title: Psoriasis_PP_944


title: Psoriasis_PP_941

status: Public on Jun 25 2024

type: SRA

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic single cell

data_processing:
The Seurat R software package (version 3.0) in R (version 3.6.2) was utilized for analysis of scRNA seq-data. Cells with nCount_RNA > 50000, nFeature > 1500, and External RNA Control Consortium (ERCC) RNA Spike-In < 15% were included in the analysis. Normalized datasets were integrated, scaled, followed by principal component analysis. Two-dimensional map coordinates were generated using the ‘RunUMAP’ procedure. Cluster analysis was performed using the ‘FindNeighbors’ and ‘FindClusters’ functions. Marker genes for clusters were identified using the ‘FindMarkers’ function. The Wilcoxon rank-sum test was used to identify differentially expressed genes (DEGs) among clusters to define cell states and was then repeated for each resultant cell type to further characterize subpopulations. The online tool EnrichR was used to perform Gene Ontology (GO) Biological Processes (BP) analysis on the significantly DEGs extracted from different pairs of comparision21. CIM-seq analysis22, an unsupervised method to analyze direct physical cell–cell interactions, was performed on RNAseq data from identified doublets/multiplets with FSC-W values exceeding 300.
Assembly: hg38
Supplementary files format and content: count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
Four-mm full-depth punch biopsies were obtained from lesional and non-lesional skin of five untreated psoriasis patients and three sex- and age-matched healthy donors. Skin biopsies were enzymatically digested with dispase (5 U/ML, Gibco) overnight to separate the epidermis from the dermis, followed by dissociation of the epidermis to single cells using a protocol optimized to achieve partial dissociation (0.5 % trypsin, 1 U ul−1 DNase, Gibco) for 7 min at 37 °C to obtain both single cells and multiplets. In the single-cell suspensions, cells were counted and diluted to 1 × 106 cells per 100 ul with ice-cold FACS buffer, followed by incubation with dye-conjugated antibodies, including anti-CD45 (APC, eBioscience). After sorting into 384-well plates with hypotonic lysis buffer using a SONY SH800S sorter, both CD45-positive and CD45-negative cells were sorted, excluding dead/dying cells, and stored at -80 °C.
cDNA synthesis was based on the Smart-seq2 protocol as implemented in (Andrews et al. Nat. Meth. 2021). In summary, single-cell lysates were thawed on ice in 384-well plates, followed by primer annealing at 72°C for 3 minutes. Subsequently, a reverse transcription (RT) mix of 3 ul was added (0.05 ul of Maxima H Minus Reverse Transcriptase [Thermo Scientific, EP0751], 0.125 ul of Recombinant RNase Inhibitor [Takara Bio, 2313B], 1 ul of 5x First strand buffer, 0.25 ul of 100mM DTT [Thermo Fisher 707265ML], 1 ul of 5M Betaine [Sigma-Aldrich, B0300-5VL], 0.03 ul of 1M MgCl2, 0.05 ul of 100uM TSO [IDT 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′], and 0.495 ul of H2O). The RT reaction was 42°C for 90 minutes, followed by 70°C for 5 minutes and a 4°C hold. Next, 7.5 ul of cDNA pre-amplification mix was added, consisting of 1.068 ul of H2O, 6.25 ul of 2X Kapa HiFi HotStart ReadyMix (Roche 07958927001), 0.125 ul of 10 uM IS_PCR primer (IDT 5′-AAGCAGTGGTATCAACGCAGAGT-3′), and 0.056 ul of Lambda Exonuclease (ThermoFisher EN0561). The PCR program was 37°C for 30 minutes, 95°C for 3 minutes, followed by [98°C for 20 seconds, 67°C for 15 seconds, 72°C for 4 minutes] repeated for 21 cycles, and a final step of 72°C for 5 minutes, with a 4°C hold. Post-PCR, cDNA clean-up was performed using 0.7X volume SPRI beads and a magnetic 384-well rack. For tagmentation, 1 ul of diluted cDNA (150 pg/ul) was mixed with 1.5 ul of tagmentation buffer (0.5 ul TAP-PEG buffer [50mM TAPS, 25mM MgCl2, 40% PEG 8k) with 0.75 ul H2O)] and 0.25 ul of Tn5 (Vasilios 2020), followed by incubation at 55°C for 10 minutes. Upon completion, Tn5 was inactivated by adding 1 ul of 0.1% SDS (Teknova S0287). Barcoding PCR was performed on the same plate by adding 19.5 ul of PCR mix (Roche7958846001, 13.25 ul of H2O, 5 ul of 5X buffer, 0.75 ul of dNTPs, and 0.5 ul of KAPA HiFi DNA Polymerase) and 2 ul of primers. The total volume of 25 ul underwent the following PCR cycling: 72°C for 3 minutes, 95°C for 30 seconds, [95°C for 15 seconds, 55°C for 30 seconds, 72°C for 45 seconds] repeated for 12 cycles, and a 10°C hold. Finally, 2 ul per well was pooled and subjected to SPRI bead clean-up at 0.9X volume twice. The finished libraries were sequenced on an Illumina NextSeq 550 sequence paired-end 37bp with 8bp dual index.

tag: tissue

value: Skin

tag: ncount rna

tag: nfeature rna

tag: donor

tag: diagnosis

value: Psoriasis

tag: region

value: PP

tag: class

value: singlet

tag: seurat clusters

tag: celltype

value: LC


title: Psoriasis_PP_945

value: Treg


title: Psoriasis_PP_942

value: pDC


title: Psoriasis_PP_940

value: doublet


title: Psoriasis_PP_938


title: Psoriasis_PP_939

value: Tc (cytokine-)


title: Psoriasis_PP_937


title: Psoriasis_PP_936

value: ILC/NK


title: Psoriasis_PP_935


title: Psoriasis_PP_934


title: Psoriasis_PP_931

value: Activated mitotic keratinocytes


title: Psoriasis_PP_932

value: Activated suprabasal keratinocytes


title: Psoriasis_PP_933


title: Psoriasis_PP_930

value: Activated basal keratinocytes


title: Psoriasis_PP_929


title: Psoriasis_PP_928


title: Psoriasis_PP_926

value: mDC


title: Psoriasis_PP_948


title: Psoriasis_PP_927

value: Mac/MoDC


title: Psoriasis_PP_924


title: Psoriasis_PP_923


title: Psoriasis_PP_922


title: Psoriasis_PP_920


title: Psoriasis_PP_925


title: Psoriasis_PP_917


title: Psoriasis_PP_921


title: Psoriasis_PP_918


title: Psoriasis_PP_910


title: Psoriasis_PP_911


title: Psoriasis_PP_913


title: Psoriasis_PP_915


title: Psoriasis_PP_916

value: ILC


title: Psoriasis_PP_909


title: Psoriasis_PP_912


title: Psoriasis_PP_908


title: Psoriasis_PP_907


title: Psoriasis_PP_906


title: Psoriasis_PP_905


title: Psoriasis_PP_903


title: Psoriasis_PP_904


title: Psoriasis_PP_895


title: Psoriasis_PP_891


title: Psoriasis_PP_898


title: Psoriasis_PP_902


title: Psoriasis_PP_958


title: Psoriasis_PP_897


title: Psoriasis_PP_919


title: Psoriasis_PP_890


title: Psoriasis_PP_887


title: Psoriasis_PP_885


title: Psoriasis_PP_894


title: Psoriasis_PP_893


title: Psoriasis_PP_914


title: Psoriasis_PP_896


title: Psoriasis_PP_881


title: Psoriasis_PP_892


title: Psoriasis_PP_883


title: Psoriasis_PP_884


title: Psoriasis_PP_900


title: Psoriasis_PP_889


title: Psoriasis_PP_888


title: Psoriasis_PP_886

value: Tc (cytokine+)


title: Psoriasis_PP_878

value: Skin


title: Psoriasis_PP_880

value: Psoriasis


title: Psoriasis_PP_901

value: PP


title: Psoriasis_PP_877

value: singlet


title: Psoriasis_PP_899


title: Psoriasis_PP_870


title: Psoriasis_PP_868


title: Psoriasis_PP_875


title: Psoriasis_PP_876


title: Psoriasis_PP_867


title: Psoriasis_PP_869


title: Psoriasis_PP_882

value: Proliferative CD8


title: Psoriasis_PP_862

value: Treg


title: Psoriasis_PP_865


title: Psoriasis_PP_866


title: Psoriasis_PP_858


title: Psoriasis_PP_859


title: Psoriasis_PP_873


title: Psoriasis_PP_879


title: Psoriasis_PP_872


title: Psoriasis_PP_856


title: Psoriasis_PP_857


title: Psoriasis_PP_854


title: Psoriasis_PP_855


title: Psoriasis_PP_863


title: Psoriasis_PP_861


title: Psoriasis_PP_860


title: Psoriasis_PP_851


title: Psoriasis_PP_874


title: Psoriasis_PP_852


title: Psoriasis_PP_850


title: Psoriasis_PP_871


title: Psoriasis_PP_853


title: Psoriasis_PP_849


title: Psoriasis_PP_847


title: Psoriasis_PP_864


title: Psoriasis_PP_848


title: Psoriasis_PP_845


title: Psoriasis_PP_846


title: Psoriasis_PP_843

value: pDC


title: Psoriasis_PP_844


title: Psoriasis_PP_842


title: Psoriasis_PP_841


title: Psoriasis_PP_839


title: Psoriasis_PP_840


title: Psoriasis_PP_836


title: Psoriasis_PP_837


title: Psoriasis_PP_832

value: doublet


title: Psoriasis_PP_834


title: Psoriasis_PP_833

value: Tc (cytokine-)


title: Psoriasis_PP_835


title: Psoriasis_PP_829


title: Psoriasis_PP_830


title: Psoriasis_PP_831


title: Psoriasis_PP_828


title: Psoriasis_PP_825


title: Psoriasis_PP_827


title: Psoriasis_PP_824


title: Psoriasis_PP_822


title: Psoriasis_PP_826


title: Psoriasis_PP_821


title: Psoriasis_PP_823


title: Psoriasis_PP_820

value: ILC/NK


title: Psoriasis_PP_818


title: Psoriasis_PP_819


title: Psoriasis_PP_816


title: Psoriasis_PP_813


title: Psoriasis_PP_812


title: Psoriasis_PP_838


title: Psoriasis_PP_814


title: Psoriasis_PP_808


title: Psoriasis_PP_810


title: Psoriasis_PP_805


title: Psoriasis_PP_806


title: Psoriasis_PP_802


title: Psoriasis_PP_807


title: Psoriasis_PP_804


title: Psoriasis_PP_800


title: Psoriasis_PP_809


title: Psoriasis_PP_798


title: Psoriasis_PP_797


title: Psoriasis_PP_794


title: Psoriasis_PP_793


title: Psoriasis_PP_799


title: Psoriasis_PP_817


title: Psoriasis_PP_792


title: Psoriasis_PP_815


title: Psoriasis_PP_791


title: Psoriasis_PP_795


title: Psoriasis_PP_788


title: Psoriasis_PP_811


title: Psoriasis_PP_787


title: Psoriasis_PP_786


title: Psoriasis_PP_785


title: Psoriasis_PP_790


title: Psoriasis_PP_784


title: Psoriasis_PP_783


title: Psoriasis_PP_803


title: Psoriasis_PP_782


title: Psoriasis_PP_801


title: Psoriasis_PP_778


title: Psoriasis_PP_779


title: Psoriasis_PP_780


title: Psoriasis_PP_777


title: Psoriasis_PP_796


title: Psoriasis_PP_776

value: Melanocytes


title: Psoriasis_PP_774


title: Psoriasis_PP_771


title: Psoriasis_PP_770


title: Psoriasis_PP_789


title: Psoriasis_PP_773


title: Psoriasis_PP_767


title: Psoriasis_PP_769


title: Psoriasis_PP_766


title: Psoriasis_PP_764


title: Psoriasis_PP_763


title: Psoriasis_PP_765


title: Psoriasis_PP_759


title: Psoriasis_PP_760


title: Psoriasis_PP_761


title: Psoriasis_PP_758


title: Psoriasis_PP_762


title: Psoriasis_PP_757


title: Psoriasis_PP_755


title: Psoriasis_PP_781


title: Psoriasis_PP_756


title: Psoriasis_PP_768


title: Psoriasis_PP_775


title: Psoriasis_PP_752


title: Psoriasis_PP_754


title: Psoriasis_PP_751


title: Psoriasis_PP_750


title: Psoriasis_PP_748


title: Psoriasis_PP_772


title: Psoriasis_PP_749


title: Psoriasis_PP_747

value: Channel keratinocytes


title: Psoriasis_PP_743


title: Psoriasis_PP_742


title: Psoriasis_PP_744


title: Psoriasis_PP_741


title: Psoriasis_PP_740


title: Psoriasis_PP_739


title: Psoriasis_PP_738


title: Psoriasis_PP_737


title: Psoriasis_PP_736


title: Psoriasis_PP_734


title: Psoriasis_PP_733


title: Psoriasis_PP_735


title: Psoriasis_PP_732


title: Psoriasis_PP_730


title: Psoriasis_PP_731


title: Psoriasis_PP_753


title: Psoriasis_PP_728


title: Psoriasis_PP_729


title: Psoriasis_PP_727


title: Psoriasis_PP_726


title: Psoriasis_PP_723


title: Psoriasis_PP_724


title: Psoriasis_PP_725


title: Psoriasis_PP_720


title: Psoriasis_PP_721


title: Psoriasis_PP_746


title: Psoriasis_PP_719


title: Psoriasis_PP_722


title: Psoriasis_PP_745


title: Psoriasis_PP_718


title: Psoriasis_PP_717


title: Psoriasis_PP_712


title: Psoriasis_PP_711


title: Psoriasis_PP_716


title: Psoriasis_PP_714


title: Psoriasis_PP_715


title: Psoriasis_PP_710


title: Psoriasis_PP_713


title: Psoriasis_PP_709


title: Psoriasis_PP_707


title: Psoriasis_PP_706


title: Psoriasis_PP_708


title: Psoriasis_PP_703


title: Psoriasis_PP_702


title: Psoriasis_PP_704


title: Psoriasis_PP_701


title: Psoriasis_PP_699


title: Psoriasis_PP_698


title: Psoriasis_PP_700


title: Psoriasis_PP_697


title: Psoriasis_PP_695


title: Psoriasis_PP_696


title: Psoriasis_PP_692


title: Psoriasis_PP_690


title: Psoriasis_PP_691


title: Psoriasis_PP_694

value: Progenitor keratinocytes


title: Psoriasis_PP_689


title: Psoriasis_PP_688


title: Psoriasis_PP_705


title: Psoriasis_PP_686


title: Psoriasis_PP_682


title: Psoriasis_PP_679


title: Psoriasis_PP_680


title: Psoriasis_PP_678


title: Psoriasis_PP_681


title: Psoriasis_PP_684


title: Psoriasis_PP_676


title: Psoriasis_PP_683


title: Psoriasis_PP_685


title: Psoriasis_PP_672


title: Psoriasis_PP_677


title: Psoriasis_PP_670


title: Psoriasis_PP_674


title: Psoriasis_PP_671


title: Psoriasis_PP_675


title: Psoriasis_PP_667


title: Psoriasis_PP_693

value: Activated suprabasal keratinocytes


title: Psoriasis_PP_668


title: Psoriasis_PP_669


title: Psoriasis_PP_687

value: LC


title: Psoriasis_PP_665

value: Mac/MoDC


title: Psoriasis_PP_664

value: ILC


title: Psoriasis_PP_666

value: Skin


title: Psoriasis_PP_663

value: Psoriasis


title: Psoriasis_PP_661

value: PP


title: Psoriasis_PP_662

value: singlet


title: Psoriasis_PP_660


title: Psoriasis_PP_659


title: Psoriasis_PP_673


title: Psoriasis_PP_652


title: Psoriasis_PP_657


title: Psoriasis_PP_655


title: Psoriasis_PP_651

value: Tc (cytokine+)


title: Psoriasis_PP_650


title: Psoriasis_PP_654

value: Treg


title: Psoriasis_PP_653


title: Psoriasis_PP_649


title: Psoriasis_PP_656


title: Psoriasis_PP_645


title: Psoriasis_PP_646


title: Psoriasis_PP_647

value: Proliferative CD8


title: Psoriasis_PP_642


title: Psoriasis_PP_648


title: Psoriasis_PP_641

value: doublet


title: Psoriasis_PP_640


title: Psoriasis_PP_638


title: Psoriasis_PP_643


title: Psoriasis_PP_637


title: Psoriasis_PP_635


title: Psoriasis_PP_634


title: Psoriasis_PP_639


title: Psoriasis_PP_632


title: Psoriasis_PP_631

value: Tc (cytokine-)


title: Psoriasis_PP_658


title: Psoriasis_PP_633


title: Psoriasis_PP_630


title: Psoriasis_PP_629


title: Psoriasis_PP_644


title: Psoriasis_PP_627


title: Psoriasis_PP_628


title: Psoriasis_PP_625


title: Psoriasis_PP_623


title: Psoriasis_PP_621


title: Psoriasis_PP_620


title: Psoriasis_PP_622


title: Psoriasis_PP_619


title: Psoriasis_PP_613


title: Psoriasis_PP_624


title: Psoriasis_PP_636


title: Psoriasis_PP_617


title: Psoriasis_PP_618


title: Psoriasis_PP_612


title: Psoriasis_PP_616


title: Psoriasis_PP_615


title: Psoriasis_PP_610


title: Psoriasis_PP_614


title: Psoriasis_PP_609


title: Psoriasis_PP_608


title: Psoriasis_PP_607


title: Psoriasis_PP_606


title: Psoriasis_PP_605


title: Psoriasis_PP_604


title: Psoriasis_PP_603


title: Psoriasis_PP_602


title: Psoriasis_PP_626


title: Psoriasis_PP_600


title: Psoriasis_PP_601


title: Psoriasis_PP_599


title: Psoriasis_PP_598


title: Psoriasis_PP_597


title: Psoriasis_PP_611


title: Psoriasis_PP_593


title: Psoriasis_PP_592


title: Psoriasis_PP_595


title: Psoriasis_PP_594


title: Psoriasis_PP_587


title: Psoriasis_PP_584


title: Psoriasis_PP_589

value: Activated mitotic keratinocytes


title: Psoriasis_PP_590


title: Psoriasis_PP_581


title: Psoriasis_PP_582


title: Psoriasis_PP_580

value: Melanocytes


title: Psoriasis_PP_588

value: Channel keratinocytes


title: Psoriasis_PP_586


title: Psoriasis_PP_579


title: Psoriasis_PP_578


title: Psoriasis_PP_577


title: Psoriasis_PP_583


title: Psoriasis_PP_576

value: Progenitor keratinocytes


title: Psoriasis_PP_575


title: Psoriasis_PP_574


title: Psoriasis_PP_573


title: Psoriasis_PP_596


title: Psoriasis_PP_570


title: Psoriasis_PP_572


title: Psoriasis_PP_591


title: Psoriasis_PP_585


title: Psoriasis_PP_566


title: Psoriasis_PP_567


title: Psoriasis_PP_571


title: Psoriasis_PP_563


title: Psoriasis_PP_558


title: Psoriasis_PP_559


title: Psoriasis_PP_564


title: Psoriasis_PP_565


title: Psoriasis_PP_553


title: Psoriasis_PP_554


title: Psoriasis_PP_561


title: Psoriasis_PP_562


title: Psoriasis_PP_560


title: Psoriasis_PP_569


title: Psoriasis_PP_556


title: Psoriasis_PP_552

value: ILC/NK


title: Psoriasis_PP_555


title: Psoriasis_PP_557


title: Psoriasis_PP_550


title: Psoriasis_PP_549


title: Psoriasis_PP_548


title: Psoriasis_PP_568

value: mDC


title: Psoriasis_PP_546


title: Psoriasis_PP_547


title: Psoriasis_PP_544


title: Psoriasis_PP_545


title: Psoriasis_PP_543


title: Psoriasis_PP_542


title: Psoriasis_PP_539


title: Psoriasis_PP_541


title: Psoriasis_PP_538


title: Psoriasis_PP_536

value: Mac/MoDC


title: Psoriasis_PP_551


title: Psoriasis_PP_535

value: ILC


title: Psoriasis_PN_533

value: Skin

value: PN


title: Psoriasis_PN_531

value: Psoriasis


title: Psoriasis_PN_528

value: singlet


title: Psoriasis_PN_532


title: Psoriasis_PN_534


title: Psoriasis_PN_527


title: Psoriasis_PN_530


title: Psoriasis_PN_525


title: Psoriasis_PN_526


title: Psoriasis_PN_529


title: Psoriasis_PN_522


title: Psoriasis_PN_524


title: Psoriasis_PN_523


title: Psoriasis_PN_521


title: Psoriasis_PN_517


title: Psoriasis_PN_518


title: Psoriasis_PN_520


title: Psoriasis_PN_519


title: Psoriasis_PN_515


title: Psoriasis_PN_516


title: Psoriasis_PP_540

value: PP


title: Psoriasis_PN_514


title: Psoriasis_PP_537


title: Psoriasis_PN_513


title: Psoriasis_PN_511


title: Psoriasis_PN_512


title: Psoriasis_PN_510


title: Psoriasis_PN_508


title: Psoriasis_PN_509


title: Psoriasis_PN_505


title: Psoriasis_PN_504


title: Psoriasis_PN_507


title: Psoriasis_PN_502


title: Psoriasis_PN_500


title: Psoriasis_PN_506

value: Activated Transition keratinocytes


title: Psoriasis_PN_498


title: Psoriasis_PN_503


title: Psoriasis_PN_501


title: Psoriasis_PN_497


title: Psoriasis_PN_494


title: Psoriasis_PN_499


title: Psoriasis_PN_496


title: Psoriasis_PN_493


title: Psoriasis_PN_490


title: Psoriasis_PN_492


title: Psoriasis_PN_491


title: Psoriasis_PN_489


title: Psoriasis_PN_488


title: Psoriasis_PN_486


title: Psoriasis_PN_487


title: Psoriasis_PN_483


title: Psoriasis_PN_484


title: Psoriasis_PN_485


title: Psoriasis_PN_482


title: Psoriasis_PN_481


title: Psoriasis_PN_480


title: Psoriasis_PN_477


title: Psoriasis_PN_479


title: Psoriasis_PN_476


title: Psoriasis_PN_495


title: Psoriasis_PN_470


title: Psoriasis_PN_468


title: Psoriasis_PN_472


title: Psoriasis_PN_467

value: Treg


title: Psoriasis_PN_465


title: Psoriasis_PN_466


title: Psoriasis_PN_463


title: Psoriasis_PN_460

value: doublet


title: Psoriasis_PN_462


title: Psoriasis_PN_464


title: Psoriasis_PN_461


title: Psoriasis_PN_459


title: Psoriasis_PN_458


title: Psoriasis_PN_455

value: Tc (cytokine-)


title: Psoriasis_PN_456


title: Psoriasis_PN_453


title: Psoriasis_PN_454


title: Psoriasis_PN_451


title: Psoriasis_PN_475


title: Psoriasis_PN_452


title: Psoriasis_PN_478


title: Psoriasis_PN_474


title: Psoriasis_PN_450


title: Psoriasis_PN_469


title: Psoriasis_PN_471


title: Psoriasis_PN_473


title: Psoriasis_PN_448


title: Psoriasis_PN_447


title: Psoriasis_PN_449


title: Psoriasis_PN_444


title: Psoriasis_PN_442

value: LC


title: Psoriasis_PN_443

value: Suprabasal keratinocytes II


title: Psoriasis_PN_457


title: Psoriasis_PN_440


title: Psoriasis_PN_437

value: Transition keratinocytes


title: Psoriasis_PN_436

value: Basal keratinocytes III


title: Psoriasis_PN_438

value: Suprabasal keratinocytes I


title: Psoriasis_PN_434


title: Psoriasis_PN_439


title: Psoriasis_PN_435

value: Activated basal keratinocytes


title: Psoriasis_PN_432


title: Psoriasis_PN_433


title: Psoriasis_PN_431


title: Psoriasis_PN_430


title: Psoriasis_PN_427

value: Progenitor keratinocytes


title: Psoriasis_PN_428


title: Psoriasis_PN_429

value: Melanocytes


title: Psoriasis_PN_446

value: Skin


title: Psoriasis_PN_426

value: PN


title: Psoriasis_PN_421

value: Psoriasis

value: Activated mitotic keratinocytes


title: Psoriasis_PN_425

value: singlet


title: Psoriasis_PN_423


title: Psoriasis_PN_424


title: Psoriasis_PN_420


title: Psoriasis_PN_418


title: Psoriasis_PN_422


title: Psoriasis_PN_419


title: Psoriasis_PN_445


title: Psoriasis_PN_441


title: Psoriasis_PN_415

value: Basal keratinocytes I


title: Psoriasis_PN_411


title: Psoriasis_PN_414


title: Psoriasis_PN_410


title: Psoriasis_PN_409


title: Psoriasis_PN_412


title: Psoriasis_PN_404

value: Mac/MoDC


title: Psoriasis_PN_408


title: Psoriasis_PN_407


title: Psoriasis_PN_406

value: doublet


title: Psoriasis_PN_403

value: Activated Transition keratinocytes


title: Psoriasis_PN_402


title: Psoriasis_PN_405


title: Psoriasis_PN_401


title: Psoriasis_PN_400


title: Psoriasis_PN_397


title: Psoriasis_PN_417


title: Psoriasis_PN_395


title: Psoriasis_PN_399


title: Psoriasis_PN_398


title: Psoriasis_PN_394


title: Psoriasis_PN_396


title: Psoriasis_PN_389


title: Psoriasis_PN_416

value: LC


title: Psoriasis_PN_388


title: Psoriasis_PN_413

value: T lymphocytes


title: Psoriasis_PN_393

value: Activated suprabasal keratinocytes


title: Psoriasis_PN_392


title: Psoriasis_PN_391


title: Psoriasis_PN_390


title: Psoriasis_PN_385

value: Suprabasal keratinocytes II


title: Psoriasis_PN_386

value: Basal keratinocytes III


title: Psoriasis_PN_383


title: Psoriasis_PN_387


title: Psoriasis_PN_382

value: Suprabasal keratinocytes I


title: Psoriasis_PN_381


title: Psoriasis_PN_379


title: Psoriasis_PN_378


title: Psoriasis_PN_377


title: Psoriasis_PN_380


title: Psoriasis_PN_376


title: Psoriasis_PN_373


title: Psoriasis_PN_374

value: Basal keratinocytes II


title: Psoriasis_PN_375


title: Psoriasis_PN_372


title: Psoriasis_PN_371

value: Activated basal keratinocytes


title: Psoriasis_PN_370

value: Skin


title: Psoriasis_PN_369

value: PN


title: Psoriasis_PN_366

value: Psoriasis

value: Transition keratinocytes


title: Psoriasis_PN_368

value: singlet

value: Melanocytes


title: Psoriasis_PN_362


title: Psoriasis_PN_365


title: Psoriasis_PN_384


title: Psoriasis_PN_364


title: Psoriasis_PN_363


title: Psoriasis_PN_359


title: Psoriasis_PN_360


title: Psoriasis_PN_361


title: Psoriasis_PN_355


title: Psoriasis_PN_358


title: Psoriasis_PN_357


title: Psoriasis_PN_356


title: Psoriasis_PN_352


title: Psoriasis_PN_353


title: Psoriasis_PN_351

value: ILC


title: Psoriasis_PN_347


title: Psoriasis_PN_349


title: Psoriasis_PN_350


title: Psoriasis_PN_348


title: Psoriasis_PN_344


title: Psoriasis_PN_343


title: Psoriasis_PN_367


title: Psoriasis_PN_345


title: Psoriasis_PN_342


title: Psoriasis_PN_339


title: Psoriasis_PN_340

value: Activated mitotic keratinocytes


title: Psoriasis_PN_338


title: Psoriasis_PN_341

value: doublet


title: Psoriasis_PN_335

value: LC


title: Psoriasis_PN_336


title: Psoriasis_PN_334


title: Psoriasis_PN_337


title: Psoriasis_PN_332


title: Psoriasis_PN_354


title: Psoriasis_PN_331


title: Psoriasis_PN_330


title: Psoriasis_PN_333


title: Psoriasis_PN_329


title: Psoriasis_PN_328


title: Psoriasis_PN_327

value: Progenitor keratinocytes


title: Psoriasis_PN_325


title: Psoriasis_PN_326

value: Activated Transition keratinocytes


title: Psoriasis_PN_346


title: Psoriasis_PN_322


title: Psoriasis_PN_323


title: Psoriasis_PN_319


title: Psoriasis_PN_318


title: Psoriasis_PN_320


title: Psoriasis_PN_317


title: Psoriasis_PN_316


title: Psoriasis_PN_315


title: Psoriasis_PN_312


title: Psoriasis_PN_314

value: T lymphocytes


title: Psoriasis_PN_311


title: Psoriasis_PN_310


title: Psoriasis_PN_313

value: Channel keratinocytes


title: Psoriasis_PN_308

value: Basal keratinocytes III


title: Psoriasis_PN_307

value: Basal keratinocytes II


title: Psoriasis_PN_309

value: Suprabasal keratinocytes I


title: Psoriasis_PN_303

value: Skin


title: Psoriasis_PN_304

value: PN

value: Activated suprabasal keratinocytes


title: Psoriasis_PN_306

value: Psoriasis


title: Psoriasis_PN_305

value: singlet


title: Psoriasis_PN_301


title: Psoriasis_PN_324


title: Psoriasis_PN_300

value: Basal keratinocytes I


title: Psoriasis_PN_299


title: Psoriasis_PN_297


title: Psoriasis_PN_298


title: Psoriasis_PN_293


title: Psoriasis_PN_295


title: Psoriasis_PN_321


title: Psoriasis_PN_291

value: Treg


title: Psoriasis_PN_292

value: Activated basal keratinocytes


title: Psoriasis_PN_290


title: Psoriasis_PN_288


title: Psoriasis_PN_289


title: Psoriasis_PN_287


title: Psoriasis_PN_283


title: Psoriasis_PN_284


title: Psoriasis_PN_286


title: Psoriasis_PN_281

value: doublet


title: Psoriasis_PN_276

value: Melanocytes


title: Psoriasis_PN_274


title: Psoriasis_PN_275


title: Psoriasis_PN_273

value: LC


title: Psoriasis_PN_280


title: Psoriasis_PN_279


title: Psoriasis_PN_302

value: Progenitor keratinocytes


title: Psoriasis_PN_277


title: Psoriasis_PN_282


title: Psoriasis_PN_272


title: Psoriasis_PN_296


title: Psoriasis_PN_285


title: Psoriasis_PN_271


title: Psoriasis_PN_269


title: Psoriasis_PN_294


title: Psoriasis_PN_278


title: Psoriasis_PN_267


title: Psoriasis_PN_266


title: Psoriasis_PN_265


title: Psoriasis_PN_264


title: Psoriasis_PN_262

value: T lymphocytes


title: Psoriasis_PN_261

value: Channel keratinocytes


title: Psoriasis_PN_260


title: Psoriasis_PN_258

value: Transition keratinocytes


title: Psoriasis_PN_259


title: Psoriasis_PN_256

value: Basal keratinocytes III


title: Psoriasis_PN_255


title: Psoriasis_PN_254


title: Psoriasis_PN_270


title: Psoriasis_PN_253


title: Psoriasis_PN_252


title: Psoriasis_PN_251

value: Activated Transition keratinocytes


title: Psoriasis_PN_249

value: Skin


title: Psoriasis_PN_247

value: PN

value: Suprabasal keratinocytes II


title: Psoriasis_PN_245

value: Psoriasis


title: Psoriasis_PN_248

value: singlet

value: Suprabasal keratinocytes I


title: Psoriasis_PN_246


title: Psoriasis_PN_244


title: Psoriasis_PN_250


title: Psoriasis_PN_268


title: Psoriasis_PN_241


title: Psoriasis_PN_240


title: Psoriasis_PN_243


title: Psoriasis_PN_242

value: Mac/MoDC


title: Psoriasis_PN_239


title: Psoriasis_PN_263

value: Activated suprabasal keratinocytes


title: Psoriasis_PN_238


title: Psoriasis_PN_236


title: Psoriasis_PN_237

value: doublet


title: Psoriasis_PN_234


title: Psoriasis_PN_233


title: Psoriasis_PN_232

value: Activated basal keratinocytes


title: Psoriasis_PN_230


title: Psoriasis_PN_231


title: Psoriasis_PN_229

value: Activated mitotic keratinocytes


title: Psoriasis_PN_228


title: Psoriasis_PN_227

value: LC


title: Psoriasis_PN_226


title: Psoriasis_PN_224


title: Psoriasis_PN_225


title: Psoriasis_PN_223


title: Psoriasis_PN_222


title: Psoriasis_PN_218


title: Psoriasis_PN_221


title: Psoriasis_PN_219


title: Psoriasis_PN_215


title: Psoriasis_PN_214


title: Psoriasis_PN_216


title: Psoriasis_PP_212

value: PP


title: Psoriasis_PN_235


title: Psoriasis_PP_213


title: Psoriasis_PN_217


title: Psoriasis_PP_204

value: T lymphocytes


title: Psoriasis_PP_211


title: Psoriasis_PP_205


title: Psoriasis_PP_208


title: Psoriasis_PP_209

value: Proliferative CD8


title: Psoriasis_PP_206


title: Psoriasis_PP_203

value: mDC


title: Psoriasis_PP_202


title: Psoriasis_PP_201


title: Psoriasis_PP_199


title: Psoriasis_PP_200


title: Psoriasis_PN_220


title: Psoriasis_PP_198


title: Psoriasis_PP_196


title: Psoriasis_PP_210


title: Psoriasis_PP_197


title: Psoriasis_PP_195


title: Psoriasis_PP_192


title: Psoriasis_PP_194


title: Psoriasis_PP_190


title: Psoriasis_PP_189


title: Psoriasis_PP_187


title: Psoriasis_PP_186


title: Psoriasis_PP_184


title: Psoriasis_PP_207


title: Psoriasis_PP_193


title: Psoriasis_PP_185


title: Psoriasis_PP_188


title: Psoriasis_PP_191


title: Psoriasis_PP_182


title: Psoriasis_PP_181


title: Psoriasis_PP_183


title: Psoriasis_PP_180


title: Psoriasis_PP_178


title: Psoriasis_PP_179


title: Psoriasis_PP_177


title: Psoriasis_PP_176


title: Psoriasis_PP_175


title: Psoriasis_PP_173


title: Psoriasis_PP_172


title: Psoriasis_PP_171


title: Psoriasis_PP_174


title: Psoriasis_PP_170


title: Psoriasis_PP_169


title: Psoriasis_PP_167


title: Psoriasis_PP_168


title: Psoriasis_PP_166


title: Psoriasis_PP_164


title: Psoriasis_PP_162

value: ILC


title: Psoriasis_PP_165

value: Skin


title: Psoriasis_PP_160


title: Psoriasis_PP_159


title: Psoriasis_PP_163


title: Psoriasis_PP_161


title: Psoriasis_PP_154


title: Psoriasis_PP_158


title: Psoriasis_PP_156


title: Psoriasis_PP_151


title: Psoriasis_PP_149


title: Psoriasis_PP_150


title: Psoriasis_PP_155


title: Psoriasis_PP_148


title: Psoriasis_PP_147


title: Psoriasis_PP_143

value: Treg


title: Psoriasis_PP_144


title: Psoriasis_PP_142


title: Psoriasis_PP_140


title: Psoriasis_PP_157


title: Psoriasis_PP_137


title: Psoriasis_PP_138

value: Tc (cytokine+)


title: Psoriasis_PP_136

value: Psoriasis


title: Psoriasis_PP_134

value: singlet


title: Psoriasis_PP_132


title: Psoriasis_PP_135


title: Psoriasis_PP_130


title: Psoriasis_PP_153


title: Psoriasis_PP_152


title: Psoriasis_PP_131


title: Psoriasis_PP_129


title: Psoriasis_PP_127


title: Psoriasis_PP_128

value: Melanocytes


title: Psoriasis_PP_125


title: Psoriasis_PP_126


title: Psoriasis_PP_123


title: Psoriasis_PP_121


title: Psoriasis_PP_124


title: Psoriasis_PP_145


title: Psoriasis_PP_146


title: Psoriasis_PP_120


title: Psoriasis_PP_117


title: Psoriasis_PP_141


title: Psoriasis_PP_139


title: Psoriasis_PP_116


title: Psoriasis_PP_115


title: Psoriasis_PP_114

value: Tc (cytokine-)


title: Psoriasis_PP_133


title: Psoriasis_PP_113

value: Activated suprabasal keratinocytes


title: Psoriasis_PP_111

value: Mac/MoDC


title: Psoriasis_PP_110


title: Psoriasis_PP_107

value: Activated basal keratinocytes


title: Psoriasis_PP_109


title: Psoriasis_PP_108


title: Psoriasis_PP_105


title: Psoriasis_PP_122


title: Psoriasis_PP_104


title: Psoriasis_PP_106


title: Psoriasis_PP_103

value: Activated Transition keratinocytes


title: Psoriasis_PP_102


title: Psoriasis_PP_99


title: Psoriasis_PP_98

value: LC


title: Psoriasis_PP_100

value: PP

value: doublet


title: Psoriasis_PP_94

value: T lymphocytes


title: Psoriasis_PP_118


title: Psoriasis_PP_101


title: Psoriasis_PP_96


title: Psoriasis_PP_97


title: Psoriasis_PP_95


title: Psoriasis_PP_91


title: Psoriasis_PP_92


title: Psoriasis_PP_93

value: mDC


title: Psoriasis_PP_89


title: Psoriasis_PP_87


title: Psoriasis_PP_112


title: Psoriasis_PP_88


title: Psoriasis_PP_86


title: Psoriasis_PP_85


title: Psoriasis_PP_83


title: Psoriasis_PP_80


title: Psoriasis_PP_81


title: Psoriasis_PP_82


title: Psoriasis_PP_76


title: Psoriasis_PP_74


title: Psoriasis_PP_79


title: Psoriasis_PP_72


title: Psoriasis_PP_70


title: Psoriasis_PP_77


title: Psoriasis_PP_68

value: Proliferative CD8


title: Psoriasis_PP_90

value: Skin


title: Psoriasis_PP_71


title: Psoriasis_PP_73


title: Psoriasis_PP_67


title: Psoriasis_PP_66

value: ILC


title: Psoriasis_PP_69


title: Psoriasis_PP_75


title: Psoriasis_PP_65


title: Psoriasis_PP_62


title: Psoriasis_PP_63


title: Psoriasis_PP_64


title: Psoriasis_PP_58


title: Psoriasis_PP_59


title: Psoriasis_PP_60


title: Psoriasis_PP_61


title: Psoriasis_PP_119


title: Psoriasis_PP_84


title: Psoriasis_PP_57


title: Psoriasis_PP_78


title: Psoriasis_PP_56


title: Psoriasis_PP_55


title: Psoriasis_PP_53


title: Psoriasis_PP_54


title: Psoriasis_PP_52


title: Psoriasis_PP_50


title: Psoriasis_PP_49


title: Psoriasis_PP_43


title: Psoriasis_PP_45


title: Psoriasis_PP_42


title: Psoriasis_PP_39


title: Psoriasis_PP_48


title: Psoriasis_PP_44


title: Psoriasis_PP_36


title: Psoriasis_PP_47


title: Psoriasis_PP_46


title: Psoriasis_PP_40


title: Psoriasis_PP_35


title: Psoriasis_PP_38


title: Psoriasis_PP_41


title: Psoriasis_PP_32


title: Psoriasis_PP_34


title: Psoriasis_PP_33

value: Treg


title: Psoriasis_PP_30

value: Psoriasis


title: Psoriasis_PP_27

value: singlet


title: Psoriasis_PP_31

value: Activated mitotic keratinocytes


title: Psoriasis_PP_29


title: Psoriasis_PP_25


title: Psoriasis_PP_26


title: Psoriasis_PP_23


title: Psoriasis_PP_22


title: Psoriasis_PP_51


title: Psoriasis_PP_24


title: Psoriasis_PP_20


title: Psoriasis_PP_37


title: Psoriasis_PP_21


title: Psoriasis_PP_14


title: Psoriasis_PP_18


title: Psoriasis_PP_17


title: Psoriasis_PP_15

value: Melanocytes


title: Psoriasis_PP_12


title: Psoriasis_PP_13


title: Psoriasis_PP_11

value: Activated suprabasal keratinocytes


title: Psoriasis_PP_9


title: Psoriasis_PP_10


title: Psoriasis_PP_7

value: Mac/MoDC


title: Psoriasis_PP_4


title: Psoriasis_PP_8


title: Psoriasis_PP_6


title: Psoriasis_PP_5


title: Psoriasis_PP_2


title: Psoriasis_PP_1


title: Psoriasis_PP_3


title: Cuttag_Sus_GCs_OP_H3K4me3

status: Public on Jun 01 2024

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

country: China

institute: Guangdong Medical University

library_source: genomic

data_processing:
FASTQC was used to measure the date quality distribution, and the clean reads were then aligned to Sscrofa11.1 genome sequences.
Peaks were called using MACS2 peak caller with q-value < 0.05.
The findMotifsGenome.pl script from HOMER was used to identify the enriched motifs.
Genome-wide normalized signal coverage tracks were visualized in the IGV.
Peaks that were greater than 2-fold changed at a false discovery rate < 0.1 were considered differential peaks, while peaks that did not have a log2 fold change significantly different from zero were termed constitutive peaks.
Assembly: Sscrofa11.1
Supplementary files format and content: bigWig files include peaks for each sample, respectively.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Sus scrofa

source_name: ovary

extract_protocol:
The CUT& Tag was conducted by using CUT&Tag Assay Kit for Illumina according to the manufacturer’s protocol with minor modifications (Vazyme, TD903). Briefly, nuclei were extracted from 5,000 GCs and incubated with ConA beads at least 10 min for comprehensively combination. The complexes were then incubated with primary antibodies overnight, while the IgG antibody were used as negative control. The samples were incubated sequentially with a secondary antibody and a diluted pA-Tn5 transposase was used to cut the genome and add a special adaptor sequence to build a library.
All sequencing libraries were established following 12 cycles of PCR amplification. The enrichment of target sites in the library was detected using qRT–PCR. The selected DNA fragments were sequenced on the Novaseq 6000 platform to at least a depth of 2.5×107 reads accordingly.

value: ovary

tag: cell type

value: granulosa cells

tag: treatment

value: WT


title: Cuttag_Sus_GCs_AP_H3K27ac


title: Cuttag_Sus_GCs_OP_H3K27ac


title: Cuttag_Sus_GCs_OP_Fosl2


title: Cuttag_Sus_GCs_OP_IgG


title: Cuttag_Sus_GCs_AP_H3K4me3


title: Psoriasis_PP_19

value: PP


title: Psoriasis_PP_16


title: Cuttag_Sus_GCs_AP_IgG


title: ATAC_Sus_GCs_Fosl2_KD_2

data_processing:
FastQC was used to evaluate the quality of the sequencing data, and Trimmomatic was explored to remove the adaptor sequences and obtain the clean data, which were subsequently aligned to the UCSC mm10 or Sscrofa11.1 reference genome using Bowtie2, under the parameters -t -q -N 1 -L 25.
All unmapped reads, non-uniquely mapped reads, and PCR duplicates were removed. For downstream analysis, the MACS2 was applied to call significant peaks with q-value < 0.05. To identify differentially expressed genes between different passaged GCs, the ATAC-seq peaks of each sample were merged to generate a consensus set of unique peaks.
The number of peaks among this set was counted using bedtools, and GAAs and GIAs were identified using DESeq2, with thresholds log2(fold-change) ≥ 1 and p value < 0.05.
Genomic features of peaks were annotated using ChIPseeker R package. Additionally, to find the sequence motifs enriched in distal ATACseq peaks, findMotifsGenome.pl from the HOMER program was used.
Motifs with known match in HOMER database were selected in GAAs and GIAs. Promoters were defined as ±2.5 kb around the TSS. Peaks at least 2.5 kb away from TSSs were defined as distal peaks by BEDTools.
The DAVID web-tool was employed to identify the GO terms using databases including Molecular Functions, Biological Functions and Cellular Components.
Genome-wide normalized signal coverage tracks were created by bam Coverage in deepTools and were visualized in the Integrative Genomics Viewer.
Assembly: Sscrofa11.1 and mm10
Supplementary files format and content: bigWig files include peaks for each sample, respectively.

extract_protocol:
In brief, a total of 50 oocytes with zona pellucida removed, and 50,000 GCs were lysed respectively in lysis buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3mM MgCl2, 0.1%Igepal CA-630, 0.1%Tween-20, 0.01%Digitonin, 1% Cytochalasin B, 0.1%collagenase I) for 10 min on ice to generate the nuclei. Nuclei were then spun at 500g for 5 min immediately to remove the supernatant. Tn5 transposome and tagmentation procedures were subjected at 37°C for 30 min (Vazyme, TD501).
DNA were purified using 2×AMPure beads (Beckman, A63881) and conducted to 16 cycles (for oocytes) or 14 cycles (for GCs) of library amplification using the following PCR conditions: 72°C for 3 min; 98°C for 30s; and thermocycling at 98 °C for 15s, 60°C for 30 s and 72°C for 3 min; following by 72°C 5 min.The amplified DNA was size-selected using AMPure beads for 200–500bp DNA fragments. All libraries were sequenced by the Novaseq 6000 platform to at least a depth of 4.0×107 reads accordingly.

value: Fosl2 knockdown


title: ATAC_Sus_GCs_Fosl2_KD_1


title: ATAC_Sus_OP_GCs_Rep2


title: ATAC_Sus_isolatedMII__oocytes_Rep1


title: ATAC_Sus_AP_GCs_Rep1


title: ATAC_Sus_MII_oocytes_Rep2

value: oocytes


title: ATAC_Sus_isolatedMII__oocytes_Rep2


title: ATAC_Sus_MII_oocytes_Rep1


title: ATAC_Sus_MI_oocytes_Rep2


title: ATAC_Sus_OP_GCs_Rep1


title: ATAC_Sus_GV_oocytes_Rep1


title: ATAC_Sus_AP_GCs_Rep2


title: ATAC_Sus_MI_oocytes_Rep1


title: RNA_Sus_GCs_Fosl2_KD_1

library_source: transcriptomic

data_processing:
The sequencing adapters were removed from the raw RNA-seq reads, and the obtained clean data were aligned to mm9 or Sscrofa11.1 genome.
Gene expressions were assembled and quantified using package RSEM with parameters of -paired-end and -star.
The averaged values were quantile normalized together with the FPKM/RPKM value in this study to allow further comparison.
Differentially expressed genes (DEGs) were identified by R package DEseq2 with log2(fold-change) ≥ 1 and p value < 0.05.
Enriched GO terms were identified with MGI Gene Ontology Term Finder using log2(fold-change) ≥ 1 and p value < 0.05 as thresholds.
Assembly: Sscrofa11.1 and mm10
Supplementary files format and content: bigWig files include peaks for each sample, respectively.

molecule: total RNA

extract_protocol:
Cells were harvested using TRIzol reagent (Invitrogen, 10296028), and total RNA was isolated according to the manufacturer’s protocol.
The RNA-seq libraries were generated from a total of 50 oocytes and 50,000 GCs. After pre-amplification and AMPure XP beads purification, cDNAs were subject to RNA library prep kit for Illumina (NEB, E7770). All libraries were sequenced on the Novaseq 6000 platform to at least a depth of 1.5×107 reads.


title: RNA_Sus_OP_GCs_Rep2


title: RNA_Sus_GCs_NC

value: Ctrl knockdown


title: RNA_Sus_AP_GCs_Rep2


title: RNA_Sus_GCs_Fosl2_KD_2


title: Cuttag_Sus_GCs_AP_Fosl2


title: RNA_Sus_isolatedMII__oocytes_Rep2


title: ATAC_Sus_GV_oocytes_Rep2


title: RNA_Sus_MI_oocytes_Rep2


title: RNA_Sus_isolatedMII__oocytes_Rep1


title: RNA_Sus_MII_oocytes_Rep1


title: Psoriasis_PP_28


title: ATAC_Sus_GCs_NC


title: RNA_Sus_AP_GCs_Rep1


title: RNA_Sus_MI_oocytes_Rep1


title: RNA_Sus_GV_oocytes_Rep1


title: RNA_Sus_GV_oocytes_Rep2


title: ATAC_Mus_OP_GCs_Rep2

organism: Mus musculus


title: ATAC_Mus_AP_GCs_Rep1


title: ATAC_Mus_AP_GCs_Rep2


title: ATAC_Mus_OP_GCs_Rep1


title: RNA_Mus_OP_GCs


title: 53N

status: Public on Apr 11 2024

city: Hershey

first: Gregory

last: Yochum

state: PA

address: 700 HMC Crescent Road

department: Biochemistry, Colorectal Surgery

country: USA

institute: Penn State College of Medicine

data_processing:
Base calling with Illumina MiSeq2500
Alignment with STAR version 2.7.3
HTSeq counting of aligned reads
Assembly: hg38
Supplementary files format and content: Count files contain raw counts for sequences aligning to each transcript.

source_name: Rectum

extract_protocol:
Tumors and adjacent colonic segments were surgically resected and aliquots were stored in RNAlater (Thermo Fisher) preservative. Samples were homogenized with a pestle and chloroform was added. The samples were centrifuged at 12,000 x g for 15 minutes. The aqueous layer was purified with RNAEasy Mini Kit (Qiagen). Samples were selected for poly-adenylation, and cDNA libraries were made and sequenced on MiSeq2500 (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rectum

tag: age at_surgery

tag: tumor stage


title: RNA_Sus_OP_GCs_Rep1


title: 51N

source_name: Hepatic flexure

value: Hepatic flexure


title: 53C


title: RNA_Sus_MII_oocytes_Rep2


title: 50N

source_name: Sigmoid

value: Sigmoid


title: 50C


title: 49N

source_name: Cecum

value: Cecum


title: 49C


title: 47N


title: 47C


title: 46C


title: 46N


title: 43N


title: RNA_Mus_AP_GCs


title: 42N


title: 43C


title: 42C


title: 41C


title: 39C


title: 39N


title: 38N


title: 41N


title: 51C


title: 37N

source_name: Rectosigmoid

value: Rectosigmoid


title: 38C


title: 36N


title: 37C


title: 35N


title: 36C


title: 35C


title: 34N


title: 34C


title: 33N


title: 33C


title: 32N


title: 32C


title: 31N


title: 31C


title: 30N

source_name: Descending colon

value: Descending colon


title: 29C


title: 29N


title: 27C


title: 27N


title: 24C


title: input12

status: Public on Apr 02 2024

city: HangZhou

first: Xiaoqin

last: Liu

state: ZheJiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake University

data_processing:
Raw reads were trimmed by TrimGalore with paired end mode and default parameter. Quality control was done with fastqc . Then UMI-tools was used to get the count matrix. Briefly, top 100 barcode list were retained using whitelist tool in UMI-tools . Then barcode and UMI information which were extracted from read2 using extract tool in UMI-tools was added to read1. After that, read1 were aligned to the mm10 genome using STAR with default parameter except that the outFilterMultimapNmax was set to 1. Finally, we got the count matrix file, in which the number of UMIs represents transcript number of each gene within each individual cell, using featurecounts and count tools in UMI-tools.
ChIP-seq reads were trimmed with TrimGalore with paired end mode and default parameter and QC was done with fastqc.  Then trimmed reads were aligned to the mm10 mouse genome with bowtie2 with default parameter. Filter alignment with samtools in which parameter were set as follows: -F 1804 -f 2 -q 30. Duplicated were marked with MarkDuplicates in picard-tools and filtered out with samtools. Finally, MACS2 call peak was used to call bcl11b binding site on the genome, with IgG as control, anti-bcl11b as treat group. Bc1llb binding site was analyzed with ChIPseeker package. ChIP-seq signal were visualized using Integrative Genomics Viewer (IGV) software .
Genome_build: mm10
Supplementary_files_format_and_content: count expression profile; peak text file

source_name: mammary gland basal cell

extract_protocol:
Single cell RNA-seq: single CD49fhiEpCAMmedLin- cell from different age mice or tumor was directly sorted into 96-well plate containing lysis buffer using FACS. Single cell was immediately lysed at 70 degree for 3min in the PCR system.;    ChIP-seq: Anti-IgG (Abcam, ab172730) and anti-Bcl11b (Benthyl laboratories.inc, A300-384A) were used for ChIP-seq assay. Briefly, after cross-linked in 1% (wt/vol) formaldehyde solution, quenched, washed and resuspended, cells were lysed using SDS lysis buffer. Then shear chromatin with AFA Focused-ultrasonicator using Covaris ME220. Take 10% as input and 90% sonicated chromatin were divided equally to two parts. The sonicated chromatin was incubated in the cold room overnight with protein G-Dynabeads (Invitrogen,10004D) which had been conjugated with 50μg appropriate antibody. After washing with RIPA buffer, LiCl buffer and TE buffer, the bound complexes were eluted, reverse cross-linked and extracted by phenol/chloroform.
Single cell RNA libraries were prepared for sequencing using 3’ UTR Smartseq protocols. The sample was reverse transcribed to cDNA using SuperScriptIIreverse transcriptase (invitrogen, 18064-071) with a template switch oligo (TSO) primer and a sample-specific 25 nt oligo dT reverse transcription primer. Then the cDNA was amplified by 16 cycles of PCR with 3’P2 primer and IS primer using KAPA HiFi HotStart Ready Mix (Kapa Biosystem, KK2602). The barcoded DNAs were amplified using biotinylated pre-index primers. After purified by AMpure XP beads, cDNA was sonicated to approximately 300 bp fragments using Covaris ME220.  3’ terminal of the cDNA was enriched using Dynabeads® MyOne Streptavidin C1 beads (Invitrogen, 65001). The RNA-seq libraries were constructed using the Kapa Hyper Prep Kit (Kapa Biosystem, KK8504) according to the manufacturer’s instructions.;       ChIP DNA library was performed by VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme, ND606). Briefly, after end preparation and adapter ligation, ChIP DNA was amplified 12 cycles and purified using AMpure XP beads (Beckman, A63881) twice and then were submitted to 150 bp paired-end sequencing on an Illumina novaseq 6000 platform (Novogene).

treatment_protocol: pInducer Bcl11b Comma D beta cells were treated with 100ng/mL Doxycycline overnight and collected

tag: strain

value: pInducer Bcl11b Comma DBeta cell line

tag: chip-antibody

value: input


title: IgG12

value: IgG


title: bclrb12


title: TmutLum

source_name: luminal cells from Bcl11b KO cells transplanted mammary gland


title: TwtLum

source_name: luminal cells from WT cells transplanted mammary gland


title: TwtBasal

source_name: basal cells from WT cells transplanted mammary gland


title: TmutBasal

source_name: basal cells from Bcl11b KO cells transplanted mammary gland


title: OT_v1

tag: month


title: OP_v1


title: 30C


title: OP_v3


title: OP_v4


title: siNFAT5 under High Na condition

status: Public on May 22 2024

type: RNA

city: Hongo, Bunkyo-ku

first: Hiroki

last: Ryuno

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

description: RMA expression value derived from Affymetrix Expression Console Software.

hyb_protocol: single stranded cDNA was hybridized for 16 hr at 45˚C on Clariom S Human Array Thermo Fisher Scientific).

scan_protocol: Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) and were scanned using GeneChip Scanner 3000 7G.

data_processing: Gene expression data were analyzed with Affymetrix Expression Console Software 1.4.1 offered SST-RMA using Affymetrix default analysis settings.

label: biotin

source_name: HeLa cells

label_protocol: Biotinylated cDNA was prepared from total RNA using GeneChip WT PLUS Reagent Kit (Affymetrix) following the manufacturer’s instructions.

extract_protocol: Total RNA were extracted using Isogen (Wako, Cat#319-90211).

treatment_protocol: HeLa cells were transfected with siControl, siNFAT5 and siHES1 using lipofectamine RNAiMax.


title: mut_v3

source_name: mammary gland basal cell in Bcl11b ko mouse


title: OT_v2


title: mut_v4


title: OT_v3


title: 24N


title: siControl under High Na condition


title: mut_v2


title: m29_v3


title: m29_v2


title: m29_v1


title: siNFAT5 under isoosmotic condition


title: m24_v1


title: siHES1 under isoosmotic condition


title: m22_v2


title: OT_v4


title: siHES1 under High Na condition


title: m22_v1


title: m19_v2


title: m19_v1


title: m17_v2


title: m17_v1


title: m15_v4


title: OP_v2


title: m15_v3


title: m13_v13


title: m15_v2


title: m15_v1


title: siControl under isoosmotic condition


title: m11_v2


title: m13_v2


title: m11_v1


title: m9_v2


title: m9_v1


title: m4_v2


title: m4_v4


title: m2_v2


title: m4_v3


title: m2_v1


title: UKE_BCN_KGU #363

status: Public on Mar 20 2024

type: genomic

city: Hamburg

first: Richard

last: Drexler

address: Martinistraße 52

department: Neurosurgery

country: Germany

institute: Medical Center Hamburg-Eppendorf

description: SAMPLE 363

hyb_protocol: Bisulfite treatment, whole-genome DNA amplification, hybridization and single-base extension, fluorescence staining and scanning of the chips were performed following the manufacturer´s instructions (Illumina).

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
All idats corresponding to methylation array data were processed similarly using the minfi package in R (version 1.40.0).52 The data was processed using the preprocessIllumina function. Only probes with detection p-values <0.01 were kept for further analysis. Also, probes with <3 beads in at least 5% of samples, as well as all non-CpG probes, SNP-related probes, and probes located on X and Y chromosomes were discarded.
normalized data matrix contains: The CpG intensities were converted into beta values representing total methylation levels (between 0 and 1).
non-normalized data matrix contains: Unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: Glioblastoma

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted with the Maxwell® 16FFPE Plus LEV DNA Kit (Promega, Fitchburg, USA) and a Maxwell DNA extractor

value: Glioblastoma

tag: age at time of surgery (years)

tag: year of surgery

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: tumor progression [0=no, 1=yes, 2=n/a]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #359

description: SAMPLE 359

tag: tissue


title: UKE_BCN_KGU #360

description: SAMPLE 360

tag: age at time of surgery (years)


title: UKE_BCN_KGU #358

description: SAMPLE 358

tag: year of surgery


title: UKE_BCN_KGU #362

description: SAMPLE 362

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #357

description: SAMPLE 357

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #355

description: SAMPLE 355

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #354

description: SAMPLE 354

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #353

description: SAMPLE 353

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #352

description: SAMPLE 352

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #356

description: SAMPLE 356

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #349

description: SAMPLE 349

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #350

description: SAMPLE 350

tag: karnofsky performance status before starting chemo-radiotherapy [%]


title: UKE_BCN_KGU #348

description: SAMPLE 348

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #347

description: SAMPLE 347

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #345

description: SAMPLE 345

tag: overall survival [months]


title: UKE_BCN_KGU #343

description: SAMPLE 343

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #344

description: SAMPLE 344

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #346

description: SAMPLE 346

tag: tissue


title: UKE_BCN_KGU #342

description: SAMPLE 342

tag: age at time of surgery (years)


title: UKE_BCN_KGU #341

description: SAMPLE 341

tag: year of surgery


title: UKE_BCN_KGU #340

description: SAMPLE 340

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #339

description: SAMPLE 339

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #361

description: SAMPLE 361

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #337

description: SAMPLE 337

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #334

description: SAMPLE 334

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #332

description: SAMPLE 332

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #335

description: SAMPLE 335

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #330

description: SAMPLE 330

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #331

description: SAMPLE 331

tag: karnofsky performance status before starting chemo-radiotherapy [%]


title: UKE_BCN_KGU #328

description: SAMPLE 328

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #351

description: SAMPLE 351

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #325

description: SAMPLE 325

tag: overall survival [months]


title: UKE_BCN_KGU #326

description: SAMPLE 326

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #327

description: SAMPLE 327

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #321

description: SAMPLE 321

tag: tissue


title: UKE_BCN_KGU #323

description: SAMPLE 323

tag: age at time of surgery (years)


title: UKE_BCN_KGU #322

description: SAMPLE 322

tag: year of surgery


title: UKE_BCN_KGU #320

description: SAMPLE 320

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #319

description: SAMPLE 319

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #318

description: SAMPLE 318

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #315

description: SAMPLE 315

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #316

description: SAMPLE 316

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #317

description: SAMPLE 317

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #314

description: SAMPLE 314

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #338

description: SAMPLE 338

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #312

description: SAMPLE 312

tag: karnofsky performance status before starting chemo-radiotherapy [%]


title: UKE_BCN_KGU #336

description: SAMPLE 336

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #311

description: SAMPLE 311

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #333

description: SAMPLE 333

tag: overall survival [months]


title: UKE_BCN_KGU #329

description: SAMPLE 329

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #310

description: SAMPLE 310

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #307

description: SAMPLE 307

tag: tissue


title: UKE_BCN_KGU #308

description: SAMPLE 308

tag: age at time of surgery (years)


title: UKE_BCN_KGU #306

description: SAMPLE 306

tag: year of surgery


title: UKE_BCN_KGU #303

description: SAMPLE 303

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #304

description: SAMPLE 304

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #300

description: SAMPLE 300

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #324

description: SAMPLE 324

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #302

description: SAMPLE 302

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #299

description: SAMPLE 299

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #297

description: SAMPLE 297

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #296

description: SAMPLE 296

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #305

description: SAMPLE 305


title: UKE_BCN_KGU #295

description: SAMPLE 295

tag: karnofsky performance status before starting chemo-radiotherapy [%]


title: UKE_BCN_KGU #301

description: SAMPLE 301

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #298

description: SAMPLE 298

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #313

description: SAMPLE 313

tag: overall survival [months]


title: UKE_BCN_KGU #294

description: SAMPLE 294

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #292

description: SAMPLE 292

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #289

description: SAMPLE 289

tag: tissue


title: UKE_BCN_KGU #290

description: SAMPLE 290

tag: age at time of surgery (years)


title: UKE_BCN_KGU #291

description: SAMPLE 291

tag: year of surgery


title: UKE_BCN_KGU #309

description: SAMPLE 309

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #293

description: SAMPLE 293

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #287

description: SAMPLE 287

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #285

description: SAMPLE 285

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #288

description: SAMPLE 288

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #284

description: SAMPLE 284

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #283

description: SAMPLE 283

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #286

description: SAMPLE 286

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #281

description: SAMPLE 281

tag: karnofsky performance status before starting chemo-radiotherapy [%]


title: UKE_BCN_KGU #282

description: SAMPLE 282

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #280

description: SAMPLE 280

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #279

description: SAMPLE 279

tag: overall survival [months]


title: UKE_BCN_KGU #278

description: SAMPLE 278

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #275

description: SAMPLE 275

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #274

description: SAMPLE 274

tag: tissue


title: UKE_BCN_KGU #273

description: SAMPLE 273

tag: age at time of surgery (years)


title: UKE_BCN_KGU #272

description: SAMPLE 272

tag: year of surgery


title: UKE_BCN_KGU #271

description: SAMPLE 271

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #270

description: SAMPLE 270

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #269

description: SAMPLE 269

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #266

description: SAMPLE 266

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #268

description: SAMPLE 268

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #267

description: SAMPLE 267

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #263

description: SAMPLE 263

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #265

description: SAMPLE 265

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #261

description: SAMPLE 261

tag: karnofsky performance status before starting chemo-radiotherapy [%]


title: UKE_BCN_KGU #259

description: SAMPLE 259

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #260

description: SAMPLE 260

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #256

description: SAMPLE 256

tag: overall survival [months]


title: UKE_BCN_KGU #258

description: SAMPLE 258

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #254

description: SAMPLE 254

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #257

description: SAMPLE 257

tag: tissue


title: UKE_BCN_KGU #255

description: SAMPLE 255

tag: age at time of surgery (years)


title: UKE_BCN_KGU #252

description: SAMPLE 252

tag: year of surgery


title: UKE_BCN_KGU #253

description: SAMPLE 253

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #276

description: SAMPLE 276

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #251

description: SAMPLE 251

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #277

description: SAMPLE 277

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #250

description: SAMPLE 250

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #249

description: SAMPLE 249

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #248

description: SAMPLE 248

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #246

description: SAMPLE 246

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #247

description: SAMPLE 247

tag: karnofsky performance status before starting chemo-radiotherapy [%]


title: UKE_BCN_KGU #245

description: SAMPLE 245

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #244

description: SAMPLE 244

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #243

description: SAMPLE 243

tag: overall survival [months]


title: UKE_BCN_KGU #264

description: SAMPLE 264

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #242

description: SAMPLE 242

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #240

description: SAMPLE 240

tag: tissue


title: UKE_BCN_KGU #262

description: SAMPLE 262

tag: age at time of surgery (years)


title: UKE_BCN_KGU #239

description: SAMPLE 239

tag: year of surgery

tag: progression-free survival [months]


title: UKE_BCN_KGU #237

description: SAMPLE 237

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #236

description: SAMPLE 236

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #238

description: SAMPLE 238

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #234

description: SAMPLE 234

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #235

description: SAMPLE 235

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #233

description: SAMPLE 233

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]

tag: overall survival [months]


title: UKE_BCN_KGU #228

description: SAMPLE 228

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #229

description: SAMPLE 229

tag: tissue

tag: age at time of surgery (years)


title: UKE_BCN_KGU #231

description: SAMPLE 231

tag: year of surgery

tag: progression-free survival [months]


title: UKE_BCN_KGU #230

description: SAMPLE 230

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #232

description: SAMPLE 232

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #224

description: SAMPLE 224

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #225

description: SAMPLE 225

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #223

description: SAMPLE 223

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #221

description: SAMPLE 221

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]

tag: overall survival [months]


title: UKE_BCN_KGU #226

description: SAMPLE 226

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #220

description: SAMPLE 220

tag: tissue

tag: age at time of surgery (years)


title: UKE_BCN_KGU #219

description: SAMPLE 219

tag: year of surgery

tag: progression-free survival [months]


title: UKE_BCN_KGU #218

description: SAMPLE 218

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #241

description: SAMPLE 241

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #217

description: SAMPLE 217

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #215

description: SAMPLE 215

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #214

description: SAMPLE 214

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #213

description: SAMPLE 213

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]

tag: overall survival [months]


title: UKE_BCN_KGU #211

description: SAMPLE 211

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #210

description: SAMPLE 210

tag: tissue

tag: age at time of surgery (years)


title: UKE_BCN_KGU #212

description: SAMPLE 212

tag: year of surgery

tag: progression-free survival [months]


title: UKE_BCN_KGU #208

description: SAMPLE 208

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #207

description: SAMPLE 207

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #206

description: SAMPLE 206

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #227

description: SAMPLE 227

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #205

description: SAMPLE 205

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #204

description: SAMPLE 204

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]

tag: overall survival [months]


title: UKE_BCN_KGU #203

description: SAMPLE 203

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #202

description: SAMPLE 202

tag: tissue

tag: age at time of surgery (years)


title: UKE_BCN_KGU #199

description: SAMPLE 199

tag: year of surgery

tag: progression-free survival [months]


title: UKE_BCN_KGU #200

description: SAMPLE 200

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)


title: UKE_BCN_KGU #198

description: SAMPLE 198

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #197

description: SAMPLE 197

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #195

description: SAMPLE 195

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #194

description: SAMPLE 194

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #196

description: SAMPLE 196

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #193

description: SAMPLE 193

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #191

description: SAMPLE 191

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #216

description: SAMPLE 216

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #189

description: SAMPLE 189

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #222

description: SAMPLE 222

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #192

description: SAMPLE 192

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #188

description: SAMPLE 188

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #190

description: SAMPLE 190

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #209

description: SAMPLE 209

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #187

description: SAMPLE 187

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #186

description: SAMPLE 186

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #185

description: SAMPLE 185

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #183

description: SAMPLE 183

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #201

description: SAMPLE 201

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #179

description: SAMPLE 179

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #180

description: SAMPLE 180

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #176

description: SAMPLE 176

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #175

description: SAMPLE 175

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #177

description: SAMPLE 177

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #172

description: SAMPLE 172

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #174

description: SAMPLE 174

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #171

description: SAMPLE 171

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #170

description: SAMPLE 170

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #168

description: SAMPLE 168

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #169

description: SAMPLE 169

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #173

description: SAMPLE 173

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #163

description: SAMPLE 163

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #165

description: SAMPLE 165

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #166

description: SAMPLE 166

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #167

description: SAMPLE 167

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #162

description: SAMPLE 162

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #184

description: SAMPLE 184

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #161

description: SAMPLE 161

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #159

description: SAMPLE 159

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #160

description: SAMPLE 160

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #157

description: SAMPLE 157

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #158

description: SAMPLE 158

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #181

description: SAMPLE 181

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #155

description: SAMPLE 155

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #182

description: SAMPLE 182

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #178

description: SAMPLE 178

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #154

description: SAMPLE 154

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #156

description: SAMPLE 156

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #152

description: SAMPLE 152

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #151

description: SAMPLE 151

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #148

description: SAMPLE 148

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #153

description: SAMPLE 153

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #145

description: SAMPLE 145

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #147

description: SAMPLE 147

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #144

description: SAMPLE 144

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #146

description: SAMPLE 146

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #142

description: SAMPLE 142

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #143

description: SAMPLE 143

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #149

description: SAMPLE 149

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #164

description: SAMPLE 164

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #141

description: SAMPLE 141

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #136

description: SAMPLE 136

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #135

description: SAMPLE 135

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #140

description: SAMPLE 140

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #139

description: SAMPLE 139

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #134

description: SAMPLE 134

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #138

description: SAMPLE 138

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #129

description: SAMPLE 129

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #127

description: SAMPLE 127

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #137

description: SAMPLE 137

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #131

description: SAMPLE 131

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #133

description: SAMPLE 133

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #128

description: SAMPLE 128

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #125

description: SAMPLE 125

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #124

description: SAMPLE 124

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #123

description: SAMPLE 123

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #150

description: SAMPLE 150

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #121

description: SAMPLE 121

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #126

description: SAMPLE 126

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #122

description: SAMPLE 122

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #119

description: SAMPLE 119

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #120

description: SAMPLE 120

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #118

description: SAMPLE 118

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #114

description: SAMPLE 114

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #117

description: SAMPLE 117

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #115

description: SAMPLE 115

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #116

description: SAMPLE 116

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #113

description: SAMPLE 113

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #108

description: SAMPLE 108

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #132

description: SAMPLE 132

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #112

description: SAMPLE 112

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #107

description: SAMPLE 107

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #111

description: SAMPLE 111

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #106

description: SAMPLE 106

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #130

description: SAMPLE 130

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #110

description: SAMPLE 110

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #109

description: SAMPLE 109

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #105

description: SAMPLE 105

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #102

description: SAMPLE 102

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #103

description: SAMPLE 103

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #104

description: SAMPLE 104

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #101

description: SAMPLE 101

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #99

description: SAMPLE 99

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #95

description: SAMPLE 95

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #93

description: SAMPLE 93

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #97

description: SAMPLE 97

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #96

description: SAMPLE 96

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #100

description: SAMPLE 100

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #90

description: SAMPLE 90

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #94

description: SAMPLE 94

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #92

description: SAMPLE 92

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #87

description: SAMPLE 87

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #85

description: SAMPLE 85

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #89

description: SAMPLE 89

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #82

description: SAMPLE 82

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #81

description: SAMPLE 81

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #78

description: SAMPLE 78

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #86

description: SAMPLE 86

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #84

description: SAMPLE 84

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #80

description: SAMPLE 80

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #88

description: SAMPLE 88

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #83

description: SAMPLE 83

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #75

description: SAMPLE 75

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #73

description: SAMPLE 73

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #76

description: SAMPLE 76

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #98

description: SAMPLE 98

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #74

description: SAMPLE 74

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #72

description: SAMPLE 72

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #71

description: SAMPLE 71

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #69

description: SAMPLE 69

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #91

description: SAMPLE 91

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #66

description: SAMPLE 66

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #65

description: SAMPLE 65

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #67

description: SAMPLE 67

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #68

description: SAMPLE 68

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #63

description: SAMPLE 63

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #62

description: SAMPLE 62

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #61

description: SAMPLE 61

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #70

description: SAMPLE 70

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #60

description: SAMPLE 60

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #79

description: SAMPLE 79

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #59

description: SAMPLE 59

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #57

description: SAMPLE 57

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #54

description: SAMPLE 54

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #64

description: SAMPLE 64

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #55

description: SAMPLE 55

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #56

description: SAMPLE 56

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #50

description: SAMPLE 50

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #58

description: SAMPLE 58

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #77

description: SAMPLE 77

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #48

description: SAMPLE 48

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #53

description: SAMPLE 53

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #52

description: SAMPLE 52

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #44

description: SAMPLE 44

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #43

description: SAMPLE 43

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #49

description: SAMPLE 49

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #41

description: SAMPLE 41

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #39

description: SAMPLE 39

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #46

description: SAMPLE 46

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #45

description: SAMPLE 45

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #33

description: SAMPLE 33

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #42

description: SAMPLE 42

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #35

description: SAMPLE 35

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #37

description: SAMPLE 37

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #36

description: SAMPLE 36

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #24

description: SAMPLE 24

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #32

description: SAMPLE 32

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #25

description: SAMPLE 25

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #34

description: SAMPLE 34

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #22

description: SAMPLE 22

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #31

description: SAMPLE 31

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #30

description: SAMPLE 30

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #20

description: SAMPLE 20

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #29

description: SAMPLE 29

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #51

description: SAMPLE 51

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #47

description: SAMPLE 47

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #28

description: SAMPLE 28

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #19

description: SAMPLE 19

tag: tissue

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #16

description: SAMPLE 16

tag: age at time of surgery (years)

tag: year of surgery


title: UKE_BCN_KGU #27

description: SAMPLE 27

tag: sex (0=male, 1=female)

tag: progression-free survival [months]


title: UKE_BCN_KGU #23

description: SAMPLE 23

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #26

description: SAMPLE 26

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #21

description: SAMPLE 21

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]


title: UKE_BCN_KGU #12

description: SAMPLE 12

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: tumor progression [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #18

description: SAMPLE 18

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #38

description: SAMPLE 38

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: overall survival [months]


title: UKE_BCN_KGU #11

description: SAMPLE 11

tag: tissue

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #14

description: SAMPLE 14

tag: age at time of surgery (years)

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: UKE_BCN_KGU #9

description: SAMPLE 9

tag: year of surgery

tag: sex (0=male, 1=female)


title: UKE_BCN_KGU #4

description: SAMPLE 4

tag: preoperative karnofsky performance status (%)

tag: progression-free survival [months]


title: UKE_BCN_KGU #7

description: SAMPLE 7

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #6

description: SAMPLE 6

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)


title: UKE_BCN_KGU #3

description: SAMPLE 3

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #2

description: SAMPLE 2

tag: tumor progression [0=no, 1=yes, 2=n/a]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]


title: UKE_BCN_KGU #13

description: SAMPLE 13

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: overall survival [months]


title: UKE_BCN_KGU #17

description: SAMPLE 17

tag: tissue

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: UKE_BCN_KGU #1

description: SAMPLE 1

tag: age at time of surgery (years)

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]