title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellD1

status: Public on Jun 05 2023

type: SRA

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

country: USA

institute: Walter Reed Army Institute of Research

library_source: transcriptomic single cell

data_processing:
Sequencing reads were trimmed with Trimmomatic(v0.36) (options: SLIDINGWINDOW:15:30 MINLEN:50)
Trimmed reads were aligned to the Macaca mulatta (reference assembly 8.0.1) plus SIVmac251 or SIVmac239 genomes (for AY69/T034, respectively) using HISAT2 (v2.1.0).
Global gene expression was quantified using htseq-count(v0.9.1) (options: -s no -a 2 -t exon)
Assembly: Mmul_8.0.1
Supplementary files format and content: tab-delimited text files include raw counts for each library

molecule: total RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Single cells in 96-well plates were lysed in SMART-Seq lysis buffer supplemented with RNAse inhibitor for 2 minutes at room temperature, vortexed, centrifuged, and frozen at -80C until cDNA library preparation.
Whole cDNA library was prepared using the SMART-Seq Ultra Low Input RNA kit.

tag: tissue

value: PBMC

tag: cell type

value: Memory CD4 T cell

tag: macaque id

tag: cell number

tag: d1a5 splice_characterization

value: no D1-A5 splice detected

tag: tatrev splice_characterization

value: no tat-rev splice detected

tag: siv presence

value: no SIV detected

tag: siv percent

value: SIV not > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellD2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellD12

value: D1-A5 splice detected

value: tat-rev splice detected

value: SIV detected

value: SIV > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellD1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellD12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellD11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellD10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellC10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellC10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellC10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellC10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellC10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellC10


title: PAAD_meta_resection_70

type: genomic

city: Berlin

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

department: Pathology

country: Germany

institute: Charité - Universitätsmedizin

hyb_protocol: Samples were hybridized to Infinium Human Methylation EPIC BeadChips (Illumina) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on Iscan (Illumina)

data_processing: We performed FunNorm (Minfi R package) and BMIQ (WateRmelon R package) normalization. We filtered probes with detection P>0.1, probes with a beadcount <3 in at least 5% of samples, non-cg probes, probes corresponding to SNPs, probes that align to multiple locations, and probes on sex chromosomes.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Pat 70

label_protocol: Supplier protocol (Illumina)

extract_protocol: Semi-automated DNA extraction was performed according to the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, Promega)

tag: subject

value: Pat 70

tag: disease

value: PAAD

tag: type

value: metastasis

tag: specimen

value: resection

tag: location

value: liver


title: iCCA_prim_resection_54

source_name: Pat 54

value: Pat 54

value: iCCA

value: primary


title: PAAD_meta_resection_65

source_name: Pat 65

value: Pat 65


title: PAAD_meta_resection_67

source_name: Pat 67

value: Pat 67


title: iCCA_prim_resection_60

source_name: Pat 60

value: Pat 60


title: iCCA_prim_resection_53

source_name: Pat 53

value: Pat 53

value: biopsy


title: PAAD_meta_resection_71

source_name: Pat 71

value: Pat 71


title: PAAD_meta_resection_66

source_name: Pat 66

value: Pat 66


title: iCCA_prim_resection_59

source_name: Pat 59

value: Pat 59


title: iCCA_prim_resection_56

source_name: Pat 56

value: Pat 56


title: PAAD_meta_resection_64

source_name: Pat 64

value: Pat 64


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellC10

value: PBMC

value: Memory CD4 T cell

value: no D1-A5 splice detected

value: no tat-rev splice detected

value: no SIV detected

value: SIV not > 1%


title: iCCA_prim_resection_49

source_name: Pat 49

value: Pat 49

value: iCCA

value: primary

value: resection

value: liver


title: PAAD_meta_resection_62

source_name: Pat 62

value: Pat 62

value: PAAD

value: metastasis


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellC10


title: PAAD_meta_resection_72

source_name: Pat 72

value: Pat 72


title: PAAD_meta_resection_68

source_name: Pat 68

value: Pat 68


title: iCCA_prim_resection_50

source_name: Pat 50

value: Pat 50

value: biopsy


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellC10

source_name: PBMC

value: PBMC

value: Memory CD4 T cell


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB9

value: no D1-A5 splice detected

value: no tat-rev splice detected


title: iCCA_prim_resection_55

source_name: Pat 55

value: Pat 55


title: iCCA_prim_resection_61

source_name: Pat 61

value: Pat 61


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB9

value: no SIV detected

value: SIV not > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellC10


title: iCCA_prim_resection_52

source_name: Pat 52

value: Pat 52

value: iCCA

value: primary

value: resection


title: iCCA_prim_resection_51

source_name: Pat 51

value: Pat 51

value: liver


title: PAAD_meta_resection_63

source_name: Pat 63

value: Pat 63

value: PAAD

value: metastasis


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB9

value: PBMC


title: iCCA_prim_resection_46

source_name: Pat 46

value: Pat 46


title: iCCA_prim_resection_48

source_name: Pat 48

value: Pat 48


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB9

value: Memory CD4 T cell

value: no D1-A5 splice detected

value: no tat-rev splice detected


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB9

value: tat-rev splice detected

value: SIV detected

value: SIV > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB9

value: SIV not > 1%


title: PAAD_meta_resection_69

source_name: Pat 69

value: Pat 69


title: iCCA_prim_resection_58

source_name: Pat 58

value: Pat 58

value: iCCA

value: primary

value: biopsy


title: iCCA_prim_resection_47

source_name: Pat 47

value: Pat 47

value: liver


title: iCCA_prim_resection_57

source_name: Pat 57

value: Pat 57

value: resection


title: iCCA_prim_resection_44

source_name: Pat 44

value: iCCA  type:primary  specimen:resection  location:liver

value: FFPE sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB9

value: PBMC

value: Memory CD4 T cell

value: no D1-A5 splice detected

value: no SIV detected


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB9

value: no tat-rev splice detected


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB8

value: SIV not > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB9


title: iCCA_prim_resection_43

source_name: Pat 43


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB8

value: D1-A5 splice detected

value: tat-rev splice detected

value: SIV detected

value: SIV > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB8


title: iCCA_prim_resection_45

source_name: Pat 45


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB7


title: iCCA_prim_resection_40

source_name: Pat 40


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB7


title: PAAD_meta_biopsy_37

source_name: Pat 37

value: PAAD  type:metastasis  specimen:biopsy  location:liver


title: PAAD_meta_biopsy_36

source_name: Pat 36


title: iCCA_prim_resection_39

source_name: Pat 39


title: iCCA_prim_resection_38

source_name: Pat 38


title: PAAD_prim_resection_34

source_name: Pat 34

value: PAAD  type:primary  specimen:resection  location:pancrease


title: PAAD_prim_resection_29

source_name: Pat 29


title: iCCA_prim_resection_42

source_name: Pat 42


title: PAAD_prim_resection_30

source_name: Pat 30


title: PAAD_prim_resection_26

source_name: Pat 26


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB7

source_name: PBMC


title: PAAD_prim_resection_33

source_name: Pat 33


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB7


title: PAAD_prim_resection_31

source_name: Pat 31


title: PAAD_prim_resection_24

source_name: Pat 24


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB6


title: PAAD_meta_biopsy_35

source_name: Pat 35


title: PAAD_prim_resection_32

source_name: Pat 32


title: iCCA_prim_resection_41

source_name: Pat 41


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB7


title: PAAD_prim_resection_25

source_name: Pat 25


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB6


title: PAAD_prim_resection_27

source_name: Pat 27


title: PAAD_prim_resection_28

source_name: Pat 28


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB6


title: PAAD_prim_resection_20

source_name: Pat 20


title: PAAD_prim_resection_21

source_name: Pat 21


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB6


title: PAAD_prim_resection_23

source_name: Pat 23


title: OC1371

city: Navi Mumbai

first: Manoj

middle: Balkrishna

last: Mahimkar

state: Maharashtra

address: Sector-22, Owe Village, Kharghar Node

country: India

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

description: Tumor tissue sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
RnBeads (v 1.12.1) and RnBeads.hg19 (v 1.13.1)
Normalized (Dasen method)

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted by using Qiagen simultaneous DNARNA extraction kit according to standard protocol.

tag: Sex

value: Male

value: Late


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB5


title: PAAD_prim_resection_19

source_name: Pat 19


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB6


title: PAAD_prim_resection_22

source_name: Pat 22


title: OC1656

description: Tumor tissue sample

value: Early


title: iCCA_prim_resection_17

source_name: Pat 17

value: iCCA  type:primary  specimen:resection  location:liver


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB5


title: OC1644

description: Tumor tissue sample

value: Female


title: iCCA_prim_resection_16

source_name: Pat 16

value: FFPE sample


title: OC1645

description: Tumor tissue sample


title: iCCA_prim_resection_15

source_name: Pat 15


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB5

source_name: PBMC

value: PBMC

value: Memory CD4 T cell


title: iCCA_prim_resection_14

source_name: Pat 14

value: iCCA  type:primary  specimen:biopsy  location:liver


title: OC1004

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB5

value: no D1-A5 splice detected

value: no tat-rev splice detected

value: no SIV detected


title: N74

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB5

value: SIV not > 1%


title: OC1652

description: Tumor tissue sample


title: OC1718

description: Tumor tissue sample


title: iCCA_prim_resection_18

source_name: Pat 18


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB5


title: N99

description: Normal tissue sample


title: OC1294

description: Tumor tissue sample


title: OC1716

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB4


title: OC2176

description: Tumor tissue sample


title: OC1932

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB4


title: OC1435

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB5


title: iCCA_prim_resection_13

source_name: Pat 13


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB4


title: OC1726

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB4


title: PAAD_meta_biopsy_11

source_name: Pat 11


title: OC2215

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB4


title: OC1496

description: Tumor tissue sample


title: iCCA_prim_resection_12

source_name: Pat 12


title: PAAD_meta_biopsy_10

source_name: Pat 10


title: iCCA_prim_biopsy_8

source_name: Pat 8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB4


title: OC1965

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB4


title: N71

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB4


title: N101

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB3


title: N69

description: Normal tissue sample


title: N100

description: Normal tissue sample


title: PAAD_meta_biopsy_3

source_name: Pat 3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB3


title: iCCA_prim_biopsy_5

source_name: Pat 5


title: iCCA_prim_biopsy_9

source_name: Pat 9


title: OC2201

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB3


title: OC1313

description: Tumor tissue sample


title: OC1405

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB3


title: OC1629

description: Tumor tissue sample


title: OC2185

description: Tumor tissue sample


title: OC1750

description: Tumor tissue sample


title: OC1947

description: Tumor tissue sample


title: OC2303

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB5

value: SIV detected


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB3


title: OC849

description: Tumor tissue sample


title: OC1487

description: Tumor tissue sample


title: PAAD_meta_biopsy_4

source_name: Pat 4


title: OC1445

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB3


title: PAAD_meta_biopsy_2

source_name: Pat 2


title: iCCA_prim_biopsy_7

source_name: Pat 7


title: iCCA_prim_biopsy_6

source_name: Pat 6


title: OC2202

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB2


title: N65

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB3


title: N97

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB2


title: OC1666

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB2

value: D1-A5 splice detected

value: tat-rev splice detected

value: SIV > 1%


title: OC1914

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB2


title: OC1440

description: Tumor tissue sample

value: Male


title: OC2300

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB2


title: OC996

description: Tumor tissue sample

value: Late


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB2


title: OC1910

description: Tumor tissue sample

value: Early


title: OC2192

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB1


title: N63

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB1


title: N62

description: Normal tissue sample


title: N61

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB1


title: N64

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB1


title: OC811

description: Tumor tissue sample


title: N43

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB1


title: OC2299

description: Leukoplakia tissue sample


title: OC1462

description: Tumor tissue sample


title: OC860

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB1


title: OC1896

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB12


title: OC1884

description: Leukoplakia tissue sample


title: OC2118

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB12


title: OC1649

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB12


title: PAAD_meta_biopsy_1

source_name: Pat 1

value: PAAD  type:metastasis  specimen:biopsy  location:liver


title: OC1508

description: Tumor tissue sample


title: OC1653

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB12


title: OC1984

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB12


title: OC1658

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB12


title: N96

description: Normal tissue sample

value: Female


title: OC2209

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB11


title: OC1566

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB11


title: OC1719

description: Tumor tissue sample


title: OC1667

description: Tumor tissue sample


title: OC2184

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB11


title: OC1846

description: Tumor tissue sample


title: OC2102

description: Tumor tissue sample


title: OC1358

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB11


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellB10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellB10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB12


title: N50

description: Normal tissue sample


title: N58

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellB10


title: OC1418

description: Tumor tissue sample


title: N59

description: Normal tissue sample


title: OC1323

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellB10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellB10


title: OC1760

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellB10


title: OC1845

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellB10


title: OC2214

description: Tumor tissue sample


title: OC2061

description: Leukoplakia tissue sample


title: OC2203

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellB10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellB10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA9


title: OC1001

description: Tumor tissue sample


title: N57

description: Normal tissue sample


title: OC2213

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA9


title: OC2067

description: Leukoplakia tissue sample


title: OC2122

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA9


title: OC1844

description: Tumor tissue sample


title: OC2204

description: Leukoplakia tissue sample


title: OC1565

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA9


title: OC1662

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA9


title: OC1869

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA9


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA9


title: OC1665

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA8


title: OC2052

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA8


title: OC1952

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellB10


title: OC1791

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA9


title: N56

description: Normal tissue sample


title: OC1669

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA8


title: OC1555

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA8


title: OC1501

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA8


title: OC2048

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA8


title: OC1823

description: Tumor tissue sample


title: N55

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA8


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA8


title: OC1367

description: Tumor tissue sample


title: OC1560

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA7


title: OC1663

description: Tumor tissue sample


title: N72

description: Normal tissue sample


title: OC2293

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA7


title: OC1664

description: Tumor tissue sample


title: OC1464

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA7


title: OC2112

description: Tumor tissue sample


title: N46

description: Normal tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA7


title: OC1377

description: Leukoplakia tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA6


title: OC588

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA6


title: OC1507

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA7


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA6


title: OC1722

description: Tumor tissue sample


title: OC2109

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA6


title: OC1983

description: Tumor tissue sample


title: OC1891

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA6


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA7


title: OC1651

description: Tumor tissue sample


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA6


title: TLBL39  Pediatric T-cell lymphoblastic lymphoma

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

country: Spain

institute: IDIBAPS

description:
Cytoscan HD
TLBL39

hyb_protocol: Samples were hybridized onto Cytoscan HD arrays Cytoscan HD and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Nexus biodiscovery 9.0 edition Software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: Pleural Effusion

label_protocol: CytoScan™ Reagent Kit / 901808,t/GPL16131

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

value: Pediatric T-cell lymphoblastic lymphoma

tag: gender

tag: tissue preparation

value: frozen tissue


title: OC1331

description: Tumor tissue sample


title: TLBL35 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL35

source_name: Cervical LN


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA6

source_name: PBMC

value: PBMC

value: Memory CD4 T cell


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA6

value: no D1-A5 splice detected


title: TLBL34 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL34

source_name: Laterocervical LN


title: Pat18

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description:
tumor_18
Gene expression of gastroesophageal junction cancer from patient with fast progressing

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of HTA_2.0 from Thermo Fischer Scientific. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: gastroesophageal junction cancer FFPE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RecoverAll™ Multi-Sample RNA/DNA Isolation Workflow

value: gastroesophageal junction cancer FFPE

tag: progression

value: fast progressing group (PFS<12)


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA6

tag: tissue

value: no tat-rev splice detected

value: no SIV detected

value: SIV not > 1%


title: Pat16

description:
tumor_16
Gene expression of gastroesophageal junction cancer from patient with fast progressing


title: Pat14

description:
tumor_14
Gene expression of gastroesophageal junction cancer from patient with fast progressing


title: TLBL33 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL33


title: Pat10

description:
tumor_10
Gene expression of gastric cancer from patient with fast progressing

source_name: gastric cancer FFPE

value: gastric cancer FFPE


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA5

tag: cell type


title: Pat19

description:
tumor_19
Gene expression of gastroesophageal junction cancer from patient with fast progressing


title: TLBL31 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL31

source_name: LN


title: Pat15

description:
tumor_15
Gene expression of gastric cancer from patient with fast progressing


title: TLBL30 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL30

source_name: Mediastinal mass


title: Pat13

description:
tumor_13
Gene expression of gastric cancer from patient with fast progressing


title: Pat17

description:
tumor_17
Gene expression of gastroesophageal junction cancer from patient with fast progressing


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA5

tag: macaque id


title: Pat12

description:
tumor_12
Gene expression of gastroesophageal junction cancer from patient with fast progressing


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA5

tag: cell number


title: TLBL29 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL29


title: Pat11

description:
tumor_11
Gene expression of gastric cancer from patient with fast progressing


title: Pat6

description:
tumor_6
Gene expression of gastric cancer from patient with long-term responding

value: long-term responding (PFS>=12)


title: Pat8

description:
tumor_8
Gene expression of gastric cancer from patient with fast progressing


title: Pat9

description:
tumor_9
Gene expression of gastroesophageal junction cancer from patient with fast progressing


title: Pat7

description:
tumor_7
Gene expression of gastric cancer from patient with long-term responding


title: Pat4

description:
tumor_4
Gene expression of gastroesophageal junction cancer from patient with long-term responding


title: TLBL21 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL21

value: Male


title: Pat2

description:
tumor_2
Gene expression of gastric cancer from patient with long-term responding


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA5

tag: d1a5 splice_characterization


title: Nor4

description:
control_4
Gene expression from gastric mucosa in control patient

source_name: gastric mucosa FFPE

value: gastric mucosa FFPE

value: control


title: Pat5

description:
tumor_5
Gene expression of gastric cancer from patient with long-term responding


title: Pat3

description:
tumor_3
Gene expression of gastroesophageal junction cancer from patient with long-term responding


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA5

tag: tatrev splice_characterization

value: tat-rev splice detected

value: SIV detected


title: Nor5

description:
control_5
Gene expression from gastric mucosa in control patient


title: Neutrophils, FOXO3 KO,6

city: New Orleans

first: Suzana

middle: D

last: Savkovic

state: LA

address: 1430 Tulane Ave.

department: Pathology and Laboratory Medicine

institute: Tulane University

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to hg38 genome using STAR(v.2.6.1d).  Abundance levels were calculated using Kallisto(v.0.46.0) and differential expression testing performed using DESeq2.
Assembly: mouse, mm10
Supplementary files format and content: Excel files with TPMs and results of differential expression testing from DESeq2

organism: Mus musculus

source_name: Neutrophils (PMNs)

extract_protocol:
Zymogen, Dnase Treated
High Output Paired End Read

tag: strain

value: Mouse (C57BL/6)

value: Neutrophils (PMNs)

tag: genotype

value: FOXO3 KO

tag: treatment

value: PMNs were isolated from  mouse peritoneum following casein injection.


title: TLBL20 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL20

value: Pediatric T-cell lymphoblastic lymphoma

value: frozen tissue


title: Neutrophils, FOXO3 KO,4


title: TLBL19 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL19


title: Neutrophils, FOXO3 KO,5


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA5

value: PBMC

value: Memory CD4 T cell

value: no D1-A5 splice detected

tag: siv presence

tag: siv percent


title: Neutrophils, FOXO3 KO,3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA5

value: no tat-rev splice detected

value: no SIV detected

value: SIV not > 1%


title: TLBL18 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL18

value: Male


title: Neutrophils, WT, 5

value: WT


title: Nor1

description:
control_1
Gene expression from gastric mucosa in control patient

value: gastric mucosa FFPE

value: control


title: Neutrophils, FOXO3 KO,1


title: Nor2

description:
control_2
Gene expression from gastric mucosa in control patient


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA5


title: Neutrophils, WT, 4


title: TLBL17R Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL17R


title: Neutrophils, WT, 3


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA5


title: Neutrophils, WT, 2


title: TLBL17 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL17


title: Nor3

description:
control_3
Gene expression from gastric mucosa in control patient


title: TLBL16 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL16

source_name: Aspirate supraclavicular LN

value: Female


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA5


title: Neutrophils, FOXO3 KO,2

value: Mouse (C57BL/6)


title: TLBL13 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL13

source_name: Right supraclavicular LN


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA4


title: TLBL11 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL11

source_name: Left Laterocervical LN


title: TLBL12R Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL12R


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA4


title: TLBL9 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL9

source_name: Left Submandibular LN


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA4


title: R2_MUT

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

description: Short Nascent Strand Replicate 2

library_source: genomic

data_processing:
Quality control of sequenced reads was performed using FastQC (Babraham Institute)
Reads were aligned to the Homo sapiens genome (hg19 build) (Ensembl v75) using Bowtie2 (v.2.3.4.2)
Picard (v.2.18.17) (Broad Institute) was used to remove duplicate reads.
Peaks were called using MACS2 (v. 2.1.0.20151222) (threshold q=0.1) and EPIC2 (v. 0.0.40) (threshold FDR=0.1)
Bigwig files were generated with deepTools (v.3.2.0)
Assembly: hg19
Supplementary files format and content: bigWig files
Library strategy: SNS-seq

source_name: Colorectal Cancer

growth_protocol: HCT116 cells were grown in RPMI medium at 37ºC

extract_protocol:
Phenol:chlorophorm
Based on Blecher-Gonen et al. 2013

value: HCT116 cell line stably expressing MUT-ORC1-3xFlag

value: Untreated

tag: replicate

tag: molecule subtype

value: Nascent Strands (ssDNA converted to dsDNA)


title: TLBL8 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL8

value: Pediatric T-cell lymphoblastic lymphoma


title: R2_WT

description: Short Nascent Strand Replicate 2

value: HCT116 cell line stably expressing WT-ORC1-3xFlag


title: R1_MUT

description: Short Nascent Strand Replicate 1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA4

value: PBMC


title: Neutrophils, WT, 1

value: Neutrophils (PMNs)

value: PMNs were isolated from  mouse peritoneum following casein injection.


title: TLBL5 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL5

value: frozen tissue


title: MUT2_S7

description: CDC45 ChIP-seq with MUT-ORC1-3xFlag

data_processing:
Quality control of sequenced reads was performed using FastQC (Babraham Institute)
Sequenced reads were trimmed for adaptor sequence with Trimmomatic (Bolget et al., 2014)
Reads were aligned to the Homo sapiens genome (hg19 build) (Ensembl v75) using Bowtie2 (v.2.3.4.2)
Picard (v.2.18.17) (Broad Institute) was used to mark duplicate reads.
Bigwig files were generated with deepTools (v.3.2.0)
Assembly: hg19
Supplementary files format and content: bigWig files

treatment_protocol: Untreated

tag: chip antibody


title: R1_WT

description: Short Nascent Strand Replicate 1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA4

value: Memory CD4 T cell

value: no D1-A5 splice detected

value: no tat-rev splice detected

value: no SIV detected


title: MUT2_S28

description: CDC45 ChIP-seq with MUT-ORC1-3xFlag


title: WT2_S26

description: CDC45 ChIP-seq with WT-ORC1-3xFlag


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA4

value: SIV not > 1%


title: T cells from spleen - 2

city: Portland

first: Jeffrey

last: Nolz

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health & Science University

description: RMA expression value derived from Transcriptome Analysis Console; core-exon analysis

hyb_protocol: Samples were hybridized with Clariom S, mouse microarray (Affymetrix) and scanned at the OHSU Gene Profiling Shared Resource.

scan_protocol: Array scanning was performed using Affymetrix Command Console (AGCC) v3.1.1 according to the manufacturers instructions.

data_processing: Expression analysis was performed using Affymetrix Transcriptome Analysis Console v.4.0.2.

source_name: T cells from spleen

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: P14 TCR-transgenic CD8+ T cells expressing an IFNg - YFP reporter gene were transferred into naïve C57Bl/6 female mice that were then infected with Vaccinia virus expressing the GP33-41 LCMV peptide.

extract_protocol: T cells from single cells suspensions generated from tissues were stained with CD45, CD8a, and Thy1.1 antibodies and were sorted directly into 1 milliliter of TRIzol. RNA was extracted from TRIzol according to the manufacturers instructions.  Extracted RNA was further purified using an RNeasy Micro Kit (Qiagen) according to the manufacturers instructions.

treatment_protocol: Mice were infected on both the left and right ear skin with 5 x 10^6 PFU VacV-GP33. Tissue (skin and spleen) was collected on day 7 after infection.

tag: Sex


title: YFP- T cells from skin - 3

source_name: T cells from skin


title: YFP+ T cells from skin -3


title: T cells from spleen - 3


title: T cells from spleen - 1


title: YFP- T cells from skin - 2


title: YFP+ T cells from skin - 2


title: WT2_S5

description: CDC45 ChIP-seq with WT-ORC1-3xFlag


title: YFP+ T cells from skin - 1


title: MUT1_S28

description: CDC45 ChIP-seq with MUT-ORC1-3xFlag


title: YFP- T cells from skin - 1


title: MUT1_S7

description: CDC45 ChIP-seq with MUT-ORC1-3xFlag


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA4


title: TLBL2 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL2

tag: gender

value: Male

tag: tissue preparation


title: WT1_S25

description: CDC45 ChIP-seq with WT-ORC1-3xFlag


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA4

tag: tissue


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA3

tag: cell type


title: EV-A71-24h

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

country: China

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh_38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Human neuroblastoma cell line SH-SY5Y

growth_protocol: The human neuroblastoma cell line SH-SY5Y, purchased from Jennino Biological Technology, was propagated in Dulbecco’s modified Eagle’s medium (DMEM) (Corning, USA) with the addition of 10% fetal bovine serum (FBS; Gibco, USA), 2 mmol/L glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin (Gibco, USA) at 37℃ in a humidified 5% CO2/95% air atmosphere.

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EV71 (sub-genotype C4, GenBank: EU812515.1), isolated from an epidemic in Fuyang, China, in 2008, was applied throughout the study. First, SH-SY5Y cells were seeded into 6-well plates at a density of 5 × 105 cells per well. Then, EV71 was inoculated in SH-SY5Y cells at a multiplicity of infection (MOI) of 1. The infected cells were collected at 0, 12 and 24 h post infection (hpi). Cells infected with EV71 for 0 hpi were designated as the control group.

tag: cell line

value: Human neuroblastoma cell line SH-SY5Y

tag: time

value: 24 hpi


title: WT1_S4

description: CDC45 ChIP-seq with WT-ORC1-3xFlag


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA3

tag: macaque id

tag: cell number

tag: d1a5 splice_characterization

value: D1-A5 splice detected

value: tat-rev splice detected

value: SIV detected

value: SIV > 1%


title: CVS-48h

treatment_protocol: The CVS-11 strain, obtained from National Institutes for Food and Drug Control and propagated in Vero cells, was used in this study. SH-SY5Y cells were seeded into 6-well plates at a density of 5 × 105 cells/well and infected with CVS at a multiplicity of infection (MOI) of 1. Subsequently, the infected cells were harvested at 0, 12 and 24 h post infection (hpi). Moreover, cells treated with CVS for 0 hpi were defined as control group.

value: 48 hpi


title: CVS-24h


title: MSB94

city: Rochester

first: Kim

last: Lauer

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
MAP-R Seqversion 3.1.3 was usedto align the raw RNA seq reads to the reference human genome build hg38
QC was performed by FastQC pre- and post-read trimming
RNA paired end reads were aligned using the STAR 2.6.1c
Gene counts were generated using subread featuerCounts
Assembly: hg38
Supplementary files format and content: tab-delimited files with RNA-Seq gene expression

source_name: tumor

extract_protocol:
Sample metadata, including tumor purity, was determined by board-certified pathologists. Samples were required to meet a tumor cellularity as a ratio of tumor to normal nuclei of 20%. Macrodissection was utilized as needed to enrich specimens below the 20% threshold. Solid tumor total nucleic acid was extracted from the FFPE tissue sections using Chemagic 360 sample-specific extraction kits (Perkin Elmer) and digested by proteinase K. RNA was purified from the total nucleic acid by DNase-I digestion.
Tempus xT RNA-seq protocol for FFPE solid tumors using transcriptome-capture probes.

value: tumor

value: DDLPS

value: Surgical Resection


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA3

source_name: PBMC

value: PBMC

tag: tatrev splice_characterization


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA4

value: Memory CD4 T cell


title: CVS-0h

value: 0 hpi


title: TLBL1 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL1

value: Pediatric T-cell lymphoblastic lymphoma

value: frozen tissue


title: TLBL3 Pediatric T-cell lymphoblastic lymphoma

description:
Cytoscan HD
TLBL3

source_name: Right laterocervical LN


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA3

value: no D1-A5 splice detected

value: no tat-rev splice detected

value: SIV not > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA3

value: no SIV detected


title: MSB91

value: PLPS

tag: treatment


title: CV-A16-12h

treatment_protocol: The CV-A16-G20 strain (sub-genotype B, GenBank: JN590244.1), isolated from an HFMD patient in Guangxi, China, in 2010, was used in this study. SH-SY5Y cells were seeded into 6-well plates at a density of 5 × 105 cells/well and infected with CV-A16 at a multiplicity of infection (MOI) of 1. Subsequently, the infected cells were harvested at 0, 12 and 24 h post infection (hpi). Moreover, cells treated with CV-A16 for 0 hpi were defined as control group.

value: Human neuroblastoma cell line SH-SY5Y

value: 12 hpi


title: CV-A16-0h


title: MSB93

value: GIST


title: EV-A71-12h


title: MSB90


title: MSB95


title: A31N

city: Greenville

first: Ted

middle: G.

last: Graber

state: NC

address: 600 Moye BLVD., Mail Route 668

department: Physical Therapy

institute: East Carolina University

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.5.4b) using the mouse mm10 genome .
Reads were aligned to the mouse reference using the STAR software version 2.5.4b with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR. Small non-coding RNAs were not counted.
Differential gene expression was analyzed with the R (version 3.5.1) software DESeq2 (version 1.22.2)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene

source_name: tibialis anterior

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Poly-A plus RNA was enriched from  ~0.1 ug of total RNA and used to generate libraries using the NEBNext Ultra II Kit.

tag: age

value: elderly (28+ months old)

tag: type

value: Second NextSeq550 Run


title: CV-A16-24h

value: 24 hpi


title: EV-A71-0h


title: MSB99

value: tumor

value: DDLPS

value: Surgical Resection


title: A17N


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA3

value: PBMC

value: Memory CD4 T cell

tag: siv presence

tag: siv percent


title: MSB9


title: 4716-14, Restored + CsA, 72hrs

city: Philadelphia

first: Jonuelle

last: Acosta

state: PA

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Fastq files for each sample were aligned against the mouse genome mm10 (GRCm39) using HISAT2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing TPMs in all samples

extract_protocol:
RNA was isolated from cell lines using the Rneasy Mini Kit (Qiagen) per manufacturer's instructions.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) as  per the manufacturer's instructions and library quality was determined used the Agilent  DNA 1000 Kit on a 2100 BioAnalyzer.

value: Small cell lung cancer

tag: genotype

value: Type V

value: 4-OHT + CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA3

value: no D1-A5 splice detected

value: no tat-rev splice detected

value: SIV not > 1%


title: A35L


title: A35N


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA3

value: no SIV detected


title: 4716-14, Restored, 72hrs


title: MSB87


title: A19R


title: MSB92


title: 4716-14, Control + CsA, 72hrs

value: CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA3


title: 4716-14, Control, 72hrs

value: Vehicle


title: MSB86

value: UPS


title: A31B

value: elderly (28+ months old)

value: Second NextSeq550 Run


title: A34N


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA2


title: MSB83

value: tumor

value: LMS


title: MSB84

value: ULMS

value: Surgical Resection


title: A23R_repeat

value: adult (6 months old)


title: 4716-11, Control, 72hrs

value: Small cell lung cancer

value: Type D


title: A29N


title: A22B_repeat


title: 4716-10, Restored + CsA, 72hrs

value: Type V

value: 4-OHT + CsA


title: 4716-11, Control + CsA, 72hrs


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA2

value: PBMC

value: Memory CD4 T cell

value: D1-A5 splice detected

value: tat-rev splice detected

value: SIV detected

value: SIV > 1%


title: A23N_repeat


title: 4716-11, Restored + CsA, 72hrs


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA2

value: no D1-A5 splice detected

value: no tat-rev splice detected

value: no SIV detected

value: SIV not > 1%


title: MSB81

value: tumor

value: GIST


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA2


title: 4716-10, Restored, 72hrs


title: MSB8

value: Surgical Resection


title: 4716-11, Restored, 72hrs

value: Small cell lung cancer


title: MSB78

value: DESMOID


title: 4716-10, Control + CsA, 72hrs

value: Type V

value: CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA3

value: PBMC


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA2

value: Memory CD4 T cell


title: A23B_repeat

value: adult (6 months old)

value: Second NextSeq550 Run


title: MSB85

value: AS


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA2

value: SIV detected


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA2

value: no D1-A5 splice detected


title: 4716-10, Control, 72hrs

value: Vehicle


title: MSB82

value: LMS


title: MSB74


title: MSB72

value: DDLPS


title: 4711-18, Restored + CsA, 72hrs

value: Type D

value: 4-OHT + CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA2

value: no tat-rev splice detected

value: SIV not > 1%


title: A22L_repeat


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA2

value: no SIV detected


title: 4711-18, Control + CsA, 72hrs

value: Small cell lung cancer


title: MSB70

value: tumor

value: GIST

value: Surgical Resection


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA2

value: PBMC

value: Memory CD4 T cell


title: A22N_repeat

value: adult (6 months old)

value: Second NextSeq550 Run


title: MSB7

value: SFT


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA1

value: no D1-A5 splice detected


title: MSB68


title: 4711-11, Restored + CsA, 72hrs

value: Type V


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA1


title: 4711-18, Control, 72hrs

value: Vehicle


title: A7

value: older adults (24 months old)

value: First NextSeq550 Run


title: A15


title: A4


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA1

value: no tat-rev splice detected


title: A18


title: A23L_repeat


title: A13


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA1

value: SIV not > 1%


title: MSB66

value: DDLPS


title: A12


title: MSB67


title: 4711-11, Control + CsA, 72hrs

value: Small cell lung cancer

value: CsA


title: 4711-11, Restored, 72hrs


title: MSB71

value: tumor

value: MPNST


title: 4711-18, Restored, 72hrs

value: Type D


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA1

value: PBMC

value: Memory CD4 T cell

value: no SIV detected


title: A10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA1


title: MSB64

value: PARAGANGLIOMA

value: Surgical Resection


title: MSB63

value: LMS


title: A23R

value: adult (6 months old)


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA1

value: no D1-A5 splice detected


title: 4711-1, Restored + CsA, 72hrs

value: 4-OHT + CsA


title: 4711-11, Control, 72hrs

value: Type V

value: Vehicle


title: MSB62


title: 4711-1, Restored, 72hrs


title: 4711-1, Control + CsA, 72hrs


title: A22B

value: First NextSeq550 Run


title: MSB61


title: A23N


title: 4711-1, Control, 72hrs

value: Small cell lung cancer


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA1

value: no tat-rev splice detected

value: SIV not > 1%


title: A22N


title: MSB59

value: tumor

value: DFSP


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA1

value: PBMC


title: MSB60

value: DDLPS


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA12

value: Memory CD4 T cell

value: tat-rev splice detected

value: SIV detected

value: SIV > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA1

value: no SIV detected


title: MSB58

value: LMS

value: Surgical Resection


title: A23B

value: adult (6 months old)


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA12

value: no D1-A5 splice detected


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA12


title: MSB55

value: GIST


title: 4716-14, Control, Day 2

data_processing:
p53 ChIP-seq data was aligned to mouse genome mm10 (GRCm39) by bowtie2 with default parameters
Peak calling was performed by MACS2 with a p-value threshold of 1E-10.
ChIP-seq signal in a specific region was calculated by the normalized RPM. Briefly, ChIP-seq reads aligning to the region were extended by 100 bp and the density of reads per bp was calculated using featureCounts. The density of reads in each region was normalized to the total number of million mapped reads, producing read density in units of reads per million mapped reads per bp (RPM per bp).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
1 x 107 SCLC cells were harvested and cross-linked at room temperature by resuspending in PBS containing 1% formaldehyde for 2.5 minutes. The reaction was quenched by addition of glycine to a final concentration of 0.125 M. After washing with cold 1X PBS, cells were lysed in 1mL sonication buffer ( 0.25% Sarkosyl, 1 mM DTT, and protease inhibitors into RIPA buffer). Cell suspension was sonicated using a Covaris S220 Focused Ultrasonicator until chromatin was sheared to a size range of around 200bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs) size selection, as per the manufacturer's instructions, with the following conditions: 30uL ChIP sample or 5uL input sample used when end prepping, adaptor was diluted 10-fold for ChIP samples but not diluted for input, 200 bp bead based size selection used for all samples, 14 cycles used for PCR enrichment of ChIP samples and 7 cycles for input samples. Library quality was determined used the Agilent DNA 1000 Kit on a 2100 BioAnalyzer (Agilent).

value: Small cell lung cancer

value: Type V

value: Vehicle


title: 4716-14, Restored + CsA, Day 2

value: 4-OHT + CsA


title: 4716-14, Control + CsA, Day 2

value: Vehicle + CsA


title: MSB52

value: tumor


title: 4716-14, Restored, Day 2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA12

value: PBMC

value: no tat-rev splice detected

value: SIV not > 1%


title: MSB50


title: Mechanically Stimulated Implant, 4 weeks

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm9 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Assembly: mm9 (mouse)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Mechanically Stimulated Implant Capsule Tissue, 2 weeks

growth_protocol: Mice were implanted with standard or mechanically stimulated silicone implants. Capsule tissue was explanted after either 2 weeks or 4 weeks for analysis.

extract_protocol:
Tissue was enzymatically digested, cells were collected and washed. These cellular suspensions were then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: Either standard or mechanically stimulated silicone implants were implanted subcutaneously in mice. Mice who received mechanically stimulated implants underwent mechanical stimulation for 8 days.

tag: passages

value: Freshly isolated and submitted

value: Mechanically Stimulated Implant

value: Capsule Tissue

value: explanted after 4 weeks


title: MSB5

value: Surgical Resection


title: 4716-11, Control + CsA, Day 2

value: Type D


title: 4716-14, Input, Day 2

value: Input


title: Standard Murine Implant, 4 weeks

source_name: Murine Standard Silicone Implant Capsule Tissue, 4 weeks

value: Standard Murine Implant


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA12

value: Memory CD4 T cell

value: no D1-A5 splice detected

value: no SIV detected


title: MSB49

value: DESMOID


title: Standard Murine Implant, 2 weeks

source_name: Murine Standard Silicone Implant Capsule Tissue, 2 weeks

value: explanted after 2 weeks


title: Mechanically Stimulated Implant, 2 weeks


title: 4716-11, Restored + CsA, Day 2

value: Small cell lung cancer

value: 4-OHT + CsA


title: MSB47

value: tumor

value: ULMS


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA12

value: PBMC

value: no tat-rev splice detected

value: SIV not > 1%


title: 4716-11, Restored, Day 2


title: MSB46

value: SFT


title: A23L

value: adult (6 months old)

value: First NextSeq550 Run


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA12


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA12


title: Pushen2，Day28

city: Nanjing

first: Yuan

last: Zhang

address: No. 87 Dingjiaqiao

institute: School of Medicine, Southeast University,

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: brain

growth_protocol: The functional recovery research of  in ischemic stroke by Photothrombotic stroke (PT) model

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pushen (drug approval number: Z20040074;  batch number: 20082403;  Suzhong pharma) was dissolved in the vehicle of ultrapure water, and it was administered by oral gavage at 24 hours after surgery continuously for 28 days.  Mice in the Sham and Vehicle group were administered with a vehicle of ultrapure water equal to the Pushen group.

value: brain

value: WT

value: Pushen (392mg/kg)


title: Pushen1，Day28

value: Pushen (391mg/kg)


title: PT3，Day28

value: ultrapure water


title: 4716-11, Control, Day 2

value: Type D

value: Vehicle


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA11

value: Memory CD4 T cell

value: no D1-A5 splice detected

value: no SIV detected


title: A22L


title: 4716-11, Input, Day 2

value: Small cell lung cancer

value: Input


title: 4716-10, Control, Day 2

value: Type V


title: Pushen3，Day28

value: Pushen (393mg/kg)


title: MSB45

value: tumor

value: UPS

value: Surgical Resection


title: 4716-10, Restored + CsA, Day 2

value: 4-OHT + CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA12

value: PBMC

value: no tat-rev splice detected

value: SIV not > 1%


title: PT1，Day28

value: brain

value: WT

value: ultrapure water


title: MSB44

value: GIST


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA11

value: Memory CD4 T cell

value: no D1-A5 splice detected


title: 4716-10, Restored, Day 2

value: Small cell lung cancer


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA11

value: no SIV detected


title: MSB41

value: DFSP


title: MSB42


title: 4716-10, Control + CsA, Day 2

value: Type V

value: Vehicle + CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA12

value: SIV detected


title: Sham2，Day28


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA11


title: Sham3，Day28


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA11


title: MSB40

value: tumor

value: DDLPS

value: Surgical Resection


title: 4716-10, Input, Day 2

value: Input


title: MSB39


title: Sham1，Day28


title: PT2，Day28


title: MSB37


title: MSB43


title: 4711-18, Control, Day 2

value: Type D

value: Vehicle


title: 4711-18, Restored + CsA, Day 2

value: 4-OHT + CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA11

value: PBMC

value: no tat-rev splice detected

value: SIV not > 1%


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA11

value: Memory CD4 T cell

value: no D1-A5 splice detected


title: MSB36

value: GIST


title: 4711-18, Restored, Day 2

value: Small cell lung cancer


title: MSB35

value: WDLPS


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA11

value: no SIV detected


title: MSB33

value: PLPS


title: 4711-18, Control + CsA, Day 2

value: Vehicle + CsA


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA11


title: MSB3

value: tumor

value: DDLPS


title: 4711-11, Control + CsA, Day 2

value: Type V


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate9 wellA10


title: ThPOK-/- modified GMP-gate Antibody Derived Tags

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: GMP ADT

data_processing:
The 10x Genomics libraries were each sequenced to a depth of ~0.9 to 1-million reads (modGMP) or ~300 million reads for cKit. The 10x Genomics libraries were aligned to the mouse genome (mm10), with unique molecular index quantified (UMI) gene counts obtained using the Cell Ranger workflow (v2.1.0), from the automated filtered cell barcode output. Using the default filtered cellular barcodes, the associated sparse-filtered matrix files were processed in AltAnalyze, ICGS2 and cellHarmony as previously described to obtain normalized gene counts (counts per ten thousands UMIs) and cell population identitites. SoupX was used to remove ambient RNAs with a 10% threshold to produce the resultant sparse matrix results.
The antibody derived tag (ADT)-linked library for each 10x Genomics capture was sequenced separately from the same 10x Genomics sample. To obtain ADT UMIs for each cellular barcode, each ADT barcode was supplied as input in the CITE-Seq-Counts python program with the ADT fastqs files.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq.SoupX.metadata.txt: Cell Clusters: cellHarmony assigned clusters for wild-type and mutant cells with UMAP coordinates
Supplementary_files_format_and_content: Tags-mouseADT.csv: ADT: Antibody Derived Tag names and barcodes
Supplementary_files_format_and_content: cKit.cell-types.UMAP.coordinates.txt: Cell Clusters: cellHarmony assigned clusters for cKit cells with UMAP coordinates
Supplementary_files_format_and_content: cKit-reference-centroids.txt: cellHarmony reference centroids for cell-type classification

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with TotalSeq antibodies and fluorchome-conjugated antibodies for FACS-sorting, then 15,000 cells per sample were loaded in each lane of a Chromium Controller Instrument (10x Genomics).
The 10x Genomics single cell 3’ v3 assay protocol was followed as described until the cDNA amplification step. The cDNA amplification mix was modified to include 1 mL of a 2 mM dilution of ADT PCR additive primer (5’-CCTTGGCACCCGAGAATT*C*C-3’ where * indicates a phosphorotioate bond) and 1 mL of a 2 mM dilution of HTO PCR additive primer (5’-GTGACTGGAGTTCAGACGTGTGC*T*C-3’ where * indicates a phosphorotioate bond) when applicable, replacing 1-2 mL of water. An 0.6X SPRI selection was performed, and the resulting supernatant was set aside (contains ADTs and HTOs) while the beads (mRNA-derived cDNA) were processed according to the standard 10x Genomics single cell 3’ v2 assay protocol. The ADTs and HTOs were further processed according to the CITE-Seq protocol (New York Genome Center, https://cite-seq.com/protocol/). ADT and mRNA libraries were sequenced separately.
scRNA-Seq with Illumina NovaSeq and ADT with Illumina HiSeq 4000

tag: strain

value: Bone marrow derived Modified GMP

value: ThPOK-/-

tag: cdna synthesis

value: ThPOK-/- ModGMP ADT


title: Wild-Type GFP modified GMP-gate Antibody Derived Tags

description: GMP ADT

value: Wild-type

value: WT GFP ModGMP ADT


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate8 wellA10

data_processing:
Sequencing reads were trimmed with Trimmomatic(v0.36) (options: SLIDINGWINDOW:15:30 MINLEN:50)
Trimmed reads were aligned to the Macaca mulatta (reference assembly 8.0.1) plus SIVmac251 or SIVmac239 genomes (for AY69/T034, respectively) using HISAT2 (v2.1.0).
Global gene expression was quantified using htseq-count(v0.9.1) (options: -s no -a 2 -t exon)
Assembly: Mmul_8.0.1
Supplementary files format and content: tab-delimited text files include raw counts for each library

tag: tissue

value: PBMC

value: no tat-rev splice detected

value: SIV not > 1%


title: 4711-11, Control, Day 2

tag: cell type

value: Vehicle


title: MSB27

value: UPS

value: Surgical Resection


title: 4711-11, Restored + CsA, Day 2

tag: cell line

value: Small cell lung cancer

value: 4-OHT + CsA


title: MSB29

value: LMS


title: 4711-11, Restored, Day 2


title: MCF7_KAT6 inhibitor_120hr_R2

city: San Diego

first: Chi-Yeh

last: Chung

state: CA

address: 10770 Science Center Drive

institute: Pfizer Inc.

data_processing:
For ATAC-seq data analysis, paired-end sequencing reads for each sample were mapped to hg38 human reference genome with Bowtie2 (Langmead and Salzberg, 2012) using the following parameters: -t -X 2000 --no-mixed --no-discordant --trim-to 3:30. Sam files were converted into Bam with Samtools. Peak calling was performed with MACS2 (Zhang et al., 2008) using these parameters: callpeak -g hs --nolambda --nomodel --shift -100 --extsize 200 --bdg --SPMR -q 5e-2. Peaks overlap with ENCODE black list regions were removed from downstream analysis using Bedtools. Bedgraph files were converted to Bigwig using bedGraphToBigWig (Kent et al., 2010) and signal tracks were visualized with IGV (Robinson et al., 2011). To correct for ATAC-seq bias, we extracted genome wide signal at 100 bp resolution using DeepTools (Ramirez et al., 2014), and performed quantile normalization on the signal data using the R package preprocessCore (https://rdrr.io/bioc/preprocessCore/).
Assembly: hg38
Supplementary files format and content: BigWig files of normalized ATAC-seq signal; bed files of differential called peaks

growth_protocol: Cells were maintained based on ATCC recommendations

extract_protocol: qPCR was performed on the DNA library to decide the optimal cycle number for library amplification. The library was then purified with Ampure XP beads (A63880, Beckman Coulter), quantified using Qubit (Qubit dsDNA HS Assay Kit, Q32851, Thermo Fisher Scientific) and checked for size distribution using 4200 TapeStation (High Sensitivity D1000 ScreenTape, 5067-5584, Agilent Technologies). Sequencing was performed with Illumina HiSeq4000 (50 bp PE, Nextera v2 libraries).

treatment_protocol: T47D, ZR751 and MCF7 cells were treated in triplicate with DMSO control or 30nM CTx-648/PF-9363 for 2 or 5 days and processed with the transposition assay. Briefly, 50,000 nuclei from each sample were used in each reaction with 20 µl of transposition mix and incubated at 37oC for 60 minutes.

value: Breast cancer cells

value: WT

value: KAT6 inhibitor

tag: time


title: MCF7_KAT6 inhibitor_120hr_R3


title: MCF7_KAT6 inhibitor_120hr_R1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate7 wellA10

extract_protocol:
Single cells in 96-well plates were lysed in SMART-Seq lysis buffer supplemented with RNAse inhibitor for 2 minutes at room temperature, vortexed, centrifuged, and frozen at -80C until cDNA library preparation.
Whole cDNA library was prepared using the SMART-Seq Ultra Low Input RNA kit.

value: Memory CD4 T cell

tag: macaque id

value: no D1-A5 splice detected

value: no SIV detected


title: MCF7_DMSO_120hr_R3

value: DMSO


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA11

tag: cell number

value: D1-A5 splice detected

value: tat-rev splice detected

value: SIV detected


title: MCF7_DMSO_120hr_R2


title: MSB26

value: tumor


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate6 wellA10

value: PBMC

tag: d1a5 splice_characterization

value: no tat-rev splice detected

value: SIV not > 1%


title: MCF7_DMSO_120hr_R1


title: MSB23

value: GIST

value: Surgical Resection


title: 4711-1, Control + CsA, Day 2

value: Small cell lung cancer

value: Type D

value: Vehicle + CsA


title: Wild-Type GMP-gate Antibody Derived Tags

description: GMP ADT

value: Bone marrow derived Modified GMP

value: Wild-type

value: WT ModGMP ADT


title: 4711-11, Input, Day 2

value: Type V

value: Input


title: MSB25


title: 4711-18, Input, Day 2


title: ZR751_KAT6 inhibitor_120hr_R3

value: Breast cancer cells

value: WT

value: KAT6 inhibitor


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate5 wellA10

value: Memory CD4 T cell

value: no D1-A5 splice detected

tag: tatrev splice_characterization

value: no SIV detected


title: 4711-1, Control, Day 2

tag: treatment

value: Vehicle


title: ZR751_KAT6 inhibitor_120hr_R2


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate3 wellA10

value: PBMC

value: no tat-rev splice detected

value: SIV not > 1%


title: MSB21

value: tumor

value: DFSP

value: Surgical Resection


title: ZR751_KAT6 inhibitor_120hr_R1


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate2 wellA10


title: 4711-1, Restored + CsA, Day 2

value: Small cell lung cancer

value: Type D

value: 4-OHT + CsA


title: 4711-1, Restored, Day 2


title: ZR751_DMSO_120hr_R2

value: DMSO


title: ZR751_DMSO_120hr_R3

value: Breast cancer cells


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate10 wellA10


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate1 wellA10


title: MSB19

value: GIST


title: MSB18


title: ZR751_DMSO_120hr_R1

value: WT


title: MSB22

value: PLS


title: Liver LMRE 20-3

city: irvine

first: Siwei

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

data_processing:
Alignment to reference assembly mm10 and known splice junctions extracted from the RefSeq database performed using Tuxedo pipeline tophat
Read counting for each gene and normalization to FPKM values  using Tuxedo pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results (FPKM) of the standard RNAseq analysis are reported in the genes_fpkm.csv file

source_name: liver

extract_protocol: none provided by the submitter

value: LMRE


title: T-cell lymphoblastic lymphoma 41

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL41

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

source_name: Mediastinal mass

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

value: T-cell lymphoblastic lymphoma

tag: gender

value: Male

tag: tissue preparation

value: FFPE


title: Memory CD4 T cell gene expression from macaque T034 PBMC, plate4 wellA10

city: Silver Spring

first: Rasmi

address: 503 Robert Grant Avenue

institute: Walter Reed Army Institute of Research

value: PBMC

value: Memory CD4 T cell

value: D1-A5 splice detected

value: tat-rev splice detected

tag: siv presence

value: SIV detected

value: SIV > 1%


title: T47D_KAT6 inhibitor_120hr_R3

value: KAT6 inhibitor


title: MSB15

value: tumor

value: WDLPS

value: Surgical Resection


title: MSB16

value: GIST


title: Liver LMRE 20-2


title: T-cell lymphoblastic lymphoma 38R

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL38R

source_name: Axilar LN


title: Liver LMRE 16-3


title: Liver LMRE 20-1


title: T47D_KAT6 inhibitor_120hr_R2

value: Breast cancer cells

value: WT


title: T47D_KAT6 inhibitor_120hr_R1


title: MSB14


title: T-cell lymphoblastic lymphoma 36

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL36

source_name: Supraclavicular LN

value: Female


title: Liver LMRE 16-2

value: LMRE


title: MSB2

value: AS


title: T-cell lymphoblastic lymphoma 28

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL28

source_name: Cervical LN

value: T-cell lymphoblastic lymphoma

value: Male

value: FFPE


title: MSB13

value: DDLPS


title: Liver LMRE 16-1


title: MSB11

value: PLPS


title: T47D_DMSO_120hr_R2

value: DMSO


title: T47D_DMSO_120hr_R3


title: Liver LMRE 12-5


title: T47D_DMSO_120hr_R1


title: T-cell lymphoblastic lymphoma 26

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL26

source_name: Mediastinal LN


title: MSB12


title: T-cell lymphoblastic lymphoma 27

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL27


title: 4711-1, Input, Day 2

value: Small cell lung cancer

value: Type D

value: Input


title: Liver LMRE 12-3


title: MCF7_KAT6 inhibitor_48hr_R3

value: KAT6 inhibitor

value: 48 hr


title: Liver LMRE 12-2


title: T-cell lymphoblastic lymphoma 14

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL14


title: T-cell lymphoblastic lymphoma 42

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL42

source_name: Pericardial biopsy

value: male


title: MSB10

value: tumor

value: ULMS

value: Surgical Resection


title: MSB1

value: UPS


title: Liver LMRE 8-3

value: LMRE


title: Suspension Cultured Pancreas Exocrine - Fresh Hu1182 D7

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-hg19-1.2.0 genome assembly using cellranger v3.0.1
Counting data of reference gene expression levels were generated by cellranger v3.0.1 (automatic identification of chemistry properties)
Assembly: hg19
Supplementary files format and content: Tab separated values; MatrixMarket

source_name: Suspension Cultured Pancreas Exocrine

growth_protocol: After islet removal, primary adult human pancreas tissue was dissociated into single cells, counted, and resuspended in suspension culture medium with Ri (“fresh”). On D1 and D4, medium was refreshed. In parallel, the same protocol was followed for cryopreserved (“cryo”) samples. On D3 and D7 of each culture, fresh and cryo spheroids were dissociated using LiberaseTM TH and TrypLE. Viability measurements were performed manually with a hemocytometer and using a BioRad cell counter.

extract_protocol:
Single cells were captured on a 10xGenomics Chromium Controller using a 10X V3 Single Cell 3’ Solution kit (10xGenomics, Chromium Single Cell 3’ Reagent kit V3, Cat. PN-1000092). All protocols were performed following the manufacturer’s instructions.
Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat. 5067-4626). The library concentration was determined with a Qubit High Sensitivity DNA Assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired-end setting of 28 cycles of read (R) 1, 101 cycles of R2, and 8 cycles of index reads on Illumina NovaSeq 6000 platform, with sequencing depth of ~0.1 million reads per cell.

value: Pancreas

value: primary adult human pancreatic cells

value: cultured in 3D suspension for 7 days


title: T-cell lymphoblastic lymphoma 12

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL12

source_name: LN

value: T-cell lymphoblastic lymphoma

value: Female

value: FFPE


title: T-cell lymphoblastic lymphoma 22

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL22


title: MCF7_KAT6 inhibitor_48hr_R1

value: Breast cancer cells

value: WT


title: Liver LMRE 8-2


title: Suspension Cultured Pancreas Exocrine - Fresh Hu1182 D3

value: cultured in 3D suspension for 3 days


title: MCF7_DMSO_48hr_R3

value: DMSO


title: Liver LMRE 8-1


title: Suspension Cultured Pancreas Exocrine - Cryo Hu958 D7


title: T-cell lymphoblastic lymphoma 4

description:
Hybridized to Affymetrix OncoScan FFPE Assay
TLBL4

source_name: Laterocervical LN

value: Male


title: MCF7_DMSO_48hr_R2

value: 48 hr


title: Suspension Cultured Pancreas Exocrine - Cryo Hu958 D3


title: MCF7_DMSO_48hr_R1


title: Triple Positive DLBCL 74

description: Hybridized to Affymetrix OncoScan FFPE Assay

value: Triple Positive DLBCL


title: Liver LMRE 4-5


title: MCF7_KAT6 inhibitor_48hr_R2

value: KAT6 inhibitor


title: Triple Positive DLBCL 44

source_name: Small intestine


title: Liver LMRE 0-4


title: Triple Positive DLBCL 71

source_name: Tonsil


title: ZR751_KAT6 inhibitor_48hr_R3


title: Triple Positive DLBCL 31

source_name: Stomach-liver


title: ZR751_KAT6 inhibitor_48hr_R2


title: ZR751_KAT6 inhibitor_48hr_R1


title: Liver LMRE 0-2