title: Embryo 12.2

description:
Embryo 12 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 12.3

status: Public on Nov 12 2014

type: genomic

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Embryo 12 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.

hyb_protocol: After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files

data_processing: .TIFF files were imported in, and processed by, BlueFuse Multi 3.1.

molecule: genomic DNA

organism: Homo sapiens

source_name: Embryo culture

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.

tag: cell type

value: Single Blastomere

source_name: female/male reference

tag: sample

value: reference


title: genomic DNA peripheral blood DNA p2C5

city: London

first: James

middle: M

last: Flanagan

state: London

address: Hammersmith Hospital, Du Cane Rd

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

description: normal blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
The in vitro methylated control samples IVM100 and IVM0 could not be pre-processed with the actual samples, but they are represented in Matrix_raw_signal.txt (linked as supplementary file on Series record).

label: Cy5 and Cy3

source_name: peripheral blood DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA samples were extracted from buffy coats using DNA Blood Mini Kits (Qiagen, Crawley, UK) according to standard instructions

tag: gender

value: Female

tag: sample type

value: peripheral blood DNA

tag: disease state

value: normal

tag: duplicate

tag: plate

tag: row

value: C

tag: col

tag: ChIP

tag: label

tag: agegap

tag: agebloodtaken

tag: round

tag: subjectid for matching


title: Embryo 12.4

description:
Embryo 12 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2D5

description: normal blood sample

value: D


title: Embryo 11.9

description:
Embryo 11 cell 9
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 11.8

description:
Embryo 11 cell 8
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 12.1

description:
Embryo 12 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2F5

description: normal blood sample

value: F


title: Embryo 11.6

description:
Embryo 11 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2G5

description: normal blood sample

value: G


title: genomic DNA peripheral blood DNA p2A5

description: normal blood sample

value: A


title: genomic DNA peripheral blood DNA p2B5

description: normal blood sample

value: B


title: Embryo 11.7

description:
Embryo 11 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2H4

description: normal blood sample

value: H


title: genomic DNA peripheral blood DNA p2G4

description: normal blood sample


title: Embryo 11.5

description:
Embryo 11 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2H5

description: normal blood sample


title: Embryo 11.2

description:
Embryo 11 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 11.1

description:
Embryo 11 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 11.4

description:
Embryo 11 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 10.5

description:
Embryo 10 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 10.6

description:
Embryo 10 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2F4

description: normal blood sample


title: genomic DNA peripheral blood DNA p2B4

description: normal blood sample


title: Embryo 11.3

description:
Embryo 11 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 10.4

description:
Embryo 10 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 10.3

description:
Embryo 10 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2E4

description: normal blood sample

value: E


title: Embryo 10.2

description:
Embryo 10 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2D4

description: normal blood sample


title: genomic DNA peripheral blood DNA p2C4

description: normal blood sample


title: Embryo 10.1

description:
Embryo 10 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2G3

description: normal blood sample


title: genomic DNA peripheral blood DNA p2H3

description: normal blood sample


title: genomic DNA peripheral blood DNA p2F3

description: normal blood sample


title: genomic DNA peripheral blood DNA p2A4

description: normal blood sample


title: Embryo 9.7

description:
Embryo 9 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2G2

description: normal blood sample


title: genomic DNA peripheral blood DNA p2E3

description: normal blood sample


title: genomic DNA peripheral blood DNA p2D3

description: normal blood sample


title: Embryo 9.10

description:
Embryo 9 cell 10
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 10.7

description:
Embryo 10 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2B3

description: normal blood sample


title: genomic DNA peripheral blood DNA p2H2

description: normal blood sample


title: genomic DNA peripheral blood DNA p2A3

description: normal blood sample


title: genomic DNA peripheral blood DNA p2B2

description: normal blood sample


title: genomic DNA peripheral blood DNA p2C3

description: normal blood sample


title: genomic DNA peripheral blood DNA p2F2

description: normal blood sample


title: Embryo 9.3

description:
Embryo 9 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 9.4

description:
Embryo 9 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 9.2

description:
Embryo 9 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 9.5

description:
Embryo 9 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2E2

description: normal blood sample


title: Embryo 9.9

description:
Embryo 9 cell 9
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2C2

description: normal blood sample


title: Embryo 9.6

description:
Embryo 9 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2D2

description: normal blood sample


title: genomic DNA peripheral blood DNA p2A2

description: normal blood sample


title: Embryo 8.5

description:
Embryo 8 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 8.4

description:
Embryo 8 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 9.8

description:
Embryo 9 cell 8
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 9.1

description:
Embryo 9 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 8.3

description:
Embryo 8 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 8.1

description:
Embryo 8 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2H1

description: normal blood sample


title: Embryo 8.2

description:
Embryo 8 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 7.4

description:
Embryo 7 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 7.5

description:
Embryo 7 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 7.6

description:
Embryo 7 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 7.3

description:
Embryo 7 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2D1

description: normal blood sample


title: Embryo 7.1

description:
Embryo 7 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 7.2

description:
Embryo 7 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2G1

description: normal blood sample


title: Embryo 6.8

description:
Embryo 6 cell 8
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 6.7

description:
Embryo 6 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2B1

description: normal blood sample


title: Embryo 6.6

description:
Embryo 6 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1E12

description: normal blood sample


title: genomic DNA peripheral blood DNA p1D12

description: normal blood sample


title: Embryo 6.5

description:
Embryo 6 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 6.3

description:
Embryo 6 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 6.2

description:
Embryo 6 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2A1

description: normal blood sample


title: genomic DNA peripheral blood DNA p1F11

description: normal blood sample


title: genomic DNA peripheral blood DNA p1H11

description: normal blood sample


title: Embryo 6.1

description:
Embryo 6 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 5.6

description:
Embryo 5 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 5.5

description:
Embryo 5 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1C12

description: normal blood sample


title: genomic DNA peripheral blood DNA p1G11

description: normal blood sample


title: genomic DNA peripheral blood DNA p1A12

description: normal blood sample


title: genomic DNA peripheral blood DNA p2C1

description: normal blood sample


title: genomic DNA peripheral blood DNA p1D11

description: normal blood sample


title: genomic DNA peripheral blood DNA p1H10

description: normal blood sample


title: genomic DNA peripheral blood DNA p1B12

description: normal blood sample


title: Embryo 5.4

description:
Embryo 5 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1E11

description: normal blood sample


title: Embryo 5.3

description:
Embryo 5 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1A11

description: normal blood sample


title: genomic DNA peripheral blood DNA p1F10

description: normal blood sample


title: Embryo 5.2

description:
Embryo 5 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p2E1

description: normal blood sample


title: Embryo 4.8

description:
Embryo 4 cell 8
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 5.1

description:
Embryo 5 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1C11

description: normal blood sample


title: genomic DNA peripheral blood DNA p1G10

description: normal blood sample


title: genomic DNA peripheral blood DNA p2F1

description: normal blood sample


title: genomic DNA peripheral blood DNA p1F12

description: normal blood sample


title: genomic DNA peripheral blood DNA p1B11

description: normal blood sample


title: Embryo 6.4

description:
Embryo 6 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 4.6

description:
Embryo 4 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1B10

description: normal blood sample


title: genomic DNA peripheral blood DNA p1C10

description: normal blood sample


title: genomic DNA peripheral blood DNA p1A10

description: normal blood sample


title: Embryo 4.5

description:
Embryo 4 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 4.4

description:
Embryo 4 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 4.2

description:
Embryo 4 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1H9

description: normal blood sample


title: genomic DNA peripheral blood DNA p1D10

description: normal blood sample


title: Embryo 4.1

description:
Embryo 4 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1G9

description: normal blood sample


title: Embryo 4.3

description:
Embryo 4 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 3.6

description:
Embryo 3 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 3.7

description:
Embryo 3 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1E10

description: normal blood sample


title: Embryo 3.5

description:
Embryo 3 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1D9

description: normal blood sample


title: Embryo 3.4

description:
Embryo 3 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1F9

description: normal blood sample


title: genomic DNA peripheral blood DNA p1E9

description: normal blood sample


title: Embryo 2.7

description:
Embryo 2 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 2.6

description:
Embryo 2 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 3.2

description:
Embryo 3 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1B9

description: normal blood sample


title: Embryo 2.5

description:
Embryo 2 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 2.4

description:
Embryo 2 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 4.7

description:
Embryo 4 cell 7
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 2.3

description:
Embryo 2 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 2.2

description:
Embryo 2 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 2.1

description:
Embryo 2 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1G8

description: normal blood sample


title: Embryo 3.1

description:
Embryo 3 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1C8

description: normal blood sample


title: genomic DNA peripheral blood DNA p1H8

description: normal blood sample


title: genomic DNA peripheral blood DNA p1B8

description: normal blood sample


title: genomic DNA peripheral blood DNA p1H7

description: normal blood sample


title: genomic DNA peripheral blood DNA p1C9

description: normal blood sample


title: genomic DNA peripheral blood DNA p1D8

description: normal blood sample


title: genomic DNA peripheral blood DNA p1F7

description: normal blood sample


title: Embryo 1.4

description:
Embryo 1 cell 4
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 1.2

description:
Embryo 1 cell 2
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1A9

description: normal blood sample


title: Embryo 3.3

description:
Embryo 3 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: Embryo 1.1

description:
Embryo 1 cell 1
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1G7

description: normal blood sample


title: Embryo 1.5

description:
Embryo 1 cell 5
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.


title: genomic DNA peripheral blood DNA p1A7

description: normal blood sample


title: genomic DNA peripheral blood DNA p1C7

description: normal blood sample


title: genomic DNA peripheral blood DNA p1A8

description: normal blood sample


title: genomic DNA peripheral blood DNA p1B7

description: normal blood sample


title: genomic DNA peripheral blood DNA p1F6

description: normal blood sample


title: genomic DNA peripheral blood DNA p1F8

description: normal blood sample


title: genomic DNA peripheral blood DNA p1D7

description: normal blood sample


title: genomic DNA peripheral blood DNA p1E7

description: normal blood sample


title: genomic DNA peripheral blood DNA p1E8

description: normal blood sample


title: PHH-HLCs

type: RNA

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description: PHH9-HLCsPHH9-iPS-HBC-derived hepatocyte-like cells

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

molecule: total RNA

source_name: PHH-HLCs, differentiated

label_protocol: 100 ng total RNA from all samples was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: For each human iPSC line for hepatocyte differentiation, all differentiated cells are constantly removed by manually picking up. Before the initiation of hepatocyte differentiation, human iPSCs were dissociated into clumps by using dispase (Roche) and plated onto BD Matrigel Basement Membrane Matrix Growth Factor Reduced (BD Biosciences). These cells were cultured in the MEF-conditioned medium for 3-4 days.  The differentiation protocol for the induction of definitive endoderm cells, hepatoblasts, and hepatocytes was based on our previous reports with some modifications.  Briefly, in the definitive endoderm differentiation, human iPSCs were cultured for 4 days in the L-Wnt3A-expressing cell (ATCC, CRL2647)-conditioned RPMI1640 medium (Sigma) which contains 100 ng/ml Activin A (R&D Systems), 4 mM L-Glutamine, 0.2% FBS (PAA Laboratories), and 1×B27 Supplement Minus Vitamin A (Life Technologies).  For the induction of HBCs, the definitive endoderm cells were cultured for 5 days in RPMI1640 medium (Sigma) which contains 30 ng/ml bone morphogenetic protein 4 (BMP4) (R&D Systems) and 20 ng/ml FGF4 (R&D Systems), 4 mM L-Glutamine, and 1×B27 Supplement Minus Vitamin A.  The protocol for HBC proliferation using human recombinant laminin-111 (BioLamina) was based on our previous report with some modifications. Briefly, the hPSC-derived HBCs were first purified from the hPSC-derived cells (day 9) by selecting attached cells on a human recombinant LN111-coated dish (final coating concentration was 1.0 μg/cm2) at 15 min after plating.  The hPSC-derived HBCs were cultured on a human LN111-coated dish (2.5 × 104 cells/cm2) in maintenance DMEM/F12 medium (DMEM/F12 medium (Invitrogen) was supplemented with 10% FBS (PAA laboratories), 1×insulin/transferrin/selenium, 10 mM nicotinamide, 10-7 M Dexamethasone (DEX) (Sigma), 20 mM HEPES, 25 mM NaHCO3, 1×GlutaMAX, 40 ng/ml hepatocyte growth factor (HGF) (R&D Systems) and 20 ng/ml epidermal growth factors (EGF) (R&D Systems)). The medium was refreshed every day. The HBCs were dissociated with Accutase (Millipore) into single cells, and subcultured every 6 or 7 days.  To perform the hepatocyte differentiation, the HBCs were cultured for 5 days in RPMI1640 medium (Sigma) which contains 20 ng/ml HGF, 4 mM L-Glutamine, and 1×B27 Supplement Minus Vitamin A.  And then, the cells were cultured for 11 days in Hepatocyte Culture Medium (HCM, Lonza) without EGF but with 20 ng/ml oncostatin M (OsM). Unlike our previous reports, the current differentiation method could omit the use of adenovirus-mediated overexpression of hepatic transcription factors.

value: PHH-HLCs, differentiated


title: genomic DNA peripheral blood DNA p1G6

description: normal blood sample


title: 18 h E2-treated MCF-7 cells rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: breast cancer_MCF-7_18hr E2 treated

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: The cells were cultured in phenol red-free DMEM:F12 medium with 10% charcoal/dextran stripped FBS (sFBS) for two days before treatment.

extract_protocol: Total RNA was extracted using the Rneasy Mini Kit (Qiagen).

treatment_protocol: The cells were treated with vehicle (75%EtOH) or 10 nM E2 for 18 hours.

tag: cell line

value: female

tag: tissue origin

value: breast cancer

tag: treated with

value: Estrodiol (10 nM E2) for 18hr


title: Embryo 1.3

description:
Embryo 1 cell 3
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.

tag: cell type

value: Single Blastomere

tag: sample


title: genomic DNA peripheral blood DNA p1H6

description: normal blood sample

tag: gender

tag: sample type


title: genomic DNA peripheral blood DNA p1E6

description: normal blood sample

tag: disease state

tag: duplicate


title: PHHs

source_name: PHHs, cultured, 48hr

value: PHHs, cultured, 48hr


title: 18 h E2-treated MCF-7 cells rep1


title: Embryo 1.6

description:
Embryo 1 cell 6
The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The ‘combined’ file represents combined results against both references.
The sample data tables display the combined results against both references.

value: reference


title: genomic DNA peripheral blood DNA p1B6

description: normal blood sample

value: Female

value: peripheral blood DNA

tag: plate

tag: row


title: 18 h vehicle-treated MCF-7 cells rep3

source_name: breast cancer_MCF-7_18hr vehicle treated

value: vehicle (75% EtOH) for 18hr


title: genomic DNA peripheral blood DNA p1C6

description: normal blood sample

value: normal

value: C

tag: col

tag: ChIP


title: 18 h vehicle-treated MCF-7 cells rep1


title: genomic DNA peripheral blood DNA p1A6

description: normal blood sample

tag: label

tag: agegap


title: genomic DNA peripheral blood DNA p1D6

description: normal blood sample

value: D

tag: agebloodtaken

tag: round


title: 18 h E2-treated BG-1 NIEHS cells rep3

source_name: ovarian cancer_BG-1 NIEHS_18hr_E2 treated

tag: cell line

value: BG-1 NIEHS

value: mixed cancer


title: 18 h vehicle-treated MCF-7 cells rep2

tag: tissue origin


title: genomic DNA peripheral blood DNA p1H5

description: normal blood sample

value: H

tag: subjectid for matching


title: genomic DNA peripheral blood DNA p1E5

description: normal blood sample

value: E


title: genomic DNA peripheral blood DNA p1D5

description: normal blood sample


title: 18 h vehicle-treated BG-1 NIEHS cells rep3

source_name: ovarian cancer_BG-1 NIEHS_18hr_vehicle treated

tag: treated with


title: 18 h E2-treated BG-1 NIEHS cells rep1


title: genomic DNA peripheral blood DNA p1F4

description: normal blood sample

value: F


title: genomic DNA peripheral blood DNA p1B5

description: normal blood sample

value: B


title: genomic DNA peripheral blood DNA p1G5

description: normal blood sample

value: G


title: genomic DNA peripheral blood DNA p1F5

description: normal blood sample


title: genomic DNA peripheral blood DNA p1C5

description: normal blood sample


title: 18 h vehicle-treated BG-1 NIEHS cells rep1

value: female


title: 18 h E2-treated MCF-7 cells rep2

value: breast cancer

value: Estrodiol (10 nM E2) for 18hr


title: genomic DNA peripheral blood DNA p1G4

description: normal blood sample


title: genomic DNA peripheral blood DNA p1H4

description: normal blood sample


title: 18 h E2-treated BG-1 FR cells rep3

source_name: ovarian cancer_BG-1 FR_18hr_E2 treated

value: BG-1 FR

value: ovarian cancer


title: genomic DNA peripheral blood DNA p1A5

description: normal blood sample

value: Female

value: peripheral blood DNA

value: A


title: 18 h E2-treated BG-1 FR cells rep2


title: genomic DNA peripheral blood DNA p1E4

description: normal blood sample

value: normal


title: 18 h vehicle-treated BG-1 FR cells rep3

source_name: ovarian cancer_BG-1 FR_18hr_vehicle treated

value: vehicle (75% EtOH) for 18hr


title: genomic DNA peripheral blood DNA p1D4

description: normal blood sample

value: D


title: 18 h E2-treated BG-1 NIEHS cells rep2

value: BG-1 NIEHS

value: mixed cancer


title: genomic DNA peripheral blood DNA p1B4

description: normal blood sample


title: H1993 BRMS1 KD/Twist1 KD_1

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from established lung cancer

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX human HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina BeadArray reader

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

label: biotin

source_name: human lung

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FBS

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: Lung adenocarcinoma


title: H1993 BRMS1 KD/Twist1 KD_2


title: 18 h vehicle-treated BG-1 FR cells rep2

tag: gender


title: genomic DNA peripheral blood DNA p1C4

description: normal blood sample

tag: sample type

value: C


title: genomic DNA peripheral blood DNA p1A4

description: normal blood sample

tag: disease state


title: H1993 shRNA Control _1


title: genomic DNA peripheral blood DNA p1G3

description: normal blood sample

tag: duplicate


title: HCEnC, adult, adult 11

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

description: Gene Expression data from corneal endothelium

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with Partek Genomics Suite (PGS) using the Gene Expression module. Data were RMA normalized and background corrected.

source_name: cornea

label_protocol: Affymetrix standard protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: age group

value: adult

tag: age subgroup

value: corneal endothelium


title: genomic DNA peripheral blood DNA p1F3

description: normal blood sample

tag: plate

tag: row

value: F

tag: col


title: genomic DNA peripheral blood DNA p1C3

description: normal blood sample

tag: ChIP

tag: label

tag: agegap


title: H1993 shRNA Control _2

tag: cell line


title: HPS-19I cells from LNCaP+HPS-19I co-culture, with TGF-beta (3926_3)

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: HPS_19I TGFB CM+DMSO_3926_3

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Human Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used. Combat used for batch effect correction (PMID:16632515).

label: Alexa Fluor 647

source_name: HPS-19I prostate stroma cells

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: HPS19I cells were grown to mostly confluence in T75 flasks.  5X105 of LNCaP-HA-TGF-β1(a) cells or LNCaP-Ctrl cells were then plated on top of the HPS19I cells.  We treated HPS19I cells using conditioned media collected from LNCaP- HA-TGF-β1(a) cells and LNCaP-Ctrl cells cultured in RPMI1640 supplemented with 0.2% FBS.  After 6 days of treatment, we extracted total RNA from these HPS19I cells and performed microarray.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

label: Alexa Fluor 555

source_name: Stratagene, Universal Human Reference RNA


title: HCEnC, adult, adult 10


title: HPS-19I cells from LNCaP+HPS-19I co-culture, with TGF-beta (36024_3)

description: HPS_19I TGFB CM+DMSO 36024_3

value: Stratagene, Universal Human Reference RNA


title: 18 h E2-treated BG-1 FR cells rep1

value: female

tag: tissue origin

value: Estrodiol (10 nM E2) for 18hr


title: 18 h vehicle-treated BG-1 FR cells rep1

value: BG-1 FR

value: ovarian cancer


title: 18 h vehicle-treated BG-1 NIEHS cells rep2


title: H1993 BRMS1 KD_2


title: genomic DNA peripheral blood DNA p1E3

description: normal blood sample

value: Female

value: peripheral blood DNA

value: E

tag: agebloodtaken

tag: round

tag: subjectid for matching


title: HPS-19I cells from LNCaP+HPS-19I co-culture, no TGF-beta (3926_4)

description: HPS_19I control CM+DMSO_3926_4


title: genomic DNA peripheral blood DNA p1B3

description: normal blood sample

tag: gender

value: normal

value: B


title: genomic DNA peripheral blood DNA p1A3

description: normal blood sample

tag: sample type

value: A


title: HCEnC, pediatric, preschooler 9

value: pediatric

value: preschooler

tag: tissue


title: genomic DNA peripheral blood DNA p1G2

description: normal blood sample

tag: disease state

tag: duplicate

value: G


title: HCEnC, adult, adult 6

tag: age group

value: adult

tag: age subgroup


title: HPS-19I cells from LNCaP+HPS-19I co-culture, no TGF-beta (36024_4)

description: HPS_19I control CM+DMSO 36024_4


title: genomic DNA peripheral blood DNA p1E2

description: normal blood sample

tag: plate

tag: row


title: LNCaP+HPS-19I co-culture,with TGF-beta and DMSO (33925_3)

source_name: LNCaP prostate cancer cells and HPS-19I cells

growth_protocol: HPS19I cells were grown to mostly confluence in T75 flasks.  5X105 of LNCaP-HA-TGF-β1(a) cells or LNCaP-Ctrl cells were then plated on top of the HPS19I cells.  The co-cultures were maintained in RPMI1640 supplemented with 0.2% FBS and subjected to treatments with 400 nM of SD208 or vehicle control for 6 days.


title: HCEnC, pediatric, preschooler 8

value: corneal endothelium


title: H1993 BRMS1 KD_1

value: Lung adenocarcinoma


title: MEIS1D experiment 3

city: Amsterdam

first: Daphne

middle: C.

last: Thijssen-Timmer

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Blood Supply

description: SAMPLE 9

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: VSN normalization using lumiN function in R

source_name: CD34+ cells

label_protocol: NuGen labeling

growth_protocol: Cells were kept in CellGro medium (CellGenix, Frankfurt) supplemented with 100ng/ml of each SCF (R&D Systems Abingdon, UK), TPO (Sanquin PeliKines, Amsterdam), Flt3 ligand (Miltenyi Biotech, Bergisch Gladbach, Germany) and 20ng/ml IL6 (Miltenyi Biotech, Bergisch Gladbach, Germany)

extract_protocol: RNA was isolated using Trizol reagent followed by Qiagen RNeasy Micro Kit for futher cleanup and DNAse I digestion according to the manufacturer's specifications. RNA quality was determined with an Agilent Bioanalyzer.

treatment_protocol: Human CD34+ cells were transduced with lentiviral particles containing MEIS1B or MEIS1D or empty vector constructs. A multiplicity of infection (MOI) of 1500 was used. Cells were incubated with virus over night, washed the next morning to remove free virus particles and cultured for an additional 24hours to allow for GFP expression. 48 hours after transduction, the cells were sorted for GFP-expression and lysed directly after sort for RNA isolation and transcription profiling

tag: cell source

value: mobilized peripheral blood

tag: cell type

value: CD34+ cells

tag: transduction


title: genomic DNA peripheral blood DNA p1H2

description: normal blood sample

value: H

tag: col

tag: ChIP

tag: label

tag: agegap


title: genomic DNA peripheral blood DNA p1F2

description: normal blood sample

value: F

tag: agebloodtaken

tag: round

tag: subjectid for matching


title: MEIS1B experiment 3

description: SAMPLE 8


title: MEIS1D experiment 2

description: SAMPLE 6


title: LNCaP+HPS-19I co-culture,with both TGF-beta and SD208 (33925_1)

description: HPS19I_LNCaP_TGFB_SD208_ 33925_1

tag: sample type

value: Stratagene, Universal Human Reference RNA


title: LNCaP+HPS-19I co-culture, no TGF-beta or SD208 (33925_4)


title: genomic DNA peripheral blood DNA p1C2

description: normal blood sample

tag: gender

value: Female

tag: disease state

value: C


title: HCEnC, pediatric, adolescent 5

tag: age group

value: adolescent

tag: tissue


title: MEIS1B experiment 2

description: SAMPLE 5


title: genomic DNA peripheral blood DNA p1D2

description: normal blood sample

value: peripheral blood DNA

value: normal

tag: duplicate

tag: plate

value: D


title: LNCaP+HPS-19I co-culture,with both TGF-beta and SD208 (36023_1)

description: HPS_19I  LNCaP_TGFB +SD208  36023_1


title: LNCaP+HPS-19I co-culture, no TGF-beta but with SD208 (33925_2)


title: genomic DNA peripheral blood DNA p1B2

description: normal blood sample

tag: row

value: B


title: LNCaP+HPS-19I co-culture,with TGF-beta and DMSO (36023_3)

description: HPS_19I  LNCaP_TGFB +DMSO 36023_3


title: HCEnC, pediatric, preadolescent 3

value: pediatric

tag: age subgroup

value: preadolescent


title: HCEnC, adult, adult 4

value: adult


title: MEIS1D experiment 1

description: SAMPLE 3

tag: cell source

tag: cell type

tag: transduction


title: MEIS1B experiment 1

description: SAMPLE 2


title: HCEnC, adult, adult 2

value: corneal endothelium


title: LNCaP+HPS-19I co-culture, no TGF-beta but with SD208 (36023_2)

description: HPS_19I  LNCaP_pBMN +SD208 36023_2


title: empty vector experiment 1

description: SAMPLE 1

value: empty vector


title: empty vector experiment 2

description: SAMPLE 4

value: mobilized peripheral blood


title: genomic DNA peripheral blood DNA p1A2

description: normal blood sample

value: A

tag: col

tag: ChIP

tag: label


title: HCEnC, pediatric, preadolescent 1


title: genomic DNA peripheral blood DNA p1H1

description: normal blood sample

value: H

tag: agegap

tag: agebloodtaken

tag: round


title: empty vector experiment 3

description: SAMPLE 7

value: CD34+ cells


title: HCEnC, pediatric, adolescent 7


title: genomic DNA peripheral blood DNA p1H3

description: normal blood sample

tag: gender

tag: sample type

tag: subjectid for matching


title: MDA-231 cells

status: Public on Nov 11 2014

city: Shanghai

first: XIN

last: HU

state: Shanghai

address: 270 Dong An Road, Build 7, RM303

department: Department of Breast Surgery

country: China

institute: Fudan Unversity Shanghai Cancer Center

description: microRNA expression data from MDA-231 cells.

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing:
Raw data were processed by Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: MDA-231 cells

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: The MDA-MB-231 (MDA-231) cells were obtained from the Shanghai Cell Bank Type Culture Collection Committee and maintained in complete growth medium as recommended by the distributor. The MDA-231 gemcitabine-resistant subline (MDA-231-Gem) was established by stepwise selection with increasing concentrations of gemcitabine.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: No treatment

value: Human mammary cancer cells MDA-231

tag: cell line

tag: phenotype

value: gemcitabine-sensitive


title: MDA-231-GEM cells

description: Gene expression data from gemcitabine-resistant MDA-231-Gem cells.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data were processed by Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: MDA-231-GEM cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: Human mammary cancer cells MDA-231-GEM (Induced gemcitabine-resistant cells)

value: gemcitabine-resistant


title: genomic DNA peripheral blood DNA p1D3

description: normal blood sample

source_name: peripheral blood DNA

value: Female

value: peripheral blood DNA

tag: disease state

tag: duplicate

tag: plate


title: Gastric antrum EG patient 18 03VY4 rep1

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

state: OH

address: 3333 Burnet Ave. MLC-7028

department: Allergy

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.034 μg/μL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes.  Fill probe array with 200 μL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 μL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm.  Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. The Stain and Antibody solutions are produced by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

scan_protocol: Scanning: The probe arrays are scanned using the Affymetrix GeneChip Scanner 3000 7G; Scanning software: Genechip Operating Software 1v4 (Affymetrix)

data_processing:
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array chips were used.  GeneChip CEL files were subjected to RMA normalization using GeneSpring GX 7.3.1 software (Agilent).  GeneSpring GX 7.3.1 was used for normalization, clustering, and filtering.
RMA normalized signal intensity then  each sample normalized to median of control samples

source_name: gastric antrum tissue, patient with active eosinophilic gastritis (EG)

label_protocol: TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre) was used to prepare cRNA following the manufacturer’s instructions. The TargetAmp1-Round Aminoallyl-aRNA Amplification Kit (Epicentre) is used to make double-stranded cDNA from total RNA. Specifically cDNA is prepared from total RNA using both the TargetAmp t7- Oligo (dT) Primer A (Epicentre) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences) along with SuperScript III Reverse Transcriptase (200 U/ul) (Invitrogen). An in vitro transcription reaction creates the cRNA target.  Biotin-X-X-NHS (Epicentre) is used to label the aminoallyl-aRNA with biotin following the manufacturer’s instructions.  The biotin-labeled cRNA target is then chemically fragmented and a hybridization cocktail is prepared and hybridized to an Affymetrix Genechip Array (GeneChip Human Genome U133 Plus 2.0 Array).

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA) per the manufacturer's instructions.  Quality control steps:  The quality of the Total RNA was checked by the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Assay.

treatment_protocol: Gastric antrum biopsy specimens were immediately placed into RNAlater until RNA extraction procedure was carried out.

value: active eosinophilic gastritis

tag: tissue

value: gastric antrum


title: LNCaP+HPS-19I co-culture, no TGF-beta or SD208 (36023_4)

description: HPS_19I  LNCaP_pBMN +DMSO  36023_4

value: Stratagene, Universal Human Reference RNA


title: genomic DNA peripheral blood DNA p1G1

description: normal blood sample

value: normal

tag: row

value: G


title: Tet-Treg+

first: Masahide

last: Hamaguchi

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Endocrinology and Metabolism

institute: Kyoto Prefectural University of Medicine, Graduate School of Medical Science

description: Gene expression data from antigen nonspecific CD8+ T cells produced by Treg-cell suppression

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix HG-U133-Plus-2.0 microarrays.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RAM using the R (Bioconductor) and global scaling as normalization method.

source_name: Antigen nonspecific CD8+ T cells produced by Treg-cell suppression

label_protocol: Biotinylated cRNA were prepared according to Single Primer Isothermal Amplification from 1 ug total RNA (NuGEN Technologies).

growth_protocol: Antigen presenting cells (APCs) (T-cell depleted PBMCs) were pulsed with 10 μM Melan-A26-35 (EAAGIGILTV) peptides (Operon Biotechnology) specific for HLA-A*0201 overnight. After γ-irradiation, APCs were added to round-bottom 96-well plates containing the sorted CD8+ T cells and Treg cells at graded ratios, and cultured for 10 days.

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Tet+CD8+ T cells induced at CD8+ T cells: Treg cells ratio, 1:0.5 and 1:0.

tag: cell type

value: CD8 T cells


title: Gastric antrum control patient 5 03W7J rep1

source_name: gastric antrum tissue, control patient

value: control


title: Gastric antrum EG patient 20 03W7D rep1


title: genomic DNA peripheral blood DNA p1F1

description: normal blood sample

value: F

tag: col


title: Tet+Treg+

description: Gene expression data from antigen specific CD8+ T cells produced by Treg-cell suppression

source_name: Antigen specific CD8+ T cells produced by Treg-cell suppression


title: Gastric antrum control patient 4 03W23 rep1


title: Gastric antrum control patient 2 03VAJ rep1


title: Gastric antrum EG patient 19 03W1X rep1


title: Gastric antrum control patient 3 03VXA rep1


title: MDA-231 cells

description: Gene expression data from MDA-231 cells.


title: R014

city: Ann Arbor

first: Elizabeth

middle: R.

last: Lawlor

state: MI

address: 1600 Huron Parkway

department: Pediatrics

institute: University of Michigan

hyb_protocol: Affymetrix SOP

scan_protocol: Affymetrix GeneChip scanner

data_processing: Data were processed using Affymetrix Power Tools (APT). Robust Multi-array Average (RMA) was used to generate normalized gene-level signal intensity estimates. Only core probesets uniquely mapped to the genome were used.

source_name: Primary tumor

label_protocol: Affymetrix SOP

extract_protocol: Total RNA was isolated using miRNAeasy kits (Qiagen, Valencia, CA). RNA concentrations were calculated using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE) and RNA integrity (RIN) was evaluated using the RNA 6000 PicoAssay (Agilent Technologies, Santa Clara, CA). RNA samples with RIN values of <4.0 were subjected to an RNA cleanup step using the mRNAeasy  kit (Qiagen, Valencia, CA).

tag: diagnosis

value: Ewing sarcoma

tag: study

tag: Sex

tag: age (years)

tag: efs (0=no event, 1=event)

tag: os (0=alive; 1=dead)

tag: efs-time

tag: os-time


title: Tet-Treg-

description: Gene expression data from antigen nonspecific CD8+ T cells produced without Treg

source_name: Antigen nonspecific CD8+ T cells produced without Treg


title: Gastric antrum EG patient 17 03VUC rep1


title: MDA-231-GEM cells

description: microRNA expression data from gemcitabine-resistant MDA-231-Gem cells.

tag: sample type

tag: cell line


title: Wildtype sample at d35, biological rep4 (MOE430A)

city: Ames

last: Reecy

state: IA

address: 2255 Kildee Hall, Iowa State University

department: Animal Science

institute: Iowa State University

description: Gene expression data from pectoralis muscle at d35

hyb_protocol: Target RNA was hybridized to both chip A and chip B of the GeneChip Mouse Expression Set 430 (MOE430; Affymetrix, Santa Clara, CA).  The A and B chips correspond to GPL339 and GPL340, respectively. Hybridization was carried out according to the GeneChip Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Scanning was carried out  according to the GeneChip Expression Analysis Technical Manual (Affymetrix).

data_processing: Robust multi-array analysis (RMA) (Irizarry et al., 2003. Biostatistics 4: 249-264) was performed to normalize the raw data by using R/affy package (Gautier et al., 2004. Bioinformatics 20: 307-315).

organism: Mus musculus

source_name: Mouse pectoralis muscle at d35

label_protocol: Double-stranded cDNA was synthesized from pooled RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA). T7-oligo(dT) primer and SuperScript II reverse transcriptase were used in first-strand synthesis. Biotin-labeled cRNA was generated with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY). cDNA and cRNA cleanup, as well as fragmentation of cRNA, were carried out using the GeneChip Sample Cleanup Module (Qiagen, distr. by Affymetrix).

growth_protocol: Tissues were collected from mouse whole embryos (13.5 d.p.c.), hindquarters (17.5 d.p.c.), or pectoralis muscle (d35). After collection, muscles were flash-frozen in liquid nitrogen as previously described in Steelman et al., 2006. FASEB J. Mar;20(3):580-2

extract_protocol: The frozen tissues from whole embryo or hindquarter only were immersed in RLT lysis buffer (Qiagen, Valencia, CA) and homogenized for 45 seconds, then centrifuged at 3600g for 10 min to pellet cell debris. Total RNA was isolated using the RNase Midi Kit (Qiagen) with on-column DNase digestion according to manufacturer's protocol. Isolation from pectoralis muscle was conducted as described in Steelman et al., 2006. FASEB J. Mar;20(3):580-2.

treatment_protocol: Three individual animals of a single genotype were pooled to give five pools (N=15, total number of arrays=5) for each genotype/timepoint combination for three tissues:  whole embryos (13.5 d.p.c.), hindquarters (17.5 d.p.c.), or pectoralis muscle (d35). Mice were reared, sacrificed by CO2 asphyxiation (embryonic timepoints) or cervical dislocation (d35) and tissues were flash-frozen in liquid nitrogen as previously described  in Steelman et al., 2006. FASEB J. Mar;20(3):580-2.

value: pectoralis muscle

tag: genotype

value: Wildtype C57BL/6J mice

tag: age

value: 35 days


title: Tet+Treg-

description: Gene expression data from antigen specific CD8+ T cells without Treg

source_name: Antigen specific CD8+ T cells without Treg


title: Wildtype sample at d35, biological rep5, (MOE430A)


title: R011


title: genomic DNA peripheral blood DNA p1E1

description: normal blood sample

tag: gender

tag: disease state

tag: duplicate

tag: plate

value: E

tag: ChIP

tag: label

tag: agegap

tag: agebloodtaken

tag: round

tag: subjectid for matching


title: Gastric antrum control patient 1 03UTF rep1

tag: tissue


title: genomic DNA peripheral blood DNA p1C1

description: normal blood sample

tag: row

value: C

tag: col


title: Wildtype sample at d35, biological rep3 (MOE430A)


title: genomic DNA peripheral blood DNA p1B1

description: normal blood sample

tag: sample type

value: B


title: genomic DNA peripheral blood DNA p1D1

description: normal blood sample

value: Female

value: D


title: R004

tag: diagnosis

tag: study

tag: Sex

tag: age (years)

tag: efs (0=no event, 1=event)

tag: os (0=alive; 1=dead)

tag: efs-time

tag: os-time


title: genomic DNA peripheral blood DNA p1A1

description: normal blood sample

tag: gender

value: peripheral blood DNA

tag: disease state

tag: duplicate

tag: plate

value: A

tag: ChIP

tag: label


title: R009


title: R006


title: Wildtype sample at d35, biological rep2 (MOE430A)

tag: tissue

tag: genotype

tag: age


title: Wildtype sample at d35, biological rep1 (MOE430A)


title: R007

tag: diagnosis


title: Mstn-null sample at d35, biological rep5, (MOE430A)

value: Mstn-null C57BL/6J mice


title: R002

tag: study


title: Mstn-null sample at d35, biological rep4 (MOE430A)


title: Mstn-null sample at d35, biological rep3 (MOE430A)


title: Mstn-null sample at d35, biological rep2 (MOE430A)


title: Wildtype sample at 17.5 d.p.c, biological rep2 (MOE430A)

description: Gene expression data from hindquarters at 17.5 d.p.c

source_name: Mouse hindquarters at 17.5 d.p.c

value: embryo hindquarters


title: Q954

tag: Sex


title: Q952

tag: age (years)


title: Q998

tag: efs (0=no event, 1=event)


title: Q995

tag: os (0=alive; 1=dead)


title: Mstn-null sample at d35, biological rep1 (MOE430A)


title: Wildtype sample at 17.5 d.p.c, biological rep5, (MOE430A)


title: Wildtype sample at 17.5 d.p.c, biological rep4 (MOE430A)


title: R001

tag: efs-time


title: Wildtype sample at 17.5 d.p.c, biological rep3 (MOE430A)


title: Q949

tag: os-time


title: Q950


title: Q947


title: Q932


title: Mstn-null sample at 17.5 d.p.c, biological rep5, (MOE430A)


title: Q927


title: Gastric antrum EG patient 16 03UL7 rep1

value: active eosinophilic gastritis

value: gastric antrum


title: Mstn-null sample at 17.5 d.p.c, biological rep3 (MOE430A)


title: Q937


title: Q942


title: Q938


title: Q914


title: Mstn-null sample at 17.5 d.p.c, biological rep1 (MOE430A)


title: Wildtype sample at 13.5 d.p.c, biological rep2 (MOE430A)

description: Gene expression data from embryos at 13.5 d.p.c

source_name: Mouse whole embryos at 13.5 d.p.c

value: whole embryo


title: Mstn-null sample at 13.5 d.p.c, biological rep5, (MOE430A)


title: Mstn-null sample at 17.5 d.p.c, biological rep4 (MOE430A)


title: Mstn-null sample at 17.5 d.p.c, biological rep2 (MOE430A)


title: Q916


title: Q470


title: Wildtype sample at 13.5 d.p.c, biological rep5, (MOE430A)


title: Q472


title: Q908


title: Q919


title: Wildtype sample at 13.5 d.p.c, biological rep4 (MOE430A)


title: Mstn-null sample at 13.5 d.p.c, biological rep2 (MOE430A)


title: Mstn-null sample at 13.5 d.p.c, biological rep3 (MOE430A)


title: Wildtype sample at 13.5 d.p.c, biological rep3 (MOE430A)


title: Q465


title: Q930


title: Mstn-null sample at 13.5 d.p.c, biological rep4 (MOE430A)


title: Q464


title: Wildtype sample at 13.5 d.p.c, biological rep1 (MOE430A)


title: Mstn-null sample at 13.5 d.p.c, biological rep1 (MOE430A)


title: Q460


title: Q458


title: Q455


title: Q462


title: Q456


title: Q454


title: Q171


title: P102

value: Male

tag: age at enrollment (days)

tag: primary tumor site

value: Pelvis

tag: efs event

value: Relapse

tag: efs time (days)

tag: survival status

value: Alive

tag: survival time (days)

tag: experiment date

tag: tumor content


title: P103

value: Ewing sarcoma

value: Other

value: No event


title: Q176


title: Mstn-null sample at d35, biological rep5, (MOE430B)

tag: tissue

value: pectoralis muscle

tag: genotype

tag: age

value: 35 days


title: Wildtype sample at d35, biological rep4 (MOE430B)

value: Wildtype C57BL/6J mice


title: Wildtype sample at d35, biological rep1 (MOE430B)


title: P101

tag: diagnosis

tag: study

tag: Sex

value: SMN

value: Dead


title: Q447

tag: age (years)

tag: efs (0=no event, 1=event)

tag: os (0=alive; 1=dead)


title: O967

tag: age at enrollment (days)


title: Q174

tag: efs-time

tag: os-time


title: Mstn-null sample at d35, biological rep4 (MOE430B)

value: Mstn-null C57BL/6J mice


title: Wildtype sample at 17.5 d.p.c, biological rep3 (MOE430B)

value: embryo hindquarters


title: Wildtype sample at d35, biological rep2 (MOE430B)


title: Wildtype sample at d35, biological rep5, (MOE430B)


title: Wildtype sample at 17.5 d.p.c, biological rep4 (MOE430B)


title: Co-cultured_MAF2-mCherry_DMSO A4

city: Kanazawa

first: Eishu

last: Hirata

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R.

source_name: Melanoma-associated fibroblast co-cultured with melanoma cells and stimulated with DMSO

label_protocol: Standard Illumina biotin labelling protocol

growth_protocol: Human primary melanoma-associated fibroblasts labeled with mCherry (MAF2-mCherry) were co-culture with 5555 mouse melanoma cells labeled with mEGFP (5555-mEGFP) in DMEM on plastic dishes.

extract_protocol: RNA was extracted using a Qiagen RNA extraction kit. The RNA was amplified using an Ambion Illumina TotalPrep RNA Amplification Kit.

treatment_protocol:
MAF2-mCherry and 5555-mEGFP co-cultures were treated with DMSO (0.1%) or PLX4720 (1 mM) for 24 hours.
Cherry-positive fraction (MAF2-mCherry) were FACS-sorted.

tag: cell type

value: melanoma-associated fibroblast (MAF2-mCherry) co-cultured with melanoma cells (5555-mEGFP)

tag: treatment

value: DMSO


title: Mstn-null sample at d35, biological rep3 (MOE430B)


title: Wildtype sample at 17.5 d.p.c, biological rep1 (MOE430B)


title: Wildtype sample at 17.5 d.p.c, biological rep2 (MOE430B)


title: O966

tag: primary tumor site

tag: efs event

tag: efs time (days)

tag: survival status

tag: survival time (days)


title: Co-cultured_MAF2-mCherry_DMSO B4


title: Mstn-null sample at 17.5 d.p.c, biological rep5, (MOE430B)

tag: tissue

tag: genotype

tag: age


title: Mstn-null sample at d35, biological rep2 (MOE430B)


title: O962

tag: diagnosis

tag: study

tag: Sex

value: Female

tag: experiment date

tag: tumor content


title: Mstn-null sample at 17.5 d.p.c, biological rep4 (MOE430B)


title: Mstn-null sample at d35, biological rep1 (MOE430B)


title: O442

value: Male

tag: age at enrollment (days)

value: unknown


title: Wildtype sample at 17.5 d.p.c, biological rep5, (MOE430B)


title: Co-cultured_MAF2-mCherry_PLX B8

source_name: Melanoma-associated fibroblast co-cultured with melanoma cells and stimulated with PLX4720


title: O963

value: Relapse


title: O437

value: Alive


title: Mstn-null sample at 17.5 d.p.c, biological rep3 (MOE430B)


title: AML-16 rep3

city: Herston

first: Steven

last: Lane

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: replicate 3

data_processing: The data were normalized using GenomeStudio.

source_name: AML cells

label_protocol: Biotinylated cRNA was prepared using Illumina Total Prep RNA amplification kit (Ambion) according to the manufacturer's recommendations.

growth_protocol: Primary AML patient samples were engrafted in NSGS recipients and viably sorted as human CD45+ and murine Cd45.1- cells from recipients at AML onset.

extract_protocol: Viable hCD45+ mCd45.1- cells were directly sorted into Picopure exptraction buffer and total RNA was extracted using Arcturus Picopure RNA extraction kit according to the manufacturer's recommendations including DNAse I digestion.

value: human CD45+ AML cells purified from spleens of NSGS recipients at AML onset

tag: sensitivity to telomerase inhibition (imetelstat)

value: low (2)


title: Co-cultured_MAF2-mCherry_PLX A8

tag: cell type


title: AML-18 rep3

description: replicate 3

value: medium (3)


title: AML-16 rep1

description: replicate 1


title: O436

value: Ewing sarcoma

value: Extremity

value: No event


title: AML-5 rep1

description: replicate 1

value: lowest (1)


title: Mstn-null sample at 17.5 d.p.c, biological rep2 (MOE430B)


title: Mstn-null sample at 17.5 d.p.c, biological rep1 (MOE430B)


title: AML-5 rep3

description: replicate 3


title: AML-18 rep2

description: replicate 2


title: AML-16 rep2

description: replicate 2


title: O965


title: Wildtype sample at d35, biological rep3 (MOE430B)

value: pectoralis muscle

value: Wildtype C57BL/6J mice

value: 35 days


title: Wildtype sample at 13.5 d.p.c, biological rep5, (MOE430B)

value: whole embryo


title: N856

value: Other

value: Dead


title: AML-5 rep2

description: replicate 2


title: Wildtype sample at 17.5 d.p.c, biological rep1 (MOE430A)

value: embryo hindquarters


title: Wildtype sample at 13.5 d.p.c, biological rep3 (MOE430B)


title: Wildtype sample at 13.5 d.p.c, biological rep4 (MOE430B)


title: N854

value: Male


title: N850


title: AML-X rep2

description: replicate 2

value: high (4)


title: N848

value: Alive


title: Wildtype sample at 13.5 d.p.c, biological rep2 (MOE430B)


title: AML-X rep3

description: replicate 3

value: human CD45+ AML cells purified from spleens of NSGS recipients at AML onset


title: Mstn-null sample at 13.5 d.p.c, biological rep5, (MOE430B)

value: Mstn-null C57BL/6J mice


title: Wildtype sample at 13.5 d.p.c, biological rep1 (MOE430B)


title: AML-18 rep1

description: replicate 1

value: medium (3)


title: Mstn-null sample at 13.5 d.p.c, biological rep4 (MOE430B)


title: Mstn-null sample at 13.5 d.p.c, biological rep3 (MOE430B)


title: Mstn-null sample at 13.5 d.p.c, biological rep2 (MOE430B)


title: M956

value: Ewing sarcoma

value: Female

value: Relapse


title: M955

value: Pelvis

value: No event


title: AML-X rep1

description: replicate 1


title: M954

value: Extremity


title: M953


title: N838


title: N845


title: N844


title: M952


title: Mstn-null sample at 13.5 d.p.c, biological rep1 (MOE430B)


title: N842


title: M951


title: OC1-WT embryo 3

last: Trimarchi

address: 3188 Molecular Biology Building

department: GDCB

description: e14 OC1_WT3

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the Iowa State University GeneChip Facility.

scan_protocol: Amplified RNA was scanned from Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the Iowa State University GeneChip Facility.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: OC1-WT embryonic retina at E14

label_protocol: Total RNA wa amplified, biotinylated, and fragmented using the Ambion MessageAmp III RNA amplification kit according to manufacturer's instructions.

growth_protocol:
The original Onecut1 deficient mice were obtained and cross by us to C57Bl/6 for a few generations. The mice were described in Jacquemin P. et al, 2000 and were from R1 ES cells injected into a "Swiss" strain of mice.
Littermate were allowed to develop normally in utero until age E14, when they were harvested from the pregnant dam.

extract_protocol: Trireagent extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Embryos were removed from the dam and retinas were isolated, then washed in 1X PBS.

tag: strain background

value: mixed

value: retina

tag: Stage

tag: onecut genotype

value: WT


title: 5282035052_E

city: Groningen

first: vincent

last: bloks

institute: UMCG

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalized and corrected for intra-experimental variation (Combat) generating robust gene-expression profiles (PubMed ID: 20181233).

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems).

extract_protocol: Total RNA was extracted with TriReagent (Sigma, St. Louis, MO, USA). The quality and concentration of the RNA were determined using the Experion automated electrophoresis system (Bio-Rad Laboratories, Inc). The RQI values returned ranged between 9.3-9.6.

treatment_protocol: 12 fxr-/- mice were transduced with AVV vector genomes ( 6 fxra2 and 6 fxra4) and put on a chow diet supplemented with 0.5% CA.

tag: strain/background

tag: genotype/variation

value: FXR-/-

value: liver

tag: gender

value: male

tag: transduction


title: M950

tag: primary tumor site

value: Other

tag: efs event

tag: efs time (days)

tag: survival status

tag: survival time (days)


title: M944

tag: diagnosis

tag: study

tag: Sex

value: Dead

tag: experiment date


title: KO OC2 Adult 3

description: Gene expression information from isolated adult retinas

source_name: OC2-KO adult retina

growth_protocol: Littermates were allowed to develop normally in utero until maturity

treatment_protocol: Retinas were isolated from adult eyes and rinsed in 1X PBS.

tag: tissue

value: adult


title: WT OC2 Adult 3

source_name: OC2-WT adult retina


title: 5282035052_F

tag: age


title: 5282035052_B


title: 5282035052_A


title: 5282035052_C


title: 5282035052_D


title: 5282035045_E


title: L819

tag: age at enrollment (days)

value: Alive

tag: tumor content


title: OC1-KO embryo 3

description: e14 OC1_KO3

source_name: OC1-KO embryonic retina at E14

growth_protocol:
The original Onecut1 deficient mice were obtained and cross by us to C57Bl/6 for a few generations. The mice were described in Jacquemin P. et al, 2000 and were from R1 ES cells injected into a "Swiss" strain of mice.
Littermates were allowed to develop normally in utero until age E14, when they were harvested from the pregnant dam.

tag: strain background

tag: Stage

tag: onecut genotype


title: OC2-WT adult 2


title: 5282035045_F

tag: strain/background

tag: genotype/variation

tag: gender

tag: transduction


title: 5282035045_D


title: L813

value: Male

tag: primary tumor site

tag: efs event

tag: efs time (days)

tag: survival status

value: unknown


title: L811

tag: diagnosis

value: Ewing sarcoma

tag: study

tag: Sex

tag: survival time (days)


title: 5282035045_B

tag: tissue

tag: age


title: OC2-KO adult 2


title: 5282035045_A


title: L809

tag: age at enrollment (days)

value: Relapse

tag: experiment date

tag: tumor content


title: L678


title: L676


title: 5282035045_C

tag: strain/background


title: L674

value: Female


title: MLL-AF9+pMIG-TGIF1#3

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaloesvej 5

department: Finsen Centre

country: Denmark

institute: Rigshospitalet

hyb_protocol: The labeled samples were hybridized to the Mouse Gene 1.0 ST GeneChip array (Affymetrix, Santa Clara, California, USA). The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450.

scan_protocol: The arrays were scanned in the Affymetrix GeneArray® 3000 7G scanner

data_processing: The raw data files were imported into Partek Genomics Suite (www.partek.com) band pre-processed using RMA with quantile normalization and mean summarization of probes in each transcript probe set.  Class comparsion was performed using the ANOVA tool integrated in Partek. The two groups were compared using the F - tests

source_name: GFP-sorted MLL-AF9 transduced pMIG-TGIF1

label_protocol: 300 ng total RNA from each sample was amplified using the GeneChip Whole Transcript (WT) Sense target protocol (Affymetrix INC., California, USA). Samples were fragmented and end labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix INC. , California, USA)

growth_protocol: MLL-AF9 transformed c-kit+ bone marrow cells were transduced with pMIG or pMIG-TGIF1

treatment_protocol: 3 days after first transduction, the cells were sorted for GFP, seeded 1 day in medium, wherafter the cells were harvested and transferred to Trizol

tag: cell line

tag: genotype/variation

value: TGIF1 expression


title: OC2-WT adult 1

tag: Stage

tag: onecut genotype


title: MLL-AF9+pMIG#3

source_name: GFP-sorted MLL-AF9 transduced pMIG

value: MLL-AF9 transformed c-kit+ bone marrow cells

value: control


title: L395

tag: primary tumor site

tag: efs event

value: No event


title: ΔrpoZ_ 40 °C _24 h_biol.rep2

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

hyb_protocol: 500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).

data_processing: The scanned images were analyzed with Agilent's Feature Extraction program version 10.7.3. using  protocol GE1_107_Sep09 and Grid 016989_D_F_20070606. gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method.

organism: Synechocystis sp. PCC 6803

source_name: cells from mutant ΔrpoZ, 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h, biological replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrop 40 °C _24 hometer.

growth_protocol: Cell were grown in BG-11 medium in standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2)

extract_protocol: RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959). RNA was purified and DNase treated using RNeasy mini kit (Qiagen).

treatment_protocol: Cells grown in standard growth conditions (A730=1, 40 mL) were treated at 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h.

tag: strain

value: ΔrpoZ

tag: phenotype

value: glucose tolerant

tag: treatment protocol


title: MLL-AF9+pMIG-TGIF1#2


title: satellite cell cultures, treated with A-Cre Biological replica 2

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

description:
satellite cell cultures isolated from STOPFloxBmi1 mice, activated upon A-Cre infection Biological replica 2
4661287052_C

data_processing: The data were normalised using quantile normalisation with Lumi package in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: See Robson et al. PLOS One 2011

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit, including clean-up and DNase I treatment  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: satellite cell cultures isolated from STOPFloxBmi1 mice and  induced to differentiate for 2 days

tag: treatment

value: infected with Adeno-Cre


title: satellite cell cultures, treated with A-GFP Biological replica 3

description:
satellite cell cultures isolated from STOPFloxBmi1 mice,control infection using A-GFP  Biological replica 3
4661287052_F

value: infected with Adeno-GFP


title: MLL-AF9+pMIG-TGIF1#1


title: OC2-KO adult 1

value: retina


title: L393

tag: diagnosis

tag: study

tag: Sex

value: Other

tag: efs time (days)

tag: survival status

value: Dead

tag: survival time (days)


title: satellite cell cultures, treated with A-Cre Biological replica 3

description:
satellite cell cultures isolated from STOPFloxBmi1 mice, activated upon A-Cre infection Biological replica 3
4661287052_E


title: CS_ 40 °C _24 h_biol.rep3

source_name: cells from control strain, 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h, biological replicate 3

value: control strain


title: OC1-WT embryo 1

description: Gene expression information from isolated E14 retinas

tag: strain background

value: mixed

tag: tissue

value: WT


title: satellite cell cultures, treated with A-Cre Biological replica 1

description:
satellite cell cultures isolated from STOPFloxBmi1 mice, activated upon A-Cre infection Biological replica 1
4661287052_A

tag: genotype/variation


title: OC1-WT embryo 2

tag: Stage


title: satellite cell cultures, treated with A-GFP Biological replica 2

description:
satellite cell cultures isolated from STOPFloxBmi1 mice,control infection using A-GFP  Biological replica 2
4661287052_D


title: satellite cell cultures, treated with A-GFP Biological replica 1

description:
satellite cell cultures isolated from STOPFloxBmi1 mice,control infection using A-GFP  Biological replica 1
4661287052_B


title: OC1-KO embryo 2

tag: onecut genotype


title: ΔrpoZ_ 40 °C _24 h_biol.rep1

source_name: cells from mutant ΔrpoZ, 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h, biological replicate 1


title: CS_ 40 °C _24 h_biol.rep2

source_name: cells from control strain, 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h, biological replicate 2


title: MLL-AF9+pMIG#2

tag: cell line


title: L392

source_name: Primary tumor

value: Ewing sarcoma

value: Male

tag: age at enrollment (days)

tag: primary tumor site

tag: efs event

tag: experiment date

tag: tumor content


title: OC1-KO embryo 1


title: L391

tag: diagnosis

value: Female

value: Alive


title: L389

tag: study


title: CS_ 40 °C _24 h_biol.rep1

source_name: cells from control strain, 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h, biological replicate 1

tag: strain

tag: phenotype

tag: treatment protocol


title: ΔrpoZ_ 40 °C _24 h_biol.rep3

source_name: cells from mutant ΔrpoZ, 40 °C under continuous illumination, PPFD 40 µmol m-2s-1, for 24 h, biological replicate 3


title: MLL-AF9+pMIG#1

value: MLL-AF9 transformed c-kit+ bone marrow cells


title: L313

tag: Sex

value: Pelvis

value: Relapse

tag: efs time (days)

tag: survival status

tag: survival time (days)


title: Rice seedlings roots_V Replicate 2

city: Tainan

first: Hao-Jen

last: Huang

address: No.1, University Raod,

department: Life Sciences

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 2 of 3. Rice seedling roots with or without 1 mM-treated V

hyb_protocol: The fragmented labeled cRNA was then pooled and hybridized to the Rice Oligo DNA Microarray 44K RAP-DB (G2519F#15241; Agilent Technologies) at 60  C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to 1 mM V

label_protocol: Microarray RNA pool was prepared by combining a fixed volume of rice root samples collected at the following time points: 1 and 3 h. Briefly, 0.5 mg total RNAwas amplified by use of a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP (control samples) or Cy5-CTP (V-treatment) (CyDye, PerkinElmer, USA) during in vitro transcription. RNA was labeled with Cy3 or Cy5.

growth_protocol: Seeds of rice (O. sativa L. cv. TN67) were surface-disinfected with 2.5% (v/v) sodium hypochlorite (Katayama, Japan) for 15 min, then thoroughly washed in distilled water, and placed in 9-cm Petri dishes containing 25 ml distilled water at 37 ℃ in darkness for 3 days. Then, uniformly germinated seeds were selected and placed on filter paper discs (Advantec No.1) moistened with 10 ml distilled water in Petri dishes. Each Petri dish contained 15 germinated seeds that were grown for 3 days at 26 ℃ in darkness.

extract_protocol: Total RNA was isolated from each plant sample using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany) with some modification [40]. The concentrations of total RNA samples were measured by the use of NanodropND 2000 (Nanodrop Technologies, Wilmington, DE, USA). RNA samples >2 g/ l with high purity (OD260/280 > 2, OD260/230 > 2) underwent  microarray analysis and semi-quantitative RT-PCR.

treatment_protocol: Six-dayold rice samples (100 mg) treated with 1 mM V for 1 and 3 h were harvested for total RNA extraction.

tag: cultivar

tag: age

value: 6 day

tag: treatment

value: exposed to 1 mM V

source_name: Rice seedlings roots were exposed to water

value: exposed to water


title: Rice seedlings roots_V Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots with or without 1 mM-treated V


title: BcA86, biological replicate 2

city: Montreal

first: Cynthia

last: Kanagaratham

state: Quebec

address: 1650 Cedar Ave.

department: Human Genetics

country: Canada

institute: McGill University

description: Gene expression data from mouse whole lung tissue

hyb_protocol: Hybridization of cartidge arrays was done using the Gene-Chip Hybridization, Wash and Stain Kit (Affymetrix) following the manufacturer's instructions.

scan_protocol: Followng hybridization gene chip was processed with the Hybridization Wash and Stain Kit (Affymetrix) following the manufacturer's instructions. Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Raw data was analyzed using the FlexArray software (McGill University). Data was normalized by Robust Multi-array Average (RMA) method for ST array. Strains were compared by cyber-T test and markers were deemed as significant if their fold change was <0.71 or >1.4 and p<0.05.

source_name: BcA86 whole lung tissue

label_protocol: cRNA was created using the Ambion WT expression Kit (Affymetrix) and cRNA was labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: All animals were house in a specific pathogen free facility in 12 hours of darkness and 12 hours of light, and with access to food and water ad libitum. Animals were sacrified by carbon dioxide overdose and lungs were collected in RNAlater stabilization reagent (Qiagen). Samples were left in RNAlater solution overnight at 4 degrees then at -80 degrees for long term storage. Lungs were collected from three different mice for each strain.

extract_protocol: All RNA samples were extracted at the same time in the same manner using the RNeasy mini kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: All animals were naïve and untreated.

tag: tissue

value: whole lung


title: L312

tag: age at enrollment (days)

tag: primary tumor site

value: No event


title: BcA86, biological replicate 1


title: BcA86, biological replicate 3


title: L310

value: Other

tag: efs event

tag: experiment date


title: L388

tag: diagnosis

value: Dead

tag: tumor content


title: L309

tag: study