title: LCL_unique sample 54

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 58

status: Public on May 19 2016

type: RNA

city: Chapel Hill

first: Michael

middle: R

last: Knowles

state: NC

address: 7019 Thurston-Bowles Bldg; CB7248

country: USA

institute: UNC-Chapel Hill

hyb_protocol: For hybridization, a hybridization cocktail is prepared and added to the labeled cDNA target using the Hybridization, Wash and Stain kit (Affymetrix Cat. #900720), applied to Gene ST or Exon ST arrays, and incubated at 45°C for 16 hours.

scan_protocol: Following hybridization, arrays are washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner.

data_processing:
The deliverable CEL files were normalized by RMA (Robust Multi-array Average), quantile normalization, and log2 transformed probe set expression values were summarized by median polish based on a core class of probes using the command line software package, Affymetrix Power Tools (APT).  These probe set expression values were mapped to current gene annotations by BioConductor and annotation database hugene10stprobeset.db (Affymetrix Human Gene 1.0-ST Probeset Array Revision 8 annotation data): http://www.bioconductor.org/packages/devel/data/annotation/html/hugene10stprobeset.db.html.  Quality control (QC) assessments were performed using whole array statistics, such as mean background signal, mean all probe set signal, and signal variability according to manufacture recommendations.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell lines grown to between 4x105 and 8x105 cells/ml

label_protocol: Total RNA is converted to sense strand cDNA using Ambion WT Expression kit (Life technologies Cat. # 4440536), and subsequently labeled with Affymetrix GeneChip WT terminal labeling kit (Affymetrix Cat. #900671). Starting with 200ng of total RNA, single stranded cDNA is prepared through reverse transcription using T7 promoter primers. Single strand cDNA is then converted to double stranded cDNA using DNA polymerase and RNAse H to simultaneously degrade the RNA. Double stranded cDNA acts as a template for in vitro transcription of cRNA. Further, cRNA is purified to remove enzymes, salts, inorganic phosphates and unincorporated nucleotides and to improve the stability of cRNA.  To generate labeled sense stranded cDNA, 10 ugs of purified cRNA is used to as a template to synthesize sense strand cDNA by the reverse transcription with random primers and a mix of dUTP/dNTPs.  The sense strand cDNA is purified, fragmented, and labeled using the Affymetrix GeneChip WT Terminal labeling kit.

extract_protocol: Total RNA was isolated using the Qiagen miRNeasy kit followed by an ethanol precipitation for further purification.

tag: Sex

value: Male

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

value: No

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: LCL_unique sample 52

tag: Sex

value: Female

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc7

tag: plate

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 100 fim

type: genomic

city: Manchester

first: Sacha

last: Howell

address: Oglesby Cancer Research Centre

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: The University of Manchester

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

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

data_processing: Background correction was applied using minfi.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Fallopian tube tissue

label_protocol: Standard Illumina Protocol for Infinium 450k Chip

extract_protocol: Genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions.

tag: tissue

value: fallopian tube

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

value: fim


title: LCL_unique sample 50

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

value: UNKNOWN

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: LCL_unique sample 51

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 72 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

value: prox


title: LCL_unique sample 49

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: LCL_unique sample 48

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 47

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 98 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube


title: LCL_unique sample 46

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 87 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube


title: Patient 72 fim


title: LCL_unique sample 45

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 84 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube


title: Patient 98 prox


title: Patient 105 prox

tag: brca mut


title: Patient 105 fim


title: Patient 115 fim


title: Patient 92 prox


title: Patient 92 fim


title: Patient 84 fim


title: Patient 87 prox


title: LCL_unique sample 42

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

value: Yes

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 75 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 111 prox


title: Patient 77 fim


title: Patient 109 prox


title: Patient 74 fim


title: Patient 111 fim


title: Patient 77 prox


title: Patient 109 fim


title: Patient 75 prox


title: LCL_unique sample 41

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 71 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 44

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 43

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 76 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 76 prox


title: Patient 115 prox


title: LCL_unique sample 40

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 71 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 39

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: LCL_unique sample 37

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 97 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 38

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 104 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 36

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 104 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 35

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 97 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 101 prox


title: Patient 101 fim


title: LCL_unique sample 32

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 74 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 34

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: LCL_unique sample 31

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 33

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 95 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 30

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 99 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 99 prox


title: Patient 90 prox


title: Patient 96 prox


title: Patient 73 prox


title: Patient 95 prox


title: Patient 103 prox


title: LCL_unique sample 29

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 86 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 94 fim


title: Patient 90 fim


title: Patient 82 fim


title: LCL_unique sample 25

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 26

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 96 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 93 prox


title: Patient 93 fim


title: Patient 103 fim


title: LCL_unique sample 24

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 28

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 68 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 23

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Normally developed testes from lean rat, biological replicate 2

city: Winnipeg

first: Alemu

middle: Regassa

last: Hunde

state: Manitoba

address: 12 Dafoe Road

department: Animal Science

country: Canada

institute: University of Manitoba

description: Gene expression data from normally developed testes obtained from lean rat

hyb_protocol: Following fragmentation, 12.5 µg of biotinylated total RNA were hybridized for 16 hours at 45C on Affymetrix Chicken Genome Array. Genechips were washed and stained using Fluidics station 450 (Affymetrix).

scan_protocol: The stained chips were scanned using Scanner 3000 (Affynetrix)

data_processing: Data were background corrected and normalised using RMA (Expression Command Console, Affymetrix)

organism: Rattus norvegicus

source_name: Testes

label_protocol: 15 µg of biotinylated aRNA were prepared according to the standard Affymetrix protocol (WT PLUS Kit user manual, Affymetrix)

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

treatment_protocol: Testes were collected from 14 week old, sexually mature obese Zucker (fa/fa) rats.

tag: model

value: Zucker (fa/fa)

tag: phenotype

value: Lean


title: LCL_unique sample 27

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 86 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Under developed testes from obese rat, biological replicate 3

description: Gene expression data from under developed testes obtained from obese rat

tag: model

tag: phenotype

value: Obese


title: Patient 62 fim


title: Under developed testes from obese rat, biological replicate 4


title: Patient 58 prox


title: LCL_unique sample 21

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Under developed testes from obese rat, biological replicate 2

tag: model

tag: phenotype


title: Under developed testes from obese rat, biological replicate 1


title: Normally developed testes from lean rat, biological replicate 1


title: Normally developed testes from obese rat, biological replicate 4

description: Gene expression data from normally developed testes obtained from obese rat


title: Patient 68 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 20

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: LCL_unique sample 19

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 22

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Normally developed testes from obese rat, biological replicate 3

tag: model

tag: phenotype


title: LCL_unique sample 18

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 17

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: LCL_unique sample 16

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 62 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 55 fim


title: LCL_unique sample 15

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: HAEC_Corn_4h_Rep4

city: London

first: Caroline

last: Wheeler-Jones

address: Royal College Street

department: CBS

institute: Royal Veterinary College

description:
SAMPLE 23
Corn 4
8803836027_D_Grn.idat

hyb_protocol: 750 ng of each cRNA sample in a 5 µl volume was hybridization to arrays.  Arrays were washed and stained with Streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) according to the Illumina Whole Genome Gene Expression Direct Hybridisation manual.

scan_protocol: Arrays were scanned using  BeadArray Reader (Illumina, San Diego, CA) according to the manufacturer's instructions.

data_processing: Image data were imported into GenomeStudio (Illumina, San Diego, CA). Missing values were imputed. Non-normalised data and quantile normalised data were exported from GenomeStudio.

label: Biotin

molecule: polyA RNA

source_name: HAEC, Corn, 4 hours

label_protocol: Biotinylated cRNA was prepared using Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX) according to the manufacturer's instructions (AMIL1791)

growth_protocol: Human Aortic Endothelial Cells (HAEC) from Lonza were cultured according to suppliers instructions and grown to near confluence in 6 cm petri dishes and used on passage 7.

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit in accordance with manufacturer's instructions. Quality control was performed with Agilent Bioanalyser and all samples had RIN scores >9.

treatment_protocol: Cells were serum starved overnight in Endothelial Basal Medium (EBM) prior to 4 hour incubation with controls or CRLPs as indicated at 280 µM [triglyceride] prepared in EBM

tag: cell type

value: HAEC

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: Normally developed testes from obese rat, biological replicate 1

tag: model

tag: phenotype


title: HAEC_Palm_4h_Rep4

description:
SAMPLE 24
Palm 4
8803836027_B_Grn.idat

source_name: HAEC, Palm, 4 hours


title: Normally developed testes from obese rat, biological replicate 2


title: HAEC_DHASCO_4h_Rep4

description:
SAMPLE 22
DHASCO 4
8803836027_G_Grn.idat

source_name: HAEC, DHASCO, 4 hours


title: Patient 59 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 14

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 52 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 12

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 58 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 55 prox


title: Patient 52 prox


title: LCL_unique sample 13

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 11

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15


title: Patient 51 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: HAEC_RC_4h_Rep4

description:
SAMPLE 20
RC 4
8803836027_K_Grn.idat

source_name: HAEC, RC, 4 hours

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: LCL_unique sample 10

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: HAEC_PBS_4h_Rep4

description:
SAMPLE 19
PBS 4
8803836027_A_Grn.idat

source_name: HAEC, PBS, 4 hours

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: Patient 64 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 8

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18


title: Patient 53 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: HAEC_Corn_4h_Rep3

description:
SAMPLE 17
Corn 3
8803836027_E_Grn.idat

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: HAEC_DHASCO_4h_Rep3

description:
SAMPLE 16
DHASCO 3
8803836027_C_Grn.idat


title: LCL_unique sample 7

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: LCL_unique sample 6

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18


title: HAEC_Fish_4h_Rep3

description:
SAMPLE 15
Fish 3
8803836027_H_Grn.idat

source_name: HAEC, Fish, 4 hours

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: HAEC_Fish_4h_Rep4

description:
SAMPLE 21
Fish 4
8803836027_I_Grn.idat


title: LCL_unique sample 9

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: HAEC_Palm_4h_Rep3

description:
SAMPLE 18
Palm 3
8803836027_L_Grn.idat

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: LCL_unique sample 5

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18


title: Patient 45 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 65 fim


title: Patient 64 prox


title: Patient 51 fim


title: LCL_unique sample 4

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: HAEC_PBS_4h_Rep3

description:
SAMPLE 13
PBS 3
8803836027_J_Grn.idat

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: Patient 53 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: LCL_unique sample 3

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18


title: LCL_unique sample 2

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 19

tag: meconium ileus surrogate variable 20

tag: meconium ileus surrogate variable 21

tag: meconium ileus surrogate variable 22

tag: meconium ileus surrogate variable 23

tag: meconium ileus surrogate variable 24

tag: meconium ileus surrogate variable 25

tag: meconium ileus surrogate variable 26


title: Patient 43 prox

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 59 fim


title: HAEC_DHASCO_4h_Rep2

description:
SAMPLE 10
DHASCO 2
8803836026_J_Grn.idat

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: Patient 65 prox


title: HAEC_Palm_4h_Rep2

description:
SAMPLE 12
Palm 2
8803836026_H_Grn.idat


title: LCL_unique sample 1

tag: Sex

tag: consortium lung phenotype

tag: age of enrollment

tag: cftr genotype

tag: persistent ps aer status

tag: age of onset of persistent ps aer or censored age

tag: meconium ileus status

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: genotype pc4

tag: genotype pc5

tag: genotype pc6

tag: genotype pc7

tag: plate

tag: consortium lung phenotype surrogate variable

tag: pseudomonas aeruginosa surrogate variable 1

tag: meconium ileus surrogate variable 1

tag: meconium ileus surrogate variable 2

tag: meconium ileus surrogate variable 3

tag: meconium ileus surrogate variable 4

tag: meconium ileus surrogate variable 5

tag: meconium ileus surrogate variable 6

tag: meconium ileus surrogate variable 7

tag: meconium ileus surrogate variable 8

tag: meconium ileus surrogate variable 9

tag: meconium ileus surrogate variable 10

tag: meconium ileus surrogate variable 11

tag: meconium ileus surrogate variable 12

tag: meconium ileus surrogate variable 13

tag: meconium ileus surrogate variable 14

tag: meconium ileus surrogate variable 15

tag: meconium ileus surrogate variable 16

tag: meconium ileus surrogate variable 17

tag: meconium ileus surrogate variable 18


title: HAEC_RC_4h_Rep2

description:
SAMPLE 8
RC 2
8803836026_B_Grn.idat

tag: cell type

tag: incubation condition

tag: haec donor age

tag: haec donor sex

tag: haecs  lonza lot number


title: HAEC_Fish_4h_Rep2

description:
SAMPLE 9
Fish 2
8803836026_C_Grn.idat


title: HAEC_Corn_4h_Rep2

description:
SAMPLE 11
Corn 2
8803836026_K_Grn.idat


title: Patient 43 fim

tag: tissue

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube

tag: brca mut


title: Patient 44 fim


title: HAEC_PBS_4h_Rep2

description:
SAMPLE 7
PBS 2
8803836026_D_Grn.idat


title: Patient 41 prox


title: Patient 39 fim


title: Patient 39 prox


title: HAEC_Corn_4h_Rep1

description:
SAMPLE 5
Corn 1
8803836026_E_Grn.idat


title: HAEC_Fish_4h_Rep1

description:
SAMPLE 3
Fish 1
8803836026_A_Grn.idat


title: HAEC_DHASCO_4h_Rep1

description:
SAMPLE 4
DHASCO 1
8803836026_F_Grn.idat


title: Patient 44 prox


title: HAEC_RC_4h_Rep1

description:
SAMPLE 2
RC 1
8803836026_G_Grn.idat


title: Patient 37 prox


title: Patient 60 fim


title: Patient 35 prox


title: Patient 35 fim


title: Patient 49 prox


title: Patient 37 fim


title: HAEC_PBS_4h_Rep1

description:
SAMPLE 1
PBS 1
8803836026_I_Grn.idat


title: Patient 41 fim


title: Patient 34 fim


title: Patient 38 fim


title: Patient 60 prox


title: Patient 63 prox


title: HAEC_RC_4h_Rep3

description:
SAMPLE 14
RC 3
8803836027_F_Grn.idat


title: Patient 36 fim


title: HAEC_Palm_4h_Rep1

description:
SAMPLE 6
Palm 1
8803836026_L_Grn.idat


title: Patient 63 fim


title: Patient 50 prox


title: Patient 49 fim


title: Patient 61 prox


title: Patient 61 fim


title: Patient 54 fim


title: Patient 38 prox


title: Patient 36 prox


title: Patient 70 prox


title: Krt18-/- liver tissue 12 months_female_mouse49

city: Graz

first: Vendula

last: Svendova

address: Auenbruggerplatz 2

country: Austria

institute: Medical University Graz

description: liver tissue

hyb_protocol: 1.5 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3 / µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo 4 x 44 K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) and finally air-dried before scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA  Microarray C reader using using a scan Control software version A.8.4.1 and one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: From the intensity files the columns gProcessedSignal was used as expression value and normalized between samples using the geometric mean. Only those genes that were considered as present were used for the computation of the geometric mean.

organism: Mus musculus

source_name: liver tissue, aged 12 month

label_protocol: 200 ng RNA were incubuted with T7 RNA polymerase which simultaneaously amplifies RNA and incorporate Cy3-labeled CTP dye; preparation of the one-color spike mix and labeling according to the manufacturer`s protocol

growth_protocol: animals were maintained under specific pathogen-free (SPF) conditions in a temperature-controlled room (20-24ºC and humidity of 50-60%) with 12 hours light-dark rhythm and fed a standard diet (ssniff Spezialitäten GmbH, Soest, Germany) and water ad libitum

extract_protocol: RNA was isolated using the Qiagen RNeasy Mini Kit folllowing manufacturer's instructions

treatment_protocol: the mice were aged without any chemical treatment or special diets

value: liver

tag: background strain

tag: age

value: 12 months

tag: gender

value: female

tag: genotype


title: Patient 70 fim


title: Krt18-/- liver tissue 12 months_female_mouse47

description: liver tissue


title: Patient 67 fim


title: Patient 57 fim


title: Patient 69 fim


title: Patient 48 prox


title: Patient 40 prox


title: Krt18+/- liver tissue 12 months_male_mouse39

description: liver tissue

value: male


title: Patient 33 prox


title: Krt18-/- liver tissue 12 months_male_mouse44

description: liver tissue


title: Patient 57 prox


title: Patient 69 prox


title: Krt18+/- liver tissue 12 months_female_mouse43

description: liver tissue


title: wt liver tissue 12 months_female_mouse36

description: liver tissue

value: wt


title: Patient 47 prox


title: Patient 33 fim


title: Patient 46 fim


title: Patient 47 fim


title: Patient 34 prox


title: Krt18-/- liver tissue 12 months_male_mouse46

description: liver tissue


title: Patient 48 fim


title: Patient 45 prox


title: Patient 66 prox


title: Patient 46 prox


title: wt liver tissue 12 months_male_mouse34

description: liver tissue


title: Krt18-/- liver tissue 6 months_female_mouse33

description: liver tissue

source_name: liver tissue, aged 6 month

value: 6 months


title: Krt18-/- liver tissue 6 months_female_mouse31

description: liver tissue


title: Krt18-/- liver tissue 6 months_male_mouse30

description: liver tissue


title: Krt18-/- liver tissue 6 months_male_mouse28

description: liver tissue


title: Krt18-/- liver tissue 6 months_female_mouse32

description: liver tissue


title: Patient 56 fim


title: Krt18+/- liver tissue 6 months_female_mouse27

description: liver tissue


title: Patient 67 prox


title: Krt18+/- liver tissue 6 months_female_mouse25

description: liver tissue


title: wt liver tissue 6 months_female_mouse21

description: liver tissue


title: Patient 16 prox


title: Krt18+/- liver tissue 6 months_male_mouse22

description: liver tissue


title: Patient 19 prox


title: Krt18+/- liver tissue 12 months_female_mouse40

description: liver tissue


title: wt liver tissue 6 months_male_mouse18

description: liver tissue


title: wt liver tissue 6 months_female_mouse19

description: liver tissue


title: Patient 20 prox


title: wt liver tissue 6 months_female_mouse20

description: liver tissue


title: Patient 21 prox


title: wt liver tissue 12 months_female_mouse35

description: liver tissue


title: Patient 20 fim


title: Patient 56 prox


title: Patient 40 fim


title: Patient 16 fim


title: Patient 32 prox


title: Patient 19 fim


title: MED12 KD (Set 3_2)

city: San Antonio

first: NAM HEE

last: KIM

state: TX

address: 7703 Floyd Curl Dr.

department: Molecular Medicine/IBT

institute: UTHSCSA

description: set 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using Illumina iScan System using standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with Illumina Genome Studio.

source_name: mNS-5 NSC

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit.

growth_protocol: mNS-5 cells were maintained on 0.1% (v/v) gelatin-coated tissue culture plates in RHB-A media supplemented with 10 ng/ml FGF-2, 10 ng/ml EGF, 2 mM L-glutamine, 100 units/ml penicillin, and 100 ug/ml streptomycin.

extract_protocol: RNA was isolated using the Qiagen Rneasy Mini Kit following the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: mNS-5 cells were infected with lentiviruses expressing non-silencing control or MED12 shRNAs. 24 hours after lentivirus infection, the medium was removed and replaced with fresh medium containing 600ng/ml puromycin for selection. Cells were harvested 5.5 days after virus infection.

tag: cell line

value: mouse ES cell-derived NSC

tag: lentivirus

value: MED12-specific shRNAs


title: Patient 14 prox

value: fallopian tube


title: wt liver tissue 6 months_male_mouse17

description: liver tissue


title: Patient 26 fim

value: fim


title: Patient 32 fim


title: Patient 42 prox


title: Patient 22 prox


title: MED12 KD (Set 2_2)

description: set 2


title: Patient 21 fim


title: MED12 KD (Set 1_2)

description: set 1


title: Patient 14 fim


title: Krt18-/- liver tissue 3 months_male_mouse12

description: liver tissue

source_name: liver tissue, aged 3 month

value: 3 months


title: Krt18-/- liver tissue 3 months_male_mouse13

description: liver tissue


title: Patient 18 fim


title: MED12 KD (Set 1)

description: set 1


title: MED12 KD (Set 2)

description: set 2


title: Patient 25 prox

value: prox


title: Patient 31 fim


title: Krt18-/- liver tissue 3 months_female_mouse16

description: liver tissue


title: Non-silencing (NS) control (Set 3)

description: set 3

value: nonsilencing control


title: Krt18+/- liver tissue 3 months_female_mouse10

description: liver tissue

data_processing: From the intensity files the columns gProcessedSignal was used as expression value and normalized between samples using the geometric mean.


title: Non-silencing (NS) control (Set 1)

description: set 1


title: Krt18-/- liver tissue 3 months_female_mouse14

description: liver tissue


title: Krt18+/- liver tissue 3 months_female_mouse8

description: liver tissue


title: Non-silencing (NS) control (Set 2)

description: set 2


title: MED12 KD (Set 3)

description: set 3


title: Krt18+/- liver tissue 3 months_female_mouse9

description: liver tissue


title: Patient 26 prox


title: Patient 31 prox


title: Krt18+/- liver tissue 3 months_male_mouse6

description: liver tissue

data_processing: From the intensity files the columns gProcessedSignal was used as expression value and normalized between samples using the geometric mean.Only those genes that were considered as present were used for the computation of the geometric mean.


title: [D14]-[-/-]-[3]

city: Rehovot

first: Tamar

last: Farfel-Becker

address: Weizmann Institute of sciense

country: Israel

institute: Weizmann Institute of sciense

description:
TF24_MoST.CEL
Each litter was born in a different cage i.e. has the same parents.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol. Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization. This A P value was computed using a  3-way ANOVA model
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na31.mm9.transcript.csv

source_name: Day 14_flox/flox

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Gba-flox/flox;nestin-Cre mice were used as a model of nGD. Gba-flox/flox mice were crossed with Gba-flox/wt;nestin-Cre mice to generate Gba-flox/flox;nestin-Cre mice (referred to as -/- mice) and Gba-flox/wt;nestin-Cre mice (referred to as +/- mice), which served as healthy controls. Ten and 14 day-old mice were sacrificed and their brains removed and placed on a Young Mouse Brain Slicer Matrix (BSMYS001-1, Zivic instruments, PA, USA). Single-edge razor blades were inserted into the matrix to generate 1 mm coronal sections. The section containing the VPM/VPL of the thalamus was snap-frozen on dry ice, and 17 g (1 mm diameter) blunt needles attached to a syringe used to remove this brain area.The sample was placed in an Eppendorf tube, snap-frozen in liquid N2 and stored at -80°C. All dissection tools were first cleaned with surface decontaminate RNase away (Molecular BioProducts, Inc., San Diego, CA).

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions, which included a DNase step and addition of β-mercaptoethanol.

treatment_protocol: Day 10 and day 14 RNA samples were prepared and analysed seperatly.

tag: genotype/variation

value: Gba-flox/flox;nestin-Cre

value: 14 days

value: brain; VPM/VPL of the thalamus

tag: litter number


title: Krt18+/- liver tissue 3 months_male_mouse5

description: liver tissue


title: [D14]-[+/-]-[3]

description:
TF20_MoST.CEL
Each litter was born in a different cage i.e. has the same parents.

source_name: Day 14_flox/wt

value: Gba-flox/wt;nestin-Cre


title: wt liver tissue 3 months_female_mouse4

description: liver tissue

value: liver


title: [D14]-[-/-]-[2]

description:
TF23_MoST.CEL
Each litter was born in a different cage i.e. has the same parents.


title: Embryo poly(A)+ RNA WT vs. wisp Replicate 3

status: Public on May 18 2016

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: Poly(A)+ RNA comparison of WT vs. wisp fertilized embryos biological replicate 3 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.

hyb_protocol: Drosophila oligonucleotide microarrays (Agilent Design ID 18972, Agilent, Foster City, CA) were hybridized with labeled cDNA in 1X Hi-RPM Hybridization buffer (Agilent) at 60 °C for 16 hr.

scan_protocol: Microarray images were acquired using an Axon GenePix 4000B scanner reading at wavelengths of 635 nm and 532 nm and then analyzed using GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).

data_processing:
Microarrays comparing poly(A)+ RNAs were processed differently. Our initial analyses of these data suggested that there was good correlation between each of the different experimental replicates, but that the dynamic range of enrichment values varied significantly between them. Because each of these samples was subject to poly(A)+ purification, the effectiveness of which cannot be easily assessed, the level of ‘enrichment’ detected for any given transcript is likely to vary from one microarray to the next. To account for these different dynamic ranges, quantile normalization was used to adjust the data from each of the six experimental replicates. Briefly, the data from each replicate experiment were ranked from highest to lowest enrichment. From these lists, an average value was determined for each of the ranked positions. The average values were then re-assigned to the individual transcripts from each experiment according to their ranks. Note that this approach yielded data that were different from a typical microarray in so much as the log-transformed ratio values did not fit a normal distribution centered about zero, but rather appeared skewed towards depletion in the wisp strain. The validity of this approach was empirically tested, as described in the Results section. After quantile normalization, we again used SAM to identify genes that showed either enrichment or depletion within the poly(A)+ pool of wisp RNAs. While SAM allows for a determination of statistical significance, the appropriate threshold for biological significance is not as readily apparent because of the challenge in normalizing these data. As such, we sampled the genes that were determined to be statistically significantly enriched using an independent experimental assay to determine the limits of biological significance
normalized log2 ratio (control/wisp-deficient)

organism: Drosophila melanogaster

source_name: control

label_protocol: cDNA was synthesized from 40 μg of total RNA or 800 ng of poly(A)-selected mRNA in a 200 μl reaction mixture containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 0.375 mM dATP, 0.375 mM dCTP, 0.375 mM dGTP, 0.225 mM dTTP, 0.05 mM aminoallyl-dUTP. 50 μg dN9 primer, and 20 ng murine Moloney leukemia virus (M-MLV) reverse transcriptase. Reactions were incubated at 42 °C for at least 2 hr and then cDNAs were purified using a Zymo25 DNA purification column (Zymo Research, Orange, CA).   The purified cDNA was divided into halves. One half was conjugated to Cy3 and the other to the Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) to generate dye-swap pairs. Dye conjugation was performed at 60 °C for 60 min in a 10 μl reaction containing 50 mM sodium bicarbonate (pH 9.0), 50% DMSO, and ~20 μg of NHS-derivatized fluorophore. Labeled cDNA was purified using a Zymo25 DNA purification column.

growth_protocol: Male flies carrying the wisp null allele, wisp41 were crossed to Df(1)RA47/FM7c female flies. wisp41/FM7c (wild type control) or wisp41/Df (wisp-deficient) virgin female progeny were separated from males and aged on standard yeast/glucose medium until use. Stage 14 oocytes were hand dissected from 3- to 5-day-old virgin females in hypertonic isolation buffer, which does not activate eggs. Virgin females that were 3 to 4 days old were mated to wild-type Oregon-R males and embryos were collected 0- to 1-hr post egg deposition.

extract_protocol: For each sample, total RNA was extracted from ~2000 stage 14 oocytes or 0- to 1-hr embryos using the TRIzol reagent (Invitrogen, Carlsbad, CA).  Polyadenylated RNA was then isolated from total RNA using the Oligotex mRNA isolation kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.

value: fertilized embryos

tag: Stage

value: 0-1 hour post egg deposition

tag: female strain

source_name: wisp-deficient


title: Embryo poly(A)+ RNA WT vs. wisp Replicate 2

description: Poly(A)+ RNA comparison of WT vs. wisp fertilized embryos biological replicate 2 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: [D14]-[+/-]-[2]

description:
TF19_MoST.CEL
Each litter was born in a different cage i.e. has the same parents.

value: female


title: [D14]-[+/-]-[1]

description:
TF18_MoST.CEL
Each litter was born in a different cage i.e. has the same parents.

value: male


title: wt liver tissue 3 months_male_mouse3

description: liver tissue

value: wt


title: Patient 25 fim


title: Embryo poly(A)+ RNA WT vs. wisp Replicate 3 dye-swap

description: Poly(A)+ RNA comparison of WT vs. wisp fertilized embryos biological replicate 3 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Embryo total RNA WT vs. wisp Replicate 3 dye-swap

description: Total RNA comparison of WT vs. wisp fertilized embryos biological replicate 3 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Embryo poly(A)+ RNA WT vs. wisp Replicate 2 dye-swap

description: Poly(A)+ RNA comparison of WT vs. wisp fertilized embryos biological replicate 2 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Embryo poly(A)+ RNA WT vs. wisp Replicate 1 dye-swap

description: Poly(A)+ RNA comparison of WT vs. wisp fertilized embryos biological replicate 1 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Embryo poly(A)+ RNA WT vs. wisp Replicate 1

description: Poly(A)+ RNA comparison of WT vs. wisp fertilized embryos biological replicate 1 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Embryo total RNA WT vs. wisp Replicate 2 dye-swap

description: Total RNA comparison of WT vs. wisp fertilized embryos biological replicate 2 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Embryo total RNA WT vs. wisp Replicate 2

description: Total RNA comparison of WT vs. wisp fertilized embryos biological replicate 2 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Embryo total RNA WT vs. wisp Replicate 1 dye-swap

description: Total RNA comparison of WT vs. wisp fertilized embryos biological replicate 1 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Oocyte poly(A)+ RNA WT vs. wisp Replicate 3 dye-swap

description: Poly(A)+ RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 3 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.

value: oocytes

value: stage 14


title: Embryo total RNA WT vs. wisp Replicate 1

description: Total RNA comparison of WT vs. wisp fertilized embryos biological replicate 1 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Embryo total RNA WT vs. wisp Replicate 3

description: Total RNA comparison of WT vs. wisp fertilized embryos biological replicate 3 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Oocyte poly(A)+ RNA WT vs. wisp Replicate 3

description: Poly(A)+ RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 3 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Oocyte poly(A)+ RNA WT vs. wisp Replicate 2 dye-swap

description: Poly(A)+ RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 2 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Patient 27 fim

value: fallopian tube


title: [D14]-[-/-]-[1]

description:
TF22_MoST.CEL
Each litter was born in a different cage i.e. has the same parents.


title: Patient 15 prox


title: Patient 18 prox


title: Patient 17 fim

value: fim


title: Patient 27 prox


title: Patient 24 prox


title: Patient 22 fim


title: Oocyte poly(A)+ RNA WT vs. wisp Replicate 2

description: Poly(A)+ RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 2 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Oocyte poly(A)+ RNA WT vs. wisp Replicate 1 dye-swap

description: Poly(A)+ RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 1 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Oocyte poly(A)+ RNA WT vs. wisp Replicate 1

description: Poly(A)+ RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 1 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Oocyte total RNA WT vs. wisp Replicate 3

description: Total RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 3 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: wt liver tissue 3 months_male_mouse2

description: liver tissue

value: 3 months


title: Oocyte total RNA WT vs. wisp Replicate 2 dye-swap

description: Total RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 2 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Patient 15 fim


title: Oocyte total RNA WT vs. wisp Replicate 3 dye-swap

description: Total RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 3 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Oocyte total RNA WT vs. wisp Replicate 2

description: Total RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 2 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Oocyte total RNA WT vs. wisp Replicate 1 dye-swap

description: Total RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 1 of 3. Labeling molelues are swaped. WT is labeled with Cy5 and wisp-deficient is labeled with Cy3.


title: Oocyte total RNA WT vs. wisp Replicate 1

description: Total RNA comparison of WT vs. wisp stage 14 oocytes biological replicate 1 of 3. WT is labeled with Cy3 and wisp-deficient is labeled with Cy5.


title: Patient 24 fim


title: Patient 30 prox

value: prox


title: Patient 29 fim


title: Patient 30 fim


title: Liver, high-phosphorus diet administrated for 24d, biological rep4

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were quantified with the Factor Analysis for Robust Microarray Summarization (FARMS, v1.4.1) method, using the statistical language R (R-2.13.1) and Bioconductor 2.8.

source_name: liver_high-phosphorus diet for 24d

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen Life Technologies Corp.), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Excised liver sample was immediately immersed in RNAlater and treated according to the manufacturer's protocol.

tag: strain

value: Wistar

value: Male

value: 8 weeks

tag: diet

value: 1.2% phosphorus containing diet for 24d


title: Liver, control diet administrated for 24d, biological rep4

source_name: liver_control diet for 24d

value: control AIN-93G diet for 24d


title: Liver, high-phosphorus diet administrated for 24d, biological rep1

value: liver


title: Liver, control diet administrated for 24d, biological rep3


title: Liver, high-phosphorus diet administrated for 24d, biological rep3


title: tail-1822

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description: Gene expression data from untreated P56 mouse skin

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates.  Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and a custom probe database which avoids SNPs in FVB and Spretus genomes. Data were batch-corrected for plate and genotype and then log2 transformed.

source_name: tail skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in standard conditions with standard chow and water ad libitum

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were aged to 8 weeks, untreated

value: WT

tag: plate

value: no

tag: Sex

value: F


title: Patient 23 fim

source_name: Fallopian tube tissue

tag: tissue


title: Patient 29 prox

tag: fimbrial (fim) or proximal (prox) end of the fallopian tube


title: Patient 28 fim


title: Liver, high-phosphorus diet administrated for 24d, biological rep2


title: tail-1828


title: tail-1831

value: M


title: tail-1826


title: tail-1830


title: tail-1821


title: tail-1833


title: tail-1834


title: tail-1809


title: tail-1827


title: tail-1811


title: tail-1815


title: Liver, control diet administrated for 24d, biological rep1


title: tail-1801


title: tail-1829


title: tail-1796


title: tail-1790


title: tail-1791


title: tail-1784

value: HET


title: Liver, control diet administrated for 24d, biological rep2


title: tail-1780


title: tail-1783


title: tail-1789


title: tail-1777


title: tail-1773


title: tail-1767


title: tail-1768


title: tail-1775


title: tail-1764


title: tail-1778


title: tail-1760


title: tail-1782


title: tail-1787


title: tail-1772


title: tail-1763


title: tail-1762


title: tail-1759


title: tail-1755


title: tail-1753


title: tail-1750


title: tail-1770


title: tail-1741


title: tail-1743


title: tail-1757


title: tail-1756


title: tail-1785


title: tail-1744


title: tail-1746


title: tail-1739


title: tail-1735


title: tail-1734


title: tail-1736


title: tail-1733


title: tail-1737


title: tail-1695


title: tail-1698


title: tail-1704


title: tail-1685


title: tail-1732


title: tail-1731


title: tail-1717


title: tail-1696


title: tail-1708


title: tail-1699


title: tail-1691


title: tail-1738


title: tail-1700

value: yes


title: tail-1716


title: tail-1684


title: tail-1669


title: tail-1662


title: tail-1683


title: tail-1670


title: tail-1666


title: tail-1652


title: tail-1697


title: tail-1651


title: tail-1686


title: tail-1631


title: tail-1632


title: tail-1618


title: tail-1592


title: tail-1613


title: tail-1596


title: tail-1609


title: tail-1577


title: tail-1588


title: tail-1646


title: tail-1574


title: tail-1615


title: tail-1562


title: tail-1573


title: tail-1589


title: tail-1543


title: tail-1538


title: tail-1533


title: tail-1547


title: tail-1532


title: tail-1525


title: tail-1580


title: tail-1550


title: tail-1554


title: tail-1530


title: tail-1546


title: tail-1556


title: tail-1593


title: tail-1540


title: tail-1539


title: tail-1522


title: tail-1520


title: tail-1518


title: tail-1521


title: tail-1524


title: tail-1508


title: tail-1498


title: tail-1502


title: tail-1507


title: tail-1488


title: tail-1454


title: tail-1492


title: tail-1460


title: tail-1496


title: tail-1490


title: tail-1495


title: tail-1464


title: tail-1431


title: tail-1433


title: tail-1485


title: tail-1451


title: tail-1463


title: tail-1429


title: tail-1413


title: tail-1455


title: tail-1430


title: tail-1416


title: tail-1468


title: tail-1456


title: tail-1405


title: tail-1398


title: tail-1397


title: tail-1392


title: tail-1422


title: tail-1395


title: tail-1383


title: tail-1388


title: tail-1374


title: tail-1406


title: tail-1379


title: tail-1358


title: tail-1373


title: tail-1370


title: tail-1378


title: tail-1356


title: tail-1369


title: tail-1366


title: back-1111

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and then log2 transformed

source_name: dorsal skin

value: back

tag: batch


title: tail-1105

value: tail


title: back-1105


title: tail-1102


title: tail-1094


title: tail-1101


title: back-1094


title: back-1101


title: tail-1109


title: tail-1110


title: tail-1111


title: back-1102


title: back-1110


title: back-1115


title: tail-1115


title: back-1109


title: back-1100


title: tail-1100


title: tail-1093


title: tail-1092


title: tail-1088


title: back-1088


title: tail-1086


title: back-1086


title: back-1087


title: back-1093


title: tail-1087


title: back-1085


title: back-1092


title: back-1084


title: tail-1084


title: back-1082


title: tail-1080