossa group B (PFB) ependymoma [203135920100_R08C01]


title: Neuroblastoma [203257030086_R02C01]


title: Neuroblastoma [203257030114_R04C01]


title: Neuroblastoma [203257030114_R01C01]


title: Neuroblastoma [203135920100_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [203135920100_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [203135920100_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [203135920100_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [203135920100_R02C01]


title: Neuroblastoma [203135920086_R08C01]


title: Neuroblastoma [203135920086_R03C01]


title: Angiomatoid Fibrous Histiocytoma [203259760007_R01C01]


title: Neuroblastoma [203135920086_R02C01]


title: Neuroblastoma [203135920086_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [203135920082_R06C01]


title: Neuroblastoma [203259060109_R06C01]


title: Posterior fossa group A (PFA) ependyoma [203135920082_R05C01]


title: Wilms tumor [203135920082_R04C01]


title: myoepithelial tumor [203135920060_R06C01]


title: high-grade astroctyoma, BRAF-altered [203135920082_R03C01]


title: myoepithelial tumor [203135920060_R04C01]


title: myoepithelial tumor [203135920060_R07C01]


title: myoepithelial tumor [203135920060_R05C01]


title: rhabdomyosarcoma [203135920060_R02C01]


title: rhabdomyosarcoma [202760950077_R06C01]


title: myoepithelial tumor [203135920060_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [203135920100_R06C01]


title: rhabdomyosarcoma [202760950077_R05C01]


title: Neuroblastoma [202760950077_R04C01]


title: desmoplastic small round cell tumor [202760950077_R02C01]


title: Clear cell sarcoma [202292330055_R08C01]


title: Neuroblastoma [202760950077_R03C01]


title: Neuroblastoma [203135920086_R05C01]


title: Myxoid liposarcoma [202253660005_R08C01]


title: Myxoid liposarcoma [202253660005_R05C01]


title: rhabdomyosarcoma [202292330029_R02C01]


title: Myxoid liposarcoma [202253660005_R04C01]


title: Myxoid liposarcoma [202253660005_R07C01]


title: Osteosarcoma [202253650068_R08C01]


title: Neuroblastoma [202253650094_R04C01]


title: Neuroblastoma [202253650068_R05C01]


title: epithelioid sarcoma [202253650094_R02C01]


title: Neuroblastoma [202253650068_R03C01]


title: Neuroblastoma [202253650068_R01C01]


title: Osteosarcoma [202253650034_R08C01]


title: Osteosarcoma [202253650034_R02C01]


title: Osteosarcoma [202253650034_R04C01]


title: Neuroblastoma [202253650028_R04C01]


title: Neuroblastoma [202253650028_R01C01]


title: Neuroblastoma [202253650028_R05C01]


title: Wilms tumor [202253650027_R04C01]


title: Wilms tumor [202760950073_R03C01]


title: Osteosarcoma [202253650019_R03C01]


title: Retinoblastoma [202234370115_R07C01]


title: desmoplastic small round cell tumor [202234380085_R03C01]


title: Retinoblastoma [202234370115_R06C01]


title: Retinoblastoma [202234370115_R08C01]


title: desmoplastic small round cell tumor [202234380079_R08C01]


title: lipoblastoma [202234380079_R06C01]


title: Retinoblastoma [202234370115_R04C01]


title: Retinoblastoma [202234370083_R07C01]


title: Retinoblastoma [202234370083_R06C01]


title: Retinoblastoma [202234370083_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [202234370083_R01C01]


title: Retinoblastoma [202234370034_R05C01]


title: desmoplastic small round cell tumor [202232290211_R04C01]


title: desmoplastic small round cell tumor [202232290211_R03C01]


title: Osteosarcoma [202253650034_R06C01]


title: desmoplastic small round cell tumor [202232290211_R02C01]


title: desmoplastic small round cell tumor [202232290174_R05C01]


title: desmoplastic small round cell tumor [202232290207_R01C01]


title: desmoplastic small round cell tumor [202232290174_R07C01]


title: desmoplastic small round cell tumor [202234380085_R04C01]


title: Neuroblastoma [202172220049_R07C01]


title: desmoplastic small round cell tumor [202232290174_R08C01]


title: Neuroblastoma [202172220049_R05C01]


title: Neuroblastoma [202172220049_R06C01]


title: Neuroblastoma [202172220049_R03C01]


title: Neuroblastoma [202172220049_R04C01]


title: Osteosarcoma [202253650034_R01C01]


title: Neuroblastoma [202172220049_R02C01]


title: Neuroblastoma [202163550163_R08C01]


title: Neuroblastoma [202163550163_R07C01]


title: desmoplastic small round cell tumor [202232290174_R06C01]


title: Neuroblastoma [202163550163_R06C01]


title: Neuroblastoma [202163550163_R05C01]


title: Neuroblastoma [202172220049_R08C01]


title: Neuroblastoma [202163550163_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [202234370034_R04C01]


title: Neuroblastoma [202163550163_R01C01]


title: Neuroblastoma [202163550163_R04C01]


title: Neuroblastoma [202163550163_R02C01]


title: infantile fibrosarcoma [202163550091_R02C01]


title: infantile fibrosarcoma [202163550088_R08C01]


title: infantile fibrosarcoma [202163550088_R06C01]


title: infantile fibrosarcoma [202163550088_R07C01]


title: Neuroblastoma [202253650094_R07C01]


title: infantile fibrosarcoma [202163550088_R05C01]


title: Neuroblastoma [202163550088_R02C01]


title: Neuroblastoma [202163550088_R01C01]


title: Adrenocortical tumor [201557510049_R06C01]


title: Adrenocortical tumor [201557510049_R05C01]


title: Adrenocortical tumor [201557510049_R04C01]


title: Adrenocortical tumor [201557510049_R01C01]


title: Adrenocortical tumor [201557510049_R02C01]


title: Adrenocortical tumor [201557510031_R05C01]


title: Adrenocortical tumor [201557510031_R08C01]


title: Adrenocortical tumor [201557510031_R03C01]


title: Adrenocortical tumor [201557510028_R04C01]


title: Adrenocortical tumor [201557510026_R04C01]


title: Adrenocortical tumor [201557510026_R06C01]


title: Adrenocortical tumor [201557510026_R07C01]


title: Adrenocortical tumor [201557510028_R03C01]


title: Adrenocortical tumor [201557510026_R08C01]


title: Adrenocortical tumor [201557510026_R05C01]


title: Adrenocortical tumor [201557510026_R02C01]


title: Adrenocortical tumor [201557510026_R03C01]


title: infantile fibrosarcoma [202163550088_R04C01]


title: Adrenocortical tumor [201557510014_R07C01]


title: Adrenocortical tumor [201557510049_R08C01]


title: Adrenocortical tumor [201557510014_R05C01]


title: Adrenocortical tumor [201557510049_R03C01]


title: Osteosarcoma [203496240008_R03C01]


title: Adrenocortical tumor [201557510014_R08C01]


title: Adrenocortical tumor [201557510014_R01C01]


title: Adrenocortical tumor [201557510031_R04C01]


title: Adrenocortical tumor [201557510014_R04C01]


title: rhabdomyosarcoma [201533640050_R07C01]


title: rhabdomyosarcoma [201533640050_R06C01]


title: rhabdomyosarcoma [201533640050_R02C01]


title: Adrenocortical tumor [201557510014_R02C01]


title: rhabdomyosarcoma [201533640050_R03C01]


title: Adrenocortical tumor [201557510026_R01C01]


title: Neuroblastoma [201533640048_R06C01]


title: Neuroblastoma [201533640048_R07C01]


title: Neuroblastoma [201533640048_R04C01]


title: Neuroblastoma [201533640048_R03C01]


title: Neuroblastoma [201533640048_R01C01]


title: Neuroblastoma [201533640048_R05C01]


title: rhabdomyosarcoma [201533640050_R08C01]


title: Neuroblastoma [201533640048_R02C01]


title: rhabdomyosarcoma [201533640046_R08C01]


title: rhabdomyosarcoma [201533640046_R07C01]


title: Adrenocortical tumor [201557510014_R06C01]


title: rhabdomyosarcoma [201533640046_R06C01]


title: rhabdomyosarcoma [201533640046_R05C01]


title: Adrenocortical tumor [201557510014_R03C01]


title: rhabdomyosarcoma [201533640046_R03C01]


title: Neuroblastoma [201533640043_R08C01]


title: Neuroblastoma [201533640043_R07C01]


title: rhabdomyosarcoma [201533640050_R05C01]


title: Neuroblastoma [201533640043_R06C01]


title: Neuroblastoma [201533640043_R04C01]


title: Neuroblastoma [201533640043_R03C01]


title: Osteosarcoma [201533640043_R01C01]


title: rhabdomyosarcoma [201533640042_R06C01]


title: rhabdomyosarcoma [201533640042_R04C01]


title: rhabdomyosarcoma [201533640042_R02C01]


title: rhabdomyosarcoma [201533640042_R03C01]


title: Osteosarcoma [201533640034_R07C01]


title: Osteosarcoma [201533640034_R05C01]


title: Osteosarcoma [201533640034_R04C01]


title: Osteosarcoma [201533640034_R02C01]


title: Osteosarcoma [201533640034_R01C01]


title: rhabdomyosarcoma [201533640031_R07C01]


title: rhabdomyosarcoma [201533640046_R04C01]


title: rhabdomyosarcoma [201533640031_R05C01]


title: rhabdomyosarcoma [201533640031_R04C01]


title: rhabdomyosarcoma [201533640031_R01C01]


title: rhabdomyosarcoma [201533640024_R06C01]


title: Neuroblastoma [201533640043_R05C01]


title: rhabdomyosarcoma [201533640031_R02C01]


title: Osteosarcoma [201533640034_R06C01]


title: Osteosarcoma [201533640043_R02C01]


title: Adrenocortical tumor [201557510031_R01C01]


title: rhabdomyosarcoma [201533640023_R06C01]


title: rhabdomyosarcoma [201533640023_R05C01]


title: rhabdomyosarcoma [201533640031_R03C01]


title: rhabdomyosarcoma [201533640024_R08C01]


title: Osteosarcoma [201533640034_R08C01]


title: rhabdomyosarcoma [201533640023_R03C01]


title: rhabdomyosarcoma [201533640009_R07C01]


title: rhabdomyosarcoma [201533640009_R05C01]


title: rhabdomyosarcoma [201533640042_R01C01]


title: rhabdomyosarcoma [201533640023_R04C01]


title: rhabdomyosarcoma [201533640009_R08C01]


title: rhabdomyosarcoma [201533640023_R01C01]


title: rhabdomyosarcoma [201533640009_R04C01]


title: Osteosarcoma [201533640005_R07C01]


title: rhabdomyosarcoma [201533640009_R01C01]


title: rhabdomyosarcoma [201533640009_R02C01]


title: synovial sarcoma [201533640005_R05C01]


title: Osteosarcoma [201533640034_R03C01]


title: Osteosarcoma [201533640005_R08C01]


title: Osteosarcoma [201533640005_R06C01]


title: synovial sarcoma [201533640005_R03C01]


title: rhabdomyosarcoma [201533620059_R07C01]


title: rhabdomyosarcoma [201533620059_R06C01]


title: synovial sarcoma [201533640005_R04C01]


title: synovial sarcoma [201533620050_R01C01]


title: rhabdomyosarcoma [201533620059_R05C01]


title: Neuroblastoma [201533640005_R01C01]


title: rhabdomyosarcoma [201533620059_R04C01]


title: synovial sarcoma [201533620050_R05C01]


title: synovial sarcoma [201533620048_R07C01]


title: synovial sarcoma [201533620050_R03C01]


title: rhabdomyosarcoma [201533620059_R03C01]


title: synovial sarcoma [201533620050_R02C01]


title: rhabdomyosarcoma [201533640031_R06C01]


title: rhabdomyosarcoma [201533620012_R07C01]


title: rhabdomyosarcoma [201533620039_R03C01]


title: synovial sarcoma [201533620048_R06C01]


title: rhabdomyosarcoma [201533620012_R04C01]


title: rhabdomyosarcoma [201533620012_R03C01]


title: rhabdomyosarcoma [201533620039_R08C01]


title: Neuroblastoma [201533620011_R05C01]


title: rhabdomyosarcoma [201533620012_R01C01]


title: synovial sarcoma [201533620048_R05C01]


title: rhabdomyosarcoma [201533620012_R06C01]


title: rhabdomyosarcoma [201533620012_R08C01]


title: Adrenocortical tumor [201533610012_R08C01]


title: rhabdomyosarcoma [201533620004_R01C01]


title: rhabdomyosarcoma [201533620039_R05C01]


title: Adrenocortical tumor [201533610012_R05C01]


title: rhabdomyosarcoma [201533620012_R02C01]


title: rhabdomyosarcoma [201533620012_R05C01]


title: Adrenocortical tumor [201533610012_R06C01]


title: rhabdomyosarcoma [201533620004_R06C01]


title: Adrenocortical tumor [201533610012_R03C01]


title: Adrenocortical tumor [201533610011_R07C01]


title: rhabdomyosarcoma [201533620004_R05C01]


title: rhabdomyosarcoma [201533620004_R04C01]


title: Neuroblastoma [202172220049_R01C01]


title: Adrenocortical tumor [201533610012_R07C01]


title: rhabdomyosarcoma [201533520040_R05C01]


title: Adrenocortical tumor [201533610011_R06C01]


title: Adrenocortical tumor [201533610011_R08C01]


title: Adrenocortical tumor [201533610011_R04C01]


title: Pineoblastoma [200683690043_R05C01]


title: atypical teratoid/rhabdoid tumor [200683690043_R04C01]


title: rhabdomyosarcoma [201533520026_R01C01]


title: rhabdomyosarcoma [201533520040_R06C01]


title: Embryonal tumor with multilayered rosettes [200683690043_R01C01]


title: atypical teratoid/rhabdoid tumor [200683690041_R07C01]


title: CIC-rearranged sarcoma [200683690043_R02C01]


title: rhabdomyosarcoma [201533520001_R08C01]


title: Adrenocortical tumor [201533610011_R03C01]


title: atypical teratoid/rhabdoid tumor [200683690039_R06C01]


title: atypical teratoid/rhabdoid tumor [200683690039_R08C01]


title: Pineoblastoma [200683690041_R05C01]


title: atypical teratoid/rhabdoid tumor [200683690041_R06C01]


title: Adrenocortical tumor [201533610011_R05C01]


title: CNS Neuroblastoma, FOXR2-activated [200683690041_R03C01]


title: Pineoblastoma [200683690039_R01C01]


title: Pineoblastoma [200683690039_R03C01]


title: Pineoblastoma [200683690043_R07C01]


title: Adrenocortical tumor [201533610012_R04C01]


title: diffuse midline glioma, H3 K27-altered [200683690043_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200683690039_R04C01]


title: rhabdomyosarcoma [201533520048_R02C01]


title: atypical teratoid/rhabdoid tumor [200683690036_R07C01]


title: atypical teratoid/rhabdoid tumor [200683690039_R02C01]


title: angiocentric glioma [200683690030_R05C01]


title: infantile hemispheric glioma [200683690030_R08C01]


title: supratentorial ependymoma, YAP1-fusion positive [200683690036_R03C01]


title: atypical teratoid/rhabdoid tumor [200683690036_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690036_R04C01]


title: CIC-rearranged sarcoma [200683690030_R07C01]


title: atypical teratoid/rhabdoid tumor [200683690030_R03C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200683690030_R06C01]


title: CIC-rearranged sarcoma [200683690027_R05C01]


title: Embryonal tumor with multilayered rosettes [200683690027_R02C01]


title: CNS Neuroblastoma, FOXR2-activated [200683690027_R01C01]


title: choroid plexus carcinoma [200683690024_R01C01]


title: Medulloblastoma, SHH-activated [200683690020_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690020_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690020_R02C01]


title: choroid plexus carcinoma [200683690024_R05C01]


title: infantile hemispheric glioma [200683690030_R04C01]


title: Embryonal tumor with multilayered rosettes [200683690024_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690020_R01C01]


title: atypical teratoid/rhabdoid tumor [200683690024_R02C01]


title: atypical teratoid/rhabdoid tumor [200683690024_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690019_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690019_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690019_R06C01]


title: choroid plexus carcinoma [200683690036_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690019_R04C01]


title: atypical teratoid/rhabdoid tumor [200683690017_R08C01]


title: Medulloblastoma, WNT-activated [200683690019_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200683690017_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200683690014_R08C01]


title: atypical teratoid/rhabdoid tumor [200683690024_R08C01]


title: Pineoblastoma [200683690017_R01C01]


title: atypical teratoid/rhabdoid tumor [200683690014_R06C01]


title: high-grade astroctyoma, NOS [200683690014_R07C01]


title: atypical teratoid/rhabdoid tumor [200683690014_R04C01]


title: atypical teratoid/rhabdoid tumor [200683690014_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200683690014_R01C01]


title: atypical teratoid/rhabdoid tumor [200683690004_R08C01]


title: atypical teratoid/rhabdoid tumor [200683690006_R07C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200683690006_R02C01]


title: atypical teratoid/rhabdoid tumor [200683690004_R07C01]


title: atypical teratoid/rhabdoid tumor [200683690004_R01C01]


title: atypical teratoid/rhabdoid tumor [200681380054_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200683690004_R05C01]


title: CNS tumor with BCOR-ITD [200683690014_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200683690004_R03C01]


title: atypical teratoid/rhabdoid tumor [200681380054_R04C01]


title: diffuse midline glioma, H3 K27-altered [200683690004_R04C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200681380054_R07C01]


title: Embryonal tumor with multilayered rosettes [200681380054_R03C01]


title: Pineoblastoma [200681380054_R01C01]


title: Embryonal tumor with multilayered rosettes [200681380054_R02C01]


title: Pineoblastoma [200681380053_R07C01]


title: Embryonal tumor with multilayered rosettes [200681380053_R08C01]


title: Embryonal tumor with multilayered rosettes [200681380053_R05C01]


title: Embryonal tumor with multilayered rosettes [200683690006_R04C01]


title: atypical teratoid/rhabdoid tumor [200683690006_R03C01]


title: infantile hemispheric glioma [200681380053_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200681380053_R04C01]


title: pilocytic astrocytoma [200681380052_R05C01]


title: atypical teratoid/rhabdoid tumor [200681380052_R04C01]


title: choroid plexus carcinoma [200681380052_R02C01]


title: choroid plexus papilloma [200681380052_R01C01]


title: atypical teratoid/rhabdoid tumor [200681380052_R03C01]


title: atypical teratoid/rhabdoid tumor [200683690004_R02C01]


title: choroid plexus carcinoma [200681380045_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200681380045_R07C01]


title: atypical teratoid/rhabdoid tumor [200681380045_R01C01]


title: Posterior fossa group A (PFA) ependyoma [200681380045_R06C01]


title: choroid plexus carcinoma [200681380054_R06C01]


title: atypical teratoid/rhabdoid tumor [200681380045_R04C01]


title: Posterior fossa group A (PFA) ependyoma [200681380045_R03C01]


title: Medulloblastoma, SHH-activated [200681380036_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380036_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380014_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380036_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380036_R05C01]


title: infantile hemispheric glioma [200681380052_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380014_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380036_R01C01]


title: CNS tumor with BCOR-ITD [200681380002_R04C01]


title: Medulloblastoma, WNT-activated [200681380014_R08C01]


title: atypical teratoid/rhabdoid tumor [200681380002_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380014_R07C01]


title: atypical teratoid/rhabdoid tumor [200681380053_R06C01]


title: Medulloblastoma, SHH-activated [200681380014_R05C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200681380001_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380014_R04C01]


title: atypical teratoid/rhabdoid tumor [200681380001_R08C01]


title: atypical teratoid/rhabdoid tumor [200681380001_R01C01]


title: Medulloblastoma, SHH-activated [200681380036_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200681380036_R08C01]


title: Pineoblastoma [200673760029_R06C01]


title: atypical teratoid/rhabdoid tumor [200681380001_R02C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200681380002_R07C01]


title: Pineoblastoma [200681380002_R01C01]


title: Pineoblastoma [200681380001_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200681380001_R04C01]


title: Medulloblastoma, SHH-activated [200673760029_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200673760028_R06C01]


title: Embryonal tumor with multilayered rosettes [200673760029_R04C01]


title: atypical teratoid/rhabdoid tumor [200673760029_R02C01]


title: atypical teratoid/rhabdoid tumor [200673760029_R03C01]


title: atypical teratoid/rhabdoid tumor [200673760029_R08C01]


title: CNS Neuroblastoma, FOXR2-activated [200673760008_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200673760028_R07C01]


title: atypical teratoid/rhabdoid tumor [200673760028_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200673760008_R02C01]


title: atypical teratoid/rhabdoid tumor [200673610045_R08C01]


title: atypical teratoid/rhabdoid tumor [200673610045_R04C01]


title: Posterior fossa group A (PFA) ependyoma [200673760029_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200673610045_R03C01]


title: choroid plexus carcinoma [200673610044_R07C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200673610045_R02C01]


title: supratentorial ependymoma, YAP1-fusion positive [200673760008_R07C01]


title: supratentorial ependymoma, YAP1-fusion positive [200673760028_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200673760008_R04C01]


title: Posterior fossa group A (PFA) ependyoma [200673760028_R04C01]


title: Posterior fossa group A (PFA) ependyoma [200673760008_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200673610045_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200673610045_R06C01]


title: supratentorial ependymoma, YAP1-fusion positive [200673610027_R08C01]


title: atypical teratoid/rhabdoid tumor [200673610044_R02C01]


title: Posterior fossa group A (PFA) ependyoma [200673760008_R01C01]


title: Posterior fossa group A (PFA) ependyoma [200673610045_R01C01]


title: Posterior fossa group A (PFA) ependyoma [200673610044_R08C01]


title: Embryonal tumor with multilayered rosettes [200673610044_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200673610044_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200661940004_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200661940004_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200673610027_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200661940004_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200673610027_R02C01]


title: choroid plexus carcinoma [200673610027_R06C01]


title: atypical teratoid/rhabdoid tumor [200673610027_R07C01]


title: atypical teratoid/rhabdoid tumor [200673610044_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200661940004_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200661940004_R07C01]


title: Medulloblastoma, SHH-activated [200661820053_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200661820053_R07C01]


title: Medulloblastoma, SHH-activated [200661940004_R05C01]


title: Medulloblastoma, WNT-activated [200661940004_R04C01]


title: Medulloblastoma, SHH-activated [200661820033_R06C01]


title: Medulloblastoma, SHH-activated [200661820033_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200661820053_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200661820053_R06C01]


title: atypical teratoid/rhabdoid tumor [200673610027_R04C01]


title: Medulloblastoma, SHH-activated [200661820033_R04C01]


title: Medulloblastoma, SHH-activated [200661820053_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200661820053_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200661820053_R02C01]


title: Medulloblastoma, SHH-activated [200661820033_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200661820033_R08C01]


title: Medulloblastoma, SHH-activated [200661820053_R03C01]


title: Medulloblastoma, SHH-activated [200661820033_R01C01]


title: atypical teratoid/rhabdoid tumor [200654520054_R06C01]


title: atypical teratoid/rhabdoid tumor [200673610027_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200661820033_R03C01]


title: choroid plexus carcinoma [200654520054_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200654520054_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200661940004_R01C01]


title: infantile hemispheric glioma [200654520052_R06C01]


title: Embryonal tumor with multilayered rosettes [200654520054_R04C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200654520054_R03C01]


title: choroid plexus carcinoma [200654520054_R01C01]


title: Posterior fossa group A (PFA) ependyoma [200654520052_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430024_R08C01]


title: Pineoblastoma [200654520049_R04C01]


title: Pineoblastoma [200654520049_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200654520052_R04C01]


title: Pineoblastoma [200654520052_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430024_R01C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200654520049_R08C01]


title: Pineoblastoma [200654520054_R02C01]


title: infantile hemispheric glioma [200654520049_R07C01]


title: atypical teratoid/rhabdoid tumor [200654520052_R02C01]


title: Medulloblastoma, WNT-activated [200654520049_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200654520052_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430024_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430024_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430024_R04C01]


title: Medulloblastoma, SHH-activated [200627670054_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430024_R06C01]


title: Medulloblastoma, SHH-activated [200654430024_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670054_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430023_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430023_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430023_R06C01]


title: Medulloblastoma, SHH-activated [200654430024_R03C01]


title: Medulloblastoma, SHH-activated [200627670054_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430023_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430023_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670053_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670053_R01C01]


title: Astrocytoma, IDH-mutant [200607140087_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430023_R02C01]


title: Medulloblastoma, WNT-activated [200627670053_R05C01]


title: Medulloblastoma, WNT-activated [200627670053_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670054_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670054_R01C01]


title: Medulloblastoma, SHH-activated [200654430023_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670053_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670053_R08C01]


title: diffuse astroctyoma, MAPK pathway altered [200607140085_R07C01]


title: Medulloblastoma, SHH-activated [200627670053_R06C01]


title: diffuse astroctyoma, MAPK pathway altered [200607140085_R04C01]


title: Medulloblastoma, WNT-activated [200627670053_R04C01]


title: angiocentric glioma [200607140085_R03C01]


title: Astrocytoma, IDH-mutant [200607140087_R07C01]


title: meningioma [200607140084_R06C01]


title: meningioma [200607140084_R05C01]


title: Astrocytoma, IDH-mutant [200607140087_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200654430023_R01C01]


title: meningioma [200607140087_R02C01]


title: pleomorphic xanthoastrocytoma [200607140085_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670054_R06C01]


title: angiocentric glioma [200607140085_R02C01]


title: meningioma [200607140084_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200627670054_R02C01]


title: meningioma [200607140084_R02C01]


title: Embryonal tumor, NEC [200607140080_R07C01]


title: Embryonal tumor, NEC [200607140080_R06C01]


title: Embryonal tumor, NOS [200607140080_R05C01]


title: posterior fossa group B (PFB) ependymoma [200607140078_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200607140078_R04C01]


title: Posterior fossa group A (PFA) ependyoma [200607140078_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200607140078_R02C01]


title: meningioma [200607140083_R08C01]


title: atypical teratoid/rhabdoid tumor [200607140082_R07C01]


title: posterior fossa group B (PFB) ependymoma [200607140078_R07C01]


title: dysembryoplastic neuroepithelial tumor [200607140077_R05C01]


title: angiocentric glioma [200607140077_R03C01]


title: posterior fossa group B (PFB) ependymoma [200607140078_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200607140078_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200607140076_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200607140076_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200607140076_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200607140076_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200607140076_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200607140076_R02C01]


title: Posterior fossa group A (PFA) ependyoma [200607140076_R04C01]


title: glioblastoma, IDH-wildtype [200607140074_R08C01]


title: atypical teratoid/rhabdoid tumor [200607140082_R03C01]


title: CNS tumor with BCOR-ITD [200607140075_R06C01]


title: glioblastoma, NOS [200607140080_R04C01]


title: glioblastoma, IDH-wildtype [200607140074_R06C01]


title: pediatric type diffuse glioma, IDH-wildtype/H3 wildtype [200607140074_R07C01]


title: Glioblastoma, IDH-wildtype [200607140074_R04C01]


title: pediatric type diffuse glioma, IDH-wildtype/H3 wildtype [200607140074_R05C01]


title: Astrocytoma, IDH-mutant [200607140074_R03C01]


title: dysembryoplastic neuroepithelial tumor [200607140077_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200607140067_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200607140067_R08C01]


title: choroid plexus papilloma [200607140068_R05C01]


title: pilocytic astrocytoma [200607140074_R02C01]


title: dysembryoplastic neuroepithelial tumor [200607140077_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200607140067_R04C01]


title: Posterior fossa group A (PFA) ependyoma [200607140067_R02C01]


title: Posterior fossa group A (PFA) ependyoma [200607140067_R03C01]


title: atypical choroid plexus papilloma [200607140061_R07C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200607140065_R08C01]


title: choroid plexus papilloma [200607140061_R05C01]


title: choroid plexus papilloma [200607140061_R08C01]


title: atypical choroid plexus papilloma [200607140061_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200607140060_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200607140060_R06C01]


title: diffuse midline glioma, H3 K27-altered [200607140059_R03C01]


title: diffuse midline glioma, H3 K27-altered [200607140061_R03C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140041_R07C01]


title: pilocytic astrocytoma [200607140041_R06C01]


title: diffuse midline glioma, H3 K27-altered [200607140059_R04C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140041_R03C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140041_R08C01]


title: pilocytic astrocytoma [200607140041_R04C01]


title: diffuse midline glioma, H3 K27-altered [200607140059_R02C01]


title: diffuse midline glioma, H3 K27-altered [200607140036_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200607140060_R05C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140041_R02C01]


title: diffuse midline glioma, H3 K27-altered [200607140036_R06C01]


title: diffuse midline glioma, H3 K27-altered [200607140036_R07C01]


title: pilocytic astrocytoma [200607140035_R05C01]


title: diffuse pediatric type high-grade glioma, IDH-wildtype/H3-wildtype [200607140036_R04C01]


title: pilocytic astrocytoma [200607140035_R08C01]


title: pilocytic astrocytoma [200607140035_R04C01]


title: pilocytic astrocytoma [200607140035_R06C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200607140034_R08C01]


title: Astrocytoma, IDH-mutant [200607140034_R07C01]


title: Astrocytoma, IDH-mutant [200607140034_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200607140060_R04C01]


title: Astrocytoma, IDH-mutant [200607140034_R06C01]


title: dysembryoplastic neuroepithelial tumor [200607140032_R06C01]


title: pilocytic astrocytoma [200607140035_R02C01]


title: pilocytic astrocytoma [200607140035_R03C01]


title: CNS Neuroblastoma, FOXR2-activated [200607140034_R03C01]


title: Astrocytoma, IDH-mutant [200607140034_R04C01]


title: diffuse low-grade glioma, MAPK pathway-altered [200607140032_R04C01]


title: pilocytic astrocytoma [200607140031_R04C01]


title: pilocytic astrocytoma [200607140031_R08C01]


title: diffuse low-grade glioma, MAPK pathway-altered [200607140032_R05C01]


title: Diffuse astrocytoma, NOS [200607140032_R02C01]


title: pilocytic astrocytoma [200607140032_R03C01]


title: pilocytic astrocytoma [200607140031_R07C01]


title: pilocytic astrocytoma [200607140031_R06C01]


title: pilocytic astrocytoma [200607140035_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200607140027_R07C01]


title: pleomorphic xanthoastrocytoma [200607140029_R08C01]


title: posterior fossa group B (PFB) ependymoma [200607140027_R06C01]


title: pilocytic astrocytoma [200607140031_R03C01]


title: posterior fossa group B (PFB) ependymoma [200607140027_R03C01]


title: posterior fossa group B (PFB) ependymoma [200607140027_R04C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140029_R02C01]


title: posterior fossa group B (PFB) ependymoma [200607140027_R05C01]


title: pilocytic astrocytoma [200607140029_R03C01]


title: posterior fossa group B (PFB) ependymoma [200607140027_R02C01]


title: pilocytic astrocytoma [200607140025_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200607140026_R02C01]


title: Posterior fossa group A (PFA) ependyoma [200607140026_R08C01]


title: pilocytic astrocytoma [200607140025_R02C01]


title: Posterior fossa group A (PFA) ependyoma [200607140026_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200607140026_R07C01]


title: pilocytic astrocytoma [200607140025_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200607140026_R06C01]


title: Posterior fossa group A (PFA) ependyoma [200607140026_R04C01]


title: Posterior fossa group A (PFA) ependyoma [200607140020_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200607140020_R07C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140019_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200607140020_R05C01]


title: pilocytic astrocytoma [200607140021_R08C01]


title: pilocytic astrocytoma [200607140009_R07C01]


title: pilocytic astrocytoma [200607140021_R07C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140019_R07C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140019_R02C01]


title: pilocytic astrocytoma [200607140021_R06C01]


title: pilocytic astrocytoma [200607140021_R03C01]


title: pilocytic astrocytoma [200607140021_R04C01]


title: pilocytic astrocytoma [200607140025_R06C01]


title: pilocytic astrocytoma [200607140009_R04C01]


title: pilocytic astrocytoma [200607140009_R02C01]


title: pilocytic astrocytoma [200607140009_R03C01]


title: pilocytic astrocytoma [200607140007_R06C01]


title: pilocytic astrocytoma [200607140007_R05C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140020_R02C01]


title: pilocytic astrocytoma [200607140009_R05C01]


title: pilocytic astrocytoma [200607140007_R03C01]


title: diffuse low-grade glioma, MAPK pathway-altered [200607140006_R06C01]


title: pilocytic astrocytoma [200607140025_R07C01]


title: Control brain [200607140008_R04C01]


title: pilocytic astrocytoma [200607140006_R03C01]


title: pilocytic astrocytoma [200607140007_R08C01]


title: pilocytic astrocytoma [200607140009_R06C01]


title: ganglioglioma [200607140006_R07C01]


title: pilocytic astrocytoma [200607140007_R07C01]


title: pilocytic astrocytoma [200607140007_R04C01]


title: diffuse midline glioma, H3 K27-altered [200607140005_R08C01]


title: diffuse midline glioma, H3 K27-altered [200607140005_R05C01]


title: diffuse midline glioma, H3 K27-altered [200607140005_R04C01]


title: diffuse midline glioma, H3 K27-altered [200607140005_R07C01]


title: diffuse midline glioma, H3 K27-altered [200607140005_R06C01]


title: CNS tumor with BCOR-ITD [200607140005_R02C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140019_R05C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607140019_R04C01]


title: diffuse low-grade glioma, MAPK pathway-altered [200607140006_R05C01]


title: diffuse midline glioma, H3 K27-altered [200607130057_R04C01]


title: ganglioglioma [200607140004_R06C01]


title: pilocytic astrocytoma [200607140004_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200607130056_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200607130056_R06C01]


title: Control brain [200607130063_R05C01]


title: Posterior fossa group A (PFA) ependyoma [200607130055_R08C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607130055_R06C01]


title: Control brain [200607130063_R06C01]


title: pilocytic astrocytoma [200607140004_R03C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607130055_R07C01]


title: Diffuse astrocytoma, NOS [200607130057_R08C01]


title: diffuse astrocytoma, MAPK pathway altered [200607130057_R05C01]


title: dysembryoplastic neuroepithelial tumor [200607130022_R08C01]


title: dysembryoplastic neuroepithelial tumor [200607130022_R06C01]


title: angiocentric glioma [200607120088_R06C01]


title: Diffuse astrocytoma, NOS [200607130057_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200607130056_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200607130056_R08C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607130055_R04C01]


title: angiocentric glioma [200607120088_R03C01]


title: dysembryoplastic neuroepithelial tumor [200607130022_R07C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200607130056_R02C01]


title: dysembryoplastic neuroepithelial tumor [200607120088_R02C01]


title: angiocentric glioma [200607120088_R07C01]


title: Control brain [200607130060_R05C01]


title: angiocentric glioma [200607120088_R05C01]


title: angiocentric glioma [200607120088_R04C01]


title: dysembryoplastic neuroepithelial tumor [200607120062_R08C01]


title: dysembryoplastic neuroepithelial tumor [200607120062_R03C01]


title: pilocytic astrocytoma [200607130022_R05C01]


title: dysembryoplastic neuroepithelial tumor [200607130022_R04C01]


title: Control brain [200607090068_R06C01]


title: posterior fossa group B (PFB) ependymoma [200607090069_R06C01]


title: Control brain [200607090068_R07C01]


title: Control brain [200607090069_R05C01]


title: angiocentric glioma [200607120088_R08C01]


title: Control brain [200607090069_R03C01]


title: Control brain [200607090067_R06C01]


title: Control brain [200607090068_R04C01]


title: Control brain [200607090068_R02C01]


title: Control brain [200607090067_R02C01]


title: Control brain [200607090066_R06C01]


title: Control brain [200607090066_R04C01]


title: Control brain [200607090066_R02C01]


title: Control brain [200607090066_R03C01]


title: Control brain [200607090065_R08C01]


title: Control brain [200607090065_R07C01]


title: Control brain [200607090056_R04C01]


title: Control brain [200607090056_R07C01]


title: Posterior fossa group A (PFA) ependyoma [200607140026_R05C01]


title: Control brain [200607090069_R04C01]


title: pilocytic astrocytoma [200607090050_R06C01]


title: pilocytic astrocytoma [200607090050_R05C01]


title: Control brain [200607090069_R02C01]


title: Control brain [200607090050_R04C01]


title: Control brain [200607090068_R05C01]


title: diffuse midline glioma, H3 K27-altered [200607090041_R03C01]


title: angiocentric glioma [200607090041_R02C01]


title: pilocytic astrocytoma [200607090041_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200607090012_R07C01]


title: Medulloblastoma, SHH-activated [200607090012_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200607090012_R06C01]


title: Medulloblastoma, SHH-activated [200607090012_R05C01]


title: Medulloblastoma, WNT-activated [200607090012_R04C01]


title: Control brain [200607090067_R05C01]


title: Control brain [200607090066_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200607090012_R03C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200607090011_R07C01]


title: Control brain [200607090068_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200607090012_R02C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200607090011_R06C01]


title: CNS Neuroblastoma, FOXR2-activated [200607090009_R07C01]


title: Pineoblastoma [200607090010_R05C01]


title: CNS Neuroblastoma, FOXR2-activated [200607090009_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200607090010_R08C01]


title: CNS Neuroblastoma, FOXR2-activated [200607090009_R05C01]


title: CNS Neuroblastoma, FOXR2-activated [200607090009_R04C01]


title: CNS Neuroblastoma, FOXR2-activated [200607090009_R03C01]


title: CNS Neuroblastoma, FOXR2-activated [200607090009_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290063_R08C01]


title: Medulloblastoma, WNT-activated [200603290063_R04C01]


title: Medulloblastoma, WNT-activated [200603290063_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290063_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290063_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290063_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290061_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290061_R08C01]


title: Medulloblastoma, WNT-activated [200603290061_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290061_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290061_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290061_R01C01]


title: Medulloblastoma, WNT-activated [200603290037_R08C01]


title: Medulloblastoma, WNT-activated [200603290037_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290061_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290037_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290037_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290037_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290001_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290037_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290001_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290001_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290037_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290001_R05C01]


title: Glioblastoma, IDH-wildtype/H3-wildtype [200603290001_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290001_R02C01]


title: Medulloblastoma, SHH-activated [200603290001_R03C01]


title: Medulloblastoma, SHH-activated [200603290063_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290001_R01C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360048_R06C01]


title: Medulloblastoma, WNT-activated [200598360048_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360048_R01C01]


title: Medulloblastoma, WNT-activated [200603290061_R03C01]


title: Medulloblastoma, WNT-activated [200598360029_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360048_R02C01]


title: Medulloblastoma, SHH-activated [200598360048_R04C01]


title: Medulloblastoma, SHH-activated [200598360029_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360048_R07C01]


title: atypical teratoid/rhabdoid tumor [200598340071_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200603290037_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360029_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340066_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360029_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340066_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360029_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340066_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360029_R01C01]


title: atypical teratoid/rhabdoid tumor [200598340071_R08C01]


title: atypical teratoid/rhabdoid tumor [200598340071_R02C01]


title: atypical teratoid/rhabdoid tumor [200598340071_R05C01]


title: Medulloblastoma, SHH-activated [200598340064_R03C01]


title: Pineoblastoma [200598340064_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340066_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340066_R03C01]


title: Pineoblastoma [200598340064_R06C01]


title: Pineoblastoma [200598340064_R04C01]


title: Pineoblastoma [200598340048_R08C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200598340064_R02C01]


title: Pineoblastoma [200598340048_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340048_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360048_R03C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200598340047_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340048_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340048_R02C01]


title: Medulloblastoma, WNT-activated [200598340048_R05C01]


title: CNS Neuroblastoma, FOXR2-activated [200598340047_R03C01]


title: CNS Neuroblastoma, FOXR2-activated [200598340047_R02C01]


title: Astrocytoma, IDH-mutant [200598340027_R07C01]


title: Astrocytoma, IDH-mutant [200598340026_R07C01]


title: Astrocytoma, IDH-mutant [200598340027_R06C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200598340026_R05C01]


title: Astrocytoma, IDH-mutant [200598340026_R08C01]


title: Glioblastoma, IDH-wildtype/H3-wildtype [200598340027_R08C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200598340026_R04C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200598340026_R06C01]


title: diffuse hemispheric glioma, H3 G34-mutant [200598340026_R03C01]


title: Medulloblastoma, WNT-activated [200598340026_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340024_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340024_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200598340024_R03C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720082_R08C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720082_R06C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720082_R05C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720082_R04C01]


title: Pineoblastoma [200594720074_R08C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720074_R04C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720074_R02C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720074_R03C01]


title: Medulloblastoma, SHH-activated [200594720066_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200594720066_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200594720066_R06C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720066_R05C01]


title: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted [200598340027_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200598360029_R05C01]


title: Medulloblastoma, WNT-activated [200594720066_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200594720066_R03C01]


title: Medulloblastoma, SHH-activated [200594720064_R07C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040161_R08C01]


title: Medulloblastoma, SHH-activated [200594720066_R02C01]


title: Medulloblastoma, SHH-activated [200594720064_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040161_R07C01]


title: Medulloblastoma, SHH-activated [200598340024_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040161_R06C01]


title: Medulloblastoma, SHH-activated [200594720064_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040161_R04C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720082_R07C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200594720082_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040161_R02C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040144_R06C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040144_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040144_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040144_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040144_R01C01]


title: Astrocytoma, IDH-mutant [200514040104_R05C01]


title: atypical teratoid/rhabdoid tumor [200514040104_R07C01]


title: shHMGA1_HT29-2

type: SRA

city: Kaifeng

first: yuan

last: zhao

address: Jinming Road

country: China

institute: Henan University

library_source: transcriptomic

data_processing:
SOAPnuke (V2.1.0) was used to filter the sequencing data
Reads containing sequencing joints were removed
Reads with N ratio greater than 0.5% were removed
Removal of low-quality reads (those with Qphred≤20 bases accounting for more than 50% of the length of the entire reads)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

growth_protocol: The cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the Trizol(Invitrogen, CA, USA), RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel.
The mRNA was purified from the total RNA using poly‐T oligo‐attached magnetic beads. Sequencing libraries were generated from the purified mRNA using the V AHTS Universal V6 RNA-seq Library Kit for MGI (V azyme, Nanjing, China) following the manufacturer's recommendations with unique index codes. The Library quantification and size was assessed using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Subsequently, sequencing was performed on a MGI-SEQ 2000 platform by Frasergen Bioinformatics Co., Ltd. (Wuhan, China).

tag: cell line

tag: cell type

value: colorectal cancer

tag: genotype

value: HMGA1 knockdown

tag: treatment

value: no treatment


title: shHMGA1_HT29-1


title: shNC_HT29-3

value: WT


title: shNC_HT29-1


title: Medulloblastoma, non-WNT/non-SHH [200514030162_R08C01]


title: Posterior fossa group A (PFA) ependyoma [200514040104_R04C01]


title: shNC_HT29-2


title: Medulloblastoma, non-WNT/non-SHH [200514040161_R05C01]


title: Kidney_gtop2b_4

city: Chengdu

first: Man

last: Zhu

state: Sichuan

address: No. 4, Section 2, Jianshe North Road, Chenghua District, Chengdu City, Sichuan, China

department: School of Medicine

institute: University of Electronic Science and Technology of China

data_processing:
SOAPnuke v1.5.6
Sequence reads for adaptor sequence/low-quality sequence/unknown base ('N' base) using SOAPnuke software. Low-Quality limit (base quality less than or equal to 15):20%, unknown base limit: 5%.
Clean sequence reads analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
The clean data were aligned to the reference genome using HISAT2 (v2.1.0) and  aligned to the gene set using Bowtie2.
Expression level of gene was calculated by RSEM (v1.3.1). The differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw FPKM values for each sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
RNA was harvested following the Microbial RNA BGI-NGS-TQ-RNA-002 protocol of Beijing Genomics institution
RNA libriaries for RNA-seq were prepared following the BGI-NGS-JK-RNA-001 protocol of Beijing Genomics institution

value: Kidney


title: Kidney_gtop2b_3


title: Medulloblastoma, non-WNT/non-SHH [200514030162_R04C01]


title: Medulloblastoma, non-WNT/non-SHH [200514030162_R07C01]


title: Kidney_gtop2b_2


title: Medulloblastoma, non-WNT/non-SHH [200514030162_R05C01]


title: Medulloblastoma, non-WNT/non-SHH [200514030162_R06C01]


title: Kidney_gLacz_4


title: Kidney_gtop2b_1


title: Medulloblastoma, non-WNT/non-SHH [200514040161_R03C01]


title: Medulloblastoma, non-WNT/non-SHH [200514040144_R07C01]


title: Kidney_gLacz_3


title: Medulloblastoma, SHH-activated [200514030091_R08C01]


title: Medulloblastoma, non-WNT/non-SHH [200514030162_R03C01]


title: Medulloblastoma, SHH-activated [200514030162_R02C01]


title: Medulloblastoma, SHH-activated [200514030091_R07C01]


title: Kidney_gLacz_2


title: shHMGA1_HT29-3


title: Lung_gtop2b_4

source_name: Lung

value: Lung


title: Medulloblastoma, SHH-activated [200514030091_R05C01]


title: Lung_gtop2b_3


title: Medulloblastoma, SHH-activated [200514030091_R06C01]


title: Lung_gtop2b_2


title: Lung_gtop2b_1


title: Medulloblastoma, non-WNT/non-SHH [200514030091_R02C01]


title: Lung_gLacz_3


title: Medulloblastoma, WNT-activated [200467580075_R04C01]


title: Lung_gLacz_2


title: Lung_gLacz_4


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200467580075_R08C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200467580075_R05C01]


title: Lung_gLacz_1


title: Ske_gtop2b_4

source_name: Skeletal muscle

value: Skeletal muscle


title: Kidney_gLacz_1


title: Ske_gtop2b_3


title: Medulloblastoma, WNT-activated [200467580075_R02C01]


title: pleomorphic xanthoastrocytoma [200467580040_R08C01]


title: Medulloblastoma, WNT-activated [200467580075_R03C01]


title: Ske_gtop2b_1


title: Ske_gLacz_4


title: pilocytic astrocytoma [200467580040_R06C01]


title: Ske_gtop2b_2


title: Ske_gLacz_2


title: Ske_gLacz_1


title: pleomorphic xanthoastrocytoma [200467580040_R05C01]


title: Diffuse astrocytoma, MYB-altered [200467580040_R04C01]


title: 48wksmaleWD7, replicate 3, snRNA-seq

city: Richmond

first: Nicholas

middle: J

last: Koelsch

state: Virginia

address: 1810 East Cary Street Apt MG02

department: Microbiology & Immunology

institute: Virginia Commonwealth University

description: WD tumor

library_source: transcriptomic single cell

data_processing:
All aligned data files were provided by the Novogene company, in which they analyzed sequencing results with mouse reference genome mm10-5.0.0 and CellRanger version 7.0.0
All analyses were conducted by using the filtered matrix files containing the data through Rstudio for procesing with various packages
Assembly: mm10-5.0.0
Supplementary files format and content: The matrix.mtx file contains raw read counts for each gene (rows) in each cell (columns) in a tab-delimited file
Supplementary files format and content: The barcodes.tsv file contains column names for the matrix file
Supplementary files format and content: The features.tsv file contains row names for the matrix file

molecule: nuclear RNA

source_name: Liver

growth_protocol: Feeding mice a high-fat diet coupled to high-sugar water (fructose and glucose) WD and performing dietary intervention by reversal back to a standard chow diet (CD) after 36 weeks on a WD in indicated mice

extract_protocol:
after animals reached 48 weeks of age at the end of study, the livers of mice were resected, snap-frozen in liquid nitrogen, and subjected to snRNA-seq
The Novogene company constructed chromium single cell 3' gene expression v3.1 libraries through the 10X Genomics Chromium system

value: Liver

value: All cells

value: 129A1/SvIm and C57BL/6J cross mice

tag: time on_diet

value: 48 weeks Western Diet (WD)


title: pleomorphic xanthoastrocytoma [200512330032_R08C01]


title: 48wksmaleWD5, replicate 2, snRNA-seq

description: WD tumor


title: Ske_gLacz_3


title: Medulloblastoma, WNT-activated [200467580020_R07C01]


title: Medulloblastoma, WNT-activated [200467580020_R08C01]


title: Embryonal tumor with multilayered rosettes, CH19MC-amplified [200467580075_R07C01]


title: pilocytic astrocytoma [200467580040_R03C01]


title: Medulloblastoma, WNT-activated [200467580020_R06C01]


title: Medulloblastoma, WNT-activated [200467580020_R03C01]


title: Medulloblastoma, WNT-activated [200467580020_R05C01]


title: 48wksmaleWD4, replicate 1, snRNA-seq

description: WD tumor


title: 48wksmaleR4, replicate 3, snRNA-seq

description: reverse diet normal

value: 36 weeks Western Diet (WD) then diet reversal to CD


title: 48wksmaleR2, replicate 1, snRNA-seq

description: reverse diet normal


title: Medulloblastoma, WNT-activated [200467580020_R04C01]


title: 48wksmaleR5, replicate 2, snRNA-seq

description: reverse diet tumor


title: Medulloblastoma, WNT-activated [200467580020_R02C01]


title: 48wksmaleR3, replicate 2, snRNA-seq

description: reverse diet normal


title: 48wksmaleR1, replicate 1, snRNA-seq

description: reverse diet tumor


title: pilocytic astrocytoma [200467580018_R08C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200467580018_R07C01]


title: Supratentorial ependymoma, ZFTA-fusion positive [200467580018_R03C01]


title: Posterior fossa group A (PFA) ependyoma [200467580018_R06C01]


title: Control_1_BMDC

city: Hangzhou

first: Zhejun

last: Cai

state: Zhejiang

address: 88 Jiefang Road

department: Department of Cardiology, The Second Affiliated Hospital

institute: Zhejiang University School of Medicine

data_processing:
Raw data in FASTQ format were initially processed using fastp software. During this step, clean data (clean reads) were generated by removing reads containing adapters, poly-N sequences, and low-quality reads from the raw data. Additionally, Q20, Q30, and GC content of the clean data were calculated. All subsequent analyses were conducted using the high-quality clean data.
The reference genome and gene model annotation files were directly downloaded from the genome website. The reference genome index was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome using the same tool. Hisat2 was selected as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file, providing superior mapping results compared to non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each gene was then calculated based on the gene length and the read counts. FPKM accounts for both sequencing depth and gene length, making it a widely used method for estimating gene expression levels.
For differential expression analysis with biological replicates, DESeq2 (version 1.20.0) was used. DESeq2 applies statistical routines based on the negative binomial distribution to determine differential expression in digital gene expression data. P-values were adjusted using the Benjamini and Hochberg method to control the false discovery rate, and genes with an adjusted P-value of ≤ 0.05 were considered differentially expressed.
For analysis without biological replicates, the edgeR R package (version 3.22.5) was utilized. Before differential expression analysis, the read counts for each library were adjusted using a scaling normalization factor. The P-values were adjusted using the Benjamini and Hochberg method, with a corrected P-value threshold of 0.05 and an absolute fold-change of 2 used to define significant differential expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes DEGs between groups

source_name: Bone marrow

growth_protocol: We isolated primary bone marrow cells from the tibias and femurs of 8-week-old male mice and cultured them in RPMI 1640 medium supplemented with GM-CSF and Flt3L cytokines to acquire CD103+ dendritic cells. 8-week-old male mice were euthanized by cervical dislocation, and their legs were dissected. After removing the surrounding muscle tissue, bone marrow was extracted aseptically from the tibia and femur. This was done by cutting the joints with a scalpel and flushing the marrow out with a 25-gauge needle attached to a syringe filled with 10 ml of PBS. The marrow clumps were then gently dissociated using a needle-free syringe through a 70 μm cell strainer. The cell suspension was centrifuged at 1000 g for 5 minutes at room temperature to pellet the cells. The collected bone marrow cells were resuspended in 10 ml of RPMI 1640 growth medium, supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 units/ml penicillin, 0.1 mg/ml streptomycin, 200 ng/ml recombinant murine FLT3L (14-8001, eBioscience), and 5 ng/ml granulocyte-macrophage colony-stimulating factor (GM-CSF, 315-03, Peprotech). On days 5 to 6, an additional 5 ml of complete medium was added to reduce apoptosis. Non-adherent cells were harvested on day 9, counted, and replated at a density of 3x10^6 cells in 10 ml of complete medium with FLT3L and GMCSF, as on day 0. Non-adherent iCD103-DCs were collected on days 15-16.

extract_protocol:
Non-adherent iCD103-DCs were collected on days 15-16. Total RNA were isolated with RNA Extraction Kits.
Total RNA was used as the starting material for RNA sample preparation. mRNA was purified from the total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed with divalent cations at an elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis followed, utilizing DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activity. After adenylation of the 3’ ends of DNA fragments, adaptors with a hairpin loop structure were ligated for hybridization. cDNA fragments, preferably 370–420 bp in length, were purified using the AMPure XP system. PCR was then performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. Finally, PCR products were purified using the AMPure XP system, and library quality was assessed using the Agilent Bioanalyzer 2100 system.

treatment_protocol: The cells could be stimulated with 20 ng/ml of TNF-alpha.

value: Bone marrow

value: Bone marrow derived dendritic cells

value: Dendritic cells

value: Wild type

value: GM-CSF and Flt3L cultivation; TNFa stimulation


title: Irf8-OE_1_BMDC


title: Irf8-OE_3_BMDC


title: Irf8-OE_2_BMDC


title: Melanoma, ffpe (GB124)

city: Balaclava

first: Ryan

last: Van Laar

state: VIC

address: PO Box 234

country: Australia

institute: Geneseq Biosciences

description:
ffpe_normalised_rpm.csv
ffpe_raw_counts.csv

data_processing:
Demultiplexing was done using bcl2fastq
sRNAtoolbox (microRNA=hsa miRdb=1 adapter=TGGAATTCTCGGGTGCCAAGG minReadLength=10 alignType=v mm=2 )
Sequence trimmed within sRNAtoolbox using provided adapter adapter=TGGAATTCTCGGGTGCCAAGG  and default sequence quality parameters.
Aligned with bowtie v1 using sRNAtoolbox to miRBase v22 with 'v' alignment parameter and mismatch 2
Raw counts were normalised to per million (rpm) by the total count of reads in the analysis after quality filtering.
Assembly: GRCh38
Supplementary files format and content: tab delimited file contains raw counts
Supplementary files format and content: tab delimited file contains normalised RPM values

source_name: Melanoma, ffpe

extract_protocol:
RNA was extracted using the Qiagen miRNeasy FFPE kit or Qiagen miRNeasy Serum/Plasma Advanced Kit. Extracted RNA was purified using the Amicon Ultra 0.5 Centrifugal filter columns for 90 minutes at 10,000g. Final sample concentrations were determined with the Invitrogen microRNA Qubit Assay and Bioanalyzer , to ensure an adequate quantity and quality of microRNA-enriched total-RNA necessary for next generation sequencing.
Libraries were prepared from a 5ng RNA input using the PerkinElmer NEXTFLEX Small RNA-Seq Kit v4, incorporating Unique Dual Indexes (UDIs) and tRNA/YRNA blockers for plasma samples to enrich microRNA content.

value: Melanoma, ffpe

tag: disease state

value: Melanoma


title: Melanoma, ffpe (GB120)


title: Melanoma, ffpe (GB121)


title: Control_2_BMDC


title: Melanoma, ffpe (GB123)


title: Metastatic Melanoma, ffpe (GB122)

source_name: Metastatic Melanoma, ffpe

value: Metastatic Melanoma, ffpe

value: Metastatic Melanoma


title: Melanoma, ffpe (GB119)


title: WT3

city: Shanghai

first: Yumei

last: Yang

address: No.180 Fenglin Road

department: Department of Endocrinology and Metabolism

institute: Zhongshan Hospital, Fudan University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Then, HTSeq (v0.9.1) was used to obtain the original count of transcripts as mRNA expression profile.
EdgeR software (v3.16.5) was used to standardize and calculate the multiple change and p-value between the two groups of samples or two samples to screen the differentially expressed mRNAs.
And GO and Pathway analysis were performed on these differentially expressed genes.
Assembly: MM10
Supplementary files format and content: Gene Expression Profiling.xlsx. This excel file includes RPKM values for each sample.

source_name: Islet

extract_protocol:
Total RNAs (1 μg) were extracted from islets of β-PCKO mice and WT mice using TRIZOL reagent, followed by rRNAs removal using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) as according to the manufacturer’s instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads.

value: Islet

value: WT


title: KO2

value: KO


title: KO3


title: WT2


title: KO1


title: Metastatic Melanoma, ffpe (GB115)


title: WT1


title: Metastatic Melanoma, ffpe (GB112)


title: Melanoma, ffpe (GB113)


title: Metastatic Melanoma, ffpe (GB114)


title: ZBP1ko CLP_2

city: Pittsburgh

first: Jie

last: Fan

address: 200 Lothrop Street

department: Department of Surgery

institute: University of Pittsburgh School of Medicine

description: 10x Genomics

data_processing:
We utilized Cell Ranger software (version 5.0.0) from 10x Genomics to demarcate cell barcodes and assign sequence reads to the corresponding genomic and transcriptomic profiles.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

molecule: polyA RNA

source_name: lung

extract_protocol:
Twenty-four hours post-surgery, all mice were euthanized and lung tissues were swiftly excised. Under sterile conditions, tissues were washed twice with ice-cold PBS supplemented with 0.04% BSA. Using sterile surgical scissors, the clean tissues were carefully minced into approximately 0.5 mm3 fragments and then placed in freshly prepared digestion solution. The digestion was conducted at 37°C for 30 minutes, with intermittent stirring every 10 minutes. The resulting cell suspension was filtered twice through a BD 70 μm cell strainer, followed by centrifugation at 4°C at 400 g for 5 minutes. The pellet was resuspended in an appropriate volume of medium, mixed with an equal volume of red blood cell lysis buffer, and incubated at 4°C for 5 minutes. Afterward, the sample was centrifuged at 400 g for 5 minutes, and the supernatant was discarded. The pellet was washed once with medium and centrifuged again at 400 g for 5 minutes. After discarding the supernatant, the sample was resuspended in 100 μl of medium. The freshly prepared single-cell suspension was adjusted to a concentration of 30,000 cells per sample.
Library construction followed the manufacturer's instructions for the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Catalog No. 000388).

value: lung


title: ZBP1ko Sham_4

description: 10x Genomics

value: Sham


title: ZBP1ko CLP_1

description: 10x Genomics


title: ZBP1ko Sham_3

description: 10x Genomics


title: ZBP1ko CLP_3

description: 10x Genomics


title: Metastatic Melanoma, ffpe (GB107)


title: Melanoma, ffpe (GB118)


title: WT CLP24h_3

description: 10x Genomics


title: Melanoma, ffpe (GB111)


title: ZBP1ko Sham_1

description: 10x Genomics


title: Metastatic Melanoma, ffpe (GB108)


title: Melanoma, ffpe (GB109)


title: WT CLP24h_2

description: 10x Genomics


title: Metastatic Melanoma, ffpe (GB106)


title: WT CLP24h_4

description: 10x Genomics


title: Melanoma, ffpe (GB110)


title: Metastatic Melanoma, ffpe (GB116)


title: Metastatic Melanoma, ffpe (GB117)


title: WT CLP24h_1

description: 10x Genomics


title: WT Sham_3

description: 10x Genomics


title: Melanoma, ffpe (GB105)


title: Melanoma, ffpe (GB104)


title: Melanoma, ffpe (GB103)


title: WT Sham_1

description: 10x Genomics


title: Melanoma, ffpe (GB102)


title: WT Sham_2

description: 10x Genomics


title: Melanoma, ffpe (GB101)


title: neoAgSpCD8Tcell_Control VAX

city: Houston

first: Sunita

last: Keshari

state: Texas

address: 7455 Fannin St Rm Scr, The University Of Texas Md Anderson

department: Immunology

institute: UT MD Anderson Cancer Center

data_processing:
The Cell Ranger Single-Cell Software Suite available at https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome was used to perform sample demultiplexing, barcode processing and single-cell 5' counting. Cellranger mkfastq was used to demultiplex raw base call files from the NovaSeq6000 sequencer, into sample-specific fastq files. Files were demultiplexed with 81.9% to 97.1% perfect barcode match, and 90%+ q30 reads.
fastq files for each sample were processed with Cellranger count, which was used to align samples to mm10 genome, filter and quantify
Assembly: mm10
Supplementary files format and content: tab-delimited files with metadata (tsv), matrices of count values (mtx) for each sample

source_name: Tumor

extract_protocol:
Established tumors were excised from mice at day 15 (d. 15) post-transplant, minced and dissociated using 1 mg/ml type IA collagenase
Libraries were prepared using Chromium Next GEM Single-cell 5' Reagent Kits v2 according to manufacturer’s protocol (10x Genomics)

treatment_protocol: Y1.7 mLama4.mItgb1melanoma cells were subcutaneously transplanted into mice at 0.5 x 10^6 cells  in 150 µl into the flank on day 0. Mice were treated intraperitoneally with 200 µg of control mAb, anti-CTLA4, anti-PD1 or  monoclonal antibody, used alone or in combination on days 7, 10, and 13 post-tumor transplant and subcutanously with Control VAX (10 µg of mAlg8 SLP + 50 µg of Poly I:C) and NeoAg SLP VAX (10 µg of mLama4 SLP + 50 µg of Poly I:C) on days 7, and 13 post-tumor transplant .

value: Tumor

value: Y1.7 mLama4.mItgb1

value: Wildtype

value: Control VAX


title: Melanoma, ffpe (GB099)


title: neoAgSpCD8Tcells_Control mAb

value: Control monoclonal antibody


title: Melanoma, ffpe (GB097)


title: neoAgSpCD8Tcell_NeoAg SLP VAX

value: NeoAg SLP VAX


title: Immune Checkpoint Inhibitors (ICT) teatment (anti-CTLA4, anti-PD-1, anti-CTLA4 plus anti-PD-1), Multiplexed

description: Multiplexed (see feature_reference.csv for hashtag info). Additional paired-end files with hastag sequencing raw data "neoAgSpCD8Tcells_antiCTLA4_antiPD1_antiCTLA4plusantiPD1_FBC…" included


title: Metastatic Melanoma, ffpe (GB098)


title: ZBP1ko Sham_2

description: 10x Genomics


title: CD45_Control VAX


title: Naevi, ffpe (GB095)

source_name: Naevi, ffpe

value: Naevi, ffpe

value: Naevi


title: CD45_anti-PD1

value: anti-PD-1 antibody


title: CD45_Control mAb

value: Melanoma


title: CD45_anti-CTLA4 plus anti-PD1

value: anti-CTLA-4+anti-PD-1 antibody


title: Naevi, ffpe (GB096)


title: Melanoma In-Situ, ffpe (GB092)

source_name: Melanoma In-Situ, ffpe

value: Melanoma In-Situ, ffpe

value: Melanoma In-Situ


title: Melanoma In-Situ, ffpe (GB089)


title: Naevi, ffpe (GB088)


title: RBBP5_CT44

first: Bokai

state: PA

address: 100 Technology Dr, Bridgeside point

institute: University of Pittsburgh

library_source: genomic

data_processing:
The sequences identified were mapped to the mouse genome (UCSC mm10) using BOWTIE function in Galaxy Deeptool (https://usegalaxy.org/) (Ramirez et al, 2016). Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed. Peak calling was carried out by MACS2 (version 2.1.1.20160309) in Galaxy (options --mfold 5, 50 --pvalue 1e-4), on each ChIP-seq file against input. To account for the different sequencing depths between samples, the BAM files generated from MACS2 were RPKM normalized to sequencing depth using the bamCoverage function in Galaxy Deeptool and the bigwig files were generated accordingly. The relative intensity of each RBBP5 binding site is further calculated via the computeMatrix function with the RPKM normalized bigwig files and bed files from the peak calling as inputs by calculating the area under the curve.
Assembly: mm10
Supplementary files format and content: bigwig fles

extract_protocol:
ChIP for RBBP5 was performed using anti-RBBP5 antibody (Bethyl, A300-109A) as previously described (Pan et al., 2020). Briefly, mouse liver samples were submerged in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final concentration). The tissue pieces were then treated with a TissueTearer and finally spun down and washed twice in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. The chromatin was enzymatically digested with MNase. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, Proteinase K and heated for reverse-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. An aliquot of chromatin (30 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 μg of antibody. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinking was reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
The DNA libraries were prepared at the University of Pittsburgh and sequenced at Gene by Gene, Ltd per standard protocols. DNA libraries were prepared with Ovation®Ultralow V2 DNA-Seq library preparation kit (NuGen) using 1ng input DNA. The size selection for libraries was performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The prepared libraries pooled and sequenced using Nova-Seq 6000 (Illumina), generating ~30 million 75 bp single-end reads per sample.

value: Liver

value: Wild-type

tag: chip antibody

value: anti-RBBP5 antibody (Bethyl, A300-109A)


title: RBBP5_CT40


title: Melanoma In-Situ, ffpe (GB090)


title: CD45_anti-CTLA4

value: anti-CTLA-4 antibody


title: RBBP5_CT36


title: Naevi, ffpe (GB086)


title: RBBP5_CT32


title: RBBP5_CT28


title: Naevi, ffpe (GB087)


title: Melanoma In-Situ, ffpe (GB085)


title: Melanoma In-Situ, ffpe (GB084)


title: Naevi, ffpe (GB094)


title: Naevi, ffpe (GB082)


title: RBBP5_CT24


title: Melanoma In-Situ, ffpe (GB093)


title: Melanoma In-Situ, ffpe (GB081)


title: CD45_NeoAg SLP VAX

value: Tumor


title: RBBP5_CT16


title: RBBP5_CT12


title: RBBP5_CT8


title: RBBP5_CT4


title: RBBP5_CT0


title: Naevi, ffpe (GB078)


title: Naevi, ffpe (GB077)


title: Melanoma In-Situ, ffpe (GB080)


title: Melanoma In-Situ, ffpe (GB079)


title: Melanoma In-Situ, ffpe (GB075)


title: Melanoma In-Situ, ffpe (GB074)


title: WT CT42B

data_processing:
The prepared libraries were pooled and sequenced using NoveSeq 6000 (Illumina), generating an average of 40 million 2×100 bp paired end reads per sample. RNA-Seq library preparation and sequencing were performed at UPMC Genome Center. Raw RNA-seq FASTQ files were analyzed by FastQC for quality control. Adaptors and low-quality reads were filtered by Trimmomatic (Bolger et al, 2014). Then the processed reads were aligned by HISAT2 (Kim et al, 2015) against mouse reference mm10. Gene and isoform FKPM values were calculated by Cufflinks. Since the background gene expression level is FPKM=0.1 in mouse liver (Pan et al., 2020), only those genes with average gene expression across 48 hours in Rbbp5 Flox mice larger than 0.1 were included for rhythm-identification analysis. Averaged FPKM values at each time were used for cycling transcripts identification by the eigenvalue/pencil method.
Assembly: mm10
Supplementary files format and content: excel spreadsheet includes RPKM values for each sample

extract_protocol:
Mouse liver tissues were collected from Rbbp5 Flox (n=2) and Rbbp5 LKO (n=2) mice at 2h intervals for a total of 48 hours under constant darkness condition. Total RNA was isolated from mouse liver with miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions.
RNA was assessed for quality using an Agilent TapeStation 4150/Fragment Analyzer 5300 and RNA concentration was quantified on a Qubit FLEX fluorometer. Libraries were generated with the Illumina Stranded mRNA Library Prep kit (Illumina: 20040534) according to the manufacturer’s instructions. Briefly, 200 ng of input RNA was used for each sample. Following adapter ligation, 12 cycles of indexing PCR were completed, using IDT for Illumina RNA UD Indexes (Illumina: 20040553-6). Library quantification and assessment was done using a Qubit FLEX fluorometer and an Agilent TapeStation 4150/Fragment Analyzer 5300.

value: Rbbp5 (flox/flox); alb-cre(-/-)


title: WT CT46B


title: Melanoma In-Situ, ffpe (GB076)


title: WT CT44B


title: Melanoma In-Situ, ffpe (GB073)


title: RBBP5_CT20


title: Melanoma In-Situ, ffpe (GB083)


title: Melanoma In-Situ, ffpe (GB072)


title: Naevi, ffpe (GB071)


title: WT CT40A


title: Melanoma In-Situ, ffpe (GB069)


title: WT CT38B


title: Melanoma In-Situ, ffpe (GB070)


title: WT CT38A


title: Naevi, ffpe (GB068)


title: WT CT36B


title: Melanoma In-Situ, ffpe (GB067)


title: WT CT36A


title: WT CT44A


title: WT CT34A


title: WT CT32B


title: WT CT46A


title: Naevi, ffpe (GB066)


title: Melanoma In-Situ, ffpe (GB065)


title: Naevi, ffpe (GB064)


title: WT CT42A


title: WT CT32A


title: WT CT30A


title: WT CT40B


title: Naevi, plasma (GB062)

description:
plasma_normalised_rpm.csv
plasma_raw_counts.csv

source_name: plasma

value: plasma


title: Naevi, plasma (GB063)


title: WT CT28B


title: Melanoma In-Situ, plasma (GB060)


title: WT CT30B


title: Naevi, plasma (GB058)


title: Melanoma In-Situ, plasma (GB059)


title: WT CT28A


title: Naevi, plasma (GB057)


title: WT CT26B


title: WT CT26C


title: WT CT24C


title: Naevi, plasma (GB054)


title: WT CT34B


title: Naevi, plasma (GB053)


title: Melanoma In-Situ, plasma (GB056)


title: WT CT24B


title: Melanoma In-Situ, plasma (GB052)


title: WT CT22A


title: WT CT20A


title: Melanoma, plasma (GB050)


title: WT CT20B


title: Melanoma, plasma (GB049)


title: Naevi, plasma (GB051)


title: WT CT18C


title: Metastatic Melanoma, plasma (GB048)

value: Metastatic Melanoma


title: WT CT16B


title: Melanoma, plasma (GB047)


title: WT CT16A


title: Melanoma, plasma (GB046)


title: Melanoma, plasma (GB044)


title: WT CT14A


title: Melanoma, plasma (GB045)


title: WT CT12B


title: WT CT14B


title: Naevi, plasma (GB055)


title: WT CT22B


title: WT CT18B


title: Metastatic Melanoma, plasma (GB042)


title: WT CT10C


title: Melanoma, plasma (GB041)


title: Melanoma, plasma (GB040)


title: WT CT10B


title: Melanoma, plasma (GB039)


title: WT CT8B


title: WT CT8A


title: Melanoma, plasma (GB036)


title: WT CT6B


title: Melanoma, plasma (GB038)


title: Melanoma, plasma (GB037)


title: Melanoma, plasma (GB035)


title: WT CT12A


title: Melanoma, plasma (GB034)


title: WT CT4B


title: WT CT6A


title: WT CT4A


title: Metastatic Melanoma, plasma (GB043)


title: WT CT2B


title: Melanoma, plasma (GB033)


title: WT CT2A


title: WT CT0B


title: Melanoma, plasma (GB031)


title: Melanoma, plasma (GB032)


title: WT CT0A


title: Melanoma, plasma (GB029)


title: RBBP5 LKO CT46A

value: Rbbp5 (flox/flox); alb-cre(+/-)


title: Metastatic Melanoma, plasma (GB030)


title: Melanoma, plasma (GB026)


title: RBBP5 LKO CT44B


title: Melanoma, plasma (GB027)


title: RBBP5 LKO CT46B


title: RBBP5 LKO CT44A


title: Melanoma, plasma (GB025)


title: RBBP5 LKO CT42B


title: Melanoma, plasma (GB022)


title: Metastatic Melanoma, plasma (GB024)


title: RBBP5 LKO CT40A


title: Metastatic Melanoma, plasma (GB021)


title: RBBP5 LKO CT42A


title: Metastatic Melanoma, plasma (GB023)


title: RBBP5 LKO CT40B


title: RBBP5 LKO CT38A


title: RBBP5 LKO CT38B


title: Melanoma, plasma (GB019)


title: Melanoma, plasma (GB018)


title: Melanoma, plasma (GB017)


title: Melanoma, plasma (GB020)


title: RBBP5 LKO CT36A


title: RBBP5 LKO CT34B


title: RBBP5 LKO CT36B


title: RBBP5 LKO CT34A


title: Melanoma, plasma (GB028)


title: Melanoma, plasma (GB015)


title: RBBP5 LKO CT32B


title: RBBP5 LKO CT32A


title: RBBP5 LKO CT30B


title: Melanoma, plasma (GB013)


title: RBBP5 LKO CT30A


title: Melanoma, plasma (GB012)


title: RBBP5 LKO CT28B


title: Metastatic Melanoma, plasma (GB010)


title: Melanoma, plasma (GB009)


title: RBBP5 LKO CT26B


title: RBBP5 LKO CT26A


title: Metastatic Melanoma, plasma (GB008)


title: RBBP5 LKO CT28A


title: RBBP5 LKO CT24B


title: Melanoma, plasma (GB016)


title: RBBP5 LKO CT24A


title: Melanoma, plasma (GB002)


title: RBBP5 LKO CT22A


title: RBBP5 LKO CT22B


title: Metastatic Melanoma, plasma (GB003)


title: Melanoma, plasma (GB014)


title: RBBP5 LKO CT20B


title: RBBP5 LKO CT20A


title: Melanoma, plasma (GB001)


title: P28_KO_3

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
The alignment and quantification pipeline used human reference genome GRCh38.p7 and Ensembl v102 for annotation.
Transcript-level counts were performed by kallisto v0.45.0 package and summarized to gene level using tximport v1.30.0.
Gene level counts were converted to count per million (CPM) and then TMM normalized using the edgeR v.4.0.3 package in R.
Assembly: hg38
Supplementary files format and content: Abundance measurements are summarised gene and transcript data from all samples.

source_name: Retina

extract_protocol:
RNA from Pilrb1/2+/+ and Pilrb1/2 -/- mice retinas were isolated using RNeasy Mini Kit (Qiagen, Valencia, CA), with on-column DNA digestion, following the manufacturer's instructions.
RNA-seq data was generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA), as previously described, and 125 base pair-end reads were generated on NextSeq 2000 platform (Illumina, San Diego, CA).

value: Retina


title: Metastatic Melanoma, plasma (GB011)


title: RBBP5 LKO CT16B


title: RBBP5 LKO CT18A


title: RBBP5 LKO CT18B


title: RBBP5 LKO CT16A


title: P28_WT_3


title: P28_KO_2


title: P28_KO_1


title: Melanoma, plasma (GB006)


title: Metastatic Melanoma, plasma (GB005)


title: P28_WT_2


title: Metastatic Melanoma, plasma (GB004)


title: RBBP5 LKO CT12B


title: RBBP5 LKO CT12A


title: M12_KO_3


title: P28_WT_1


title: M12_KO_2


title: M12_KO_1


title: M12_WT_3


title: RBBP5 LKO CT10A


title: RBBP5 LKO CT10B


title: M12_WT_2


title: M12_WT_1


title: RBBP5 LKO CT8A


title: RBBP5 LKO CT6B


title: Blood sample from dengue with warning sign patient 10

city: Shah Alam

first: Jeyanthi

last: Suppiah

address: Jalan Setia Murni U13/52, Setia Alam

department: Virology Unit

country: Malaysia

institute: Institute for Medical Research, National Institutes of Health Malaysia

data_processing:
To compare gene expression profile between 3 groups, healthy control, severe dengue and dengue with warning sign
Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) [3]. The heatmap was drawn by pheatmap (v1.0.8) [4] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001). Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: excel files which included TPM, FPKM and read counts for each sample.

source_name: blood/pbmc

extract_protocol:
Total RNA was extracted using the innuPREP RNA mini kit 2.0 (Analytical Jenna)
Enrichment of mRNA was performed using Dynabeads mrRNA Purification Kit (Invitrogen) and library preparation was carried out using MGIEasy RNA Library Prep Set (MGI)
2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: blood/pbmc

value: dengue virus


title: RBBP5 LKO CT8B


title: Blood sample from dengue with warning sign patient 9


title: RBBP5 LKO CT4B


title: JK3_12h_3

city: Qinhuangxdao

first: Yucui

last: Han

address: No. 360, West Section, Hebei Street

institute: Hebei Normal University Of Science and Technology

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads  were generated. About xxxxx raw reads  for each sample were generated. Raw reads of fastq format  were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.  Then about xxxxxx clean reads  for each sample were retained for subsequent analyses. The clean  reads were mapped to the reference genome  using HISAT2. FPKM of each gene was calculated and  the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R  (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and  foldchange > 2 or foldchange < 0.5  was set as the threshold for significantly differential expression  gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the  expression pattern of genes in different groups and samples. The radar map of top 30 genes was  drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways  enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0),  respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble  diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential  expression in the two types of samples. Then it is tested whether the predefined gene set was  enriched at the top or bottom of the ranking list.
Assembly: mm10
Supplementary files format and content: Setaria italica v2.2
Supplementary files format and content: tab-delimited text file include FPKM values

organism: Setaria italica

source_name: leaf

growth_protocol: mRNAsequencing experimental method

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.RNA purity and quantification were evaluated using the NanoDrop 2000  spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100  Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using  VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The  transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: RNAIsolation and Library Preparatio and RNASequencing and Differentially Expressed Genes Analysis

value: leaf


title: JK3_24h_2


title: JK3_24h_3


title: RBBP5 LKO CT14A


title: Blood sample from severe dengue patient 3


title: RBBP5 LKO CT14B


title: Blood sample from dengue with warning sign patient 8


title: JK3_12h_1


title: JK3_12h_2


title: Blood sample from severe dengue patient 2


title: JK3_0h_3


title: RBBP5 LKO CT4A


title: Blood sample from dengue with warning sign patient 7


title: RBBP5 LKO CT2B


title: RBBP5 LKO CT2A


title: JK3_0h_2


title: RBBP5 LKO CT6A


title: RBBP5 LKO CT0B


title: JK3_24h_1


title: B175_24h_1


title: B175_24h_3


title: B175_12h_2


title: B175_24h_2


title: B175_12h_3


title: Blood sample from dengue with warning sign patient 5


title: RBBP5 LKO CT0A


title: B175_12h_1


title: Blood sample from dengue with warning sign patient 4


title: Blood sample from dengue with warning sign patient 3


title: B175_0h_1


title: B175_0h_3


title: JK3_0h_1


title: Blood sample from dengue with warning sign patient 13


title: MCF-7 palbociclib + fulvestrant: palbociclib + fulvestrant + INX-315 biol rep 2

city: New York

first: Jessica

middle: Sarah

last: Armand

state: NY

department: Pathology and Cell Biology

institute: Columbia University Irving Medical Center

data_processing:
Sequence reads were trimmed to remove adaptors and low-quality reads with an average Phred quality score below 30
Trimmed sequence reads were mapped to the transcriptome reference GRCh38_tran using HISAT2 (default parameters: maximum mismatch cost = 6, minimum mismatch cost = 2, gap penalty = 5 + N * 3).
Reference annotation GTF file GRCh38 was used to generate the read count matrix. All references were obtained from Ensembl.org.
Assembly: hg38
Supplementary files format and content: Text file with raw counts for each sample

source_name: Breast, mammary gland

growth_protocol: MCF-7 cells were cultured in DMEM plus 10% FBS and housed in a humidified incubator at 37C and 5% CO2.

extract_protocol:
RNA isolation was performed using the GeneJET RNA Purification Kit (Thermo Scientific, #K0732) according to manufacturer’s instruction.
Isolated RNA was shipped to Azenta for library preparation and sequencing; please contact Azenta life sciences for further information

treatment_protocol: Cells were cultured to dual palbociclib (Selleck) + fulvestrant (Selleck) resistance for 2 months. Cells were then either discontinued, maintained in palbociclib + fulvestrant, switched to INX-315 (MedChemExpress) +fulvestrant, or switched to palbociclib + INX-315 + fulvestrant for 20 days.

value: Breast, mammary gland

value: epithelial cell

value: WT

value: Palbociclib + INX-315 + fulvestrant