title: Spinal cord G93A-SOD1 age 100 days rep1

description:
SPCT100N01
replicate 1


title: V7 tassel, biological replicate 1

status: Public on Mar 01 2013

type: RNA

city: Guelph

first: Gregory

middle: S

last: Downs

address: 50 Stone Road E

country: Canada

institute: University of Guelph

hyb_protocol: Labeled cRNAs were fragmented and applied to a maize custom GeneChip microarray for molecular hybridization.

scan_protocol: The array images with hybridization signals were acquired and quantified by GeneChip Operation System (GCOS) software (Affymetrix).

data_processing: CEL files were normalized using the Robust Multichip Average (RMA) method from the “affy” library of the BioConductor package (version 2.6) of the R statistical framework (version 2.11.0)

label: biotin

molecule: total RNA

organism: Zea mays

source_name: V7 tassel

label_protocol: Labeling followed a standard protocol recommended by Affymetrix.

growth_protocol: An elite Syngenta Zea mays (maize) inbred (SRG200) was grown in a greenhouse at the University of Guelph during the summer of 2007. Growth conditions were 16 hour days (~600 μmol m-2 s-1) at 28°C, 8 hour nights at 23°C, and 50% relative humidity. Plants were grown semi-hydroponically in pots containing Turface® clay, watered with a modified Hoagland’s solution containing: 0.4 g/L 28-14-14 fertilizer, 0.4 g/L 15-15-30 fertilizer, 0.2 g/L NH4NO3, 0.4 g/L of MgSO4•7H2O and 0.03 g/L of micronutrient mix (S, Co, Cu, Fe, Mn, Mo and Zn).

extract_protocol: Total RNA was isolated and used for cDNA, cRNA synthesis.

treatment_protocol: Three biological replicates per sample were harvested in the middle of the day to minimize complications due to diurnal changes in C and N metabolism.

tag: developmental stage

tag: tissue

value: tassel


title: Spinal cord G93A-SOD1 age 70 days rep6

city: Utrecht

first: C.

last: Saris

address: Heidelberglaan 100

department: Neurology

country: Netherlands

institute: UMC Utrecht

description:
SPCT070N06
replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Mus musculus

source_name: Mouse lumbar spinal cord

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

extract_protocol: Blood from mice was collected directly into a PreAnalytix PAXgene tube (Qiagen, Venlo, The Netherlands) and the RNA was isolated using the PreAnalytix PAXgene Blood RNA kit (Qiagen). Blood total mRNA samples were treated with the Ambion GLOBINclear Mouse/Rat kit (Ambion, Austin TX, USA) to remove mouse hemoglobin mRNA. In mice, the tibialis anterior muscles were removed; the left tibialis anterior was used for mRNA isolation. Lumbar spinal cord was homogenized in lysis buffer (RLT-β-mercaptoethanol) using a T25 Ultra-Turrax homogenizer (IKA Labor Technik, Staufen, Germany). mRNA was isolated using an RNeasy RNA isolation kit (Qiagen). All kits were used according to the manufacturers’ protocol.

tag: genotype/variation

tag: strain

tag: age

value: 70 days

value: lumbar spinal cord


title: V7 top ear shoot, biological replicate 3

source_name: V7 top ear shoot

value: top ear shoot


title: Spinal cord G93A-SOD1 age 70 days rep4

description:
SPCT070N04
replicate 4


title: V8-V9 tassel, biological replicate 1

source_name: V8-V9 tassel


title: Spinal cord G93A-SOD1 age 70 days rep5

description:
SPCT070N05
replicate 5


title: Spinal cord G93A-SOD1 age 70 days rep7

description:
SPCT070N07
replicate 7


title: V7 top ear shoot, biological replicate 1


title: V7 top ear shoot, biological replicate 2


title: Spinal cord wild type age 100 days rep7

description:
SPCW100N07
replicate 7

value: Wild type littermate

value: 100 days


title: V5 leaf, biological replicate 3

source_name: V5 leaf

value: leaf


title: Muscle wild type age 100 days rep6

description:
MUSW100N06
replicate 6

source_name: Mouse tibialis anterior muscle

value: tibialis anterior muscle


title: V5 nodal root, biological replicate 3

source_name: V5 nodal root

value: nodal root


title: Muscle wild type age 100 days rep2

description:
MUSW100N02
replicate 2


title: Muscle wild type age 100 days rep3

description:
MUSW100N03
replicate 3


title: V5 seminal root, biological replicate 3

source_name: V5 seminal root

value: seminal root


title: V5 stalk below tassel, biological replicate 1

source_name: V5 stalk below tassel

value: stalk below tassel


title: Spinal cord G93A-SOD1 age 70 days rep3

description:
SPCT070N03
replicate 3


title: Muscle wild type age 100 days rep7

description:
MUSW100N07
replicate 7


title: V5 leaf, biological replicate 2


title: V5 leaf, biological replicate 1


title: Spinal cord G93A-SOD1 age 70 days rep1

description:
SPCT070N01
replicate 1


title: Muscle wild type age 100 days rep5

description:
MUSW100N05
replicate 5


title: Muscle wild type age 100 days rep4

description:
MUSW100N04
replicate 4


title: V5 stalk below tassel, biological replicate 2


title: V5 nodal root, biological replicate 1


title: Muscle wild type age 100 days rep1

description:
MUSW100N01
replicate 1


title: V5 nodal root, biological replicate 2


title: Spinal cord G93A-SOD1 age 70 days rep2

description:
SPCT070N02
replicate 2


title: Muscle wild type age 70 days rep8

description:
MUSW070N08
replicate 8


title: Muscle wild type age 70 days rep7

description:
MUSW070N07
replicate 7


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 20 nM endoxifen, 24 h, rep 3

city: Rochester

first: John

last: Hawse

state: MN

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

country: USA

institute: Mayo Clinic

description:
Replicate 3
Sample name: 75

data_processing: The raw data was pre-processed by Illumina's beadstudio without backgroud subtraction and probe level profile was obtained. This data was exported, log2 ransformed and normalized using fast lowess normalization in R

organism: Homo sapiens

source_name: Parental MCF7 cells

label_protocol: standard Illumina protocol

growth_protocol: MCF7 cells were routinely cultured in phenol red-free Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12) medium containing 10% (v/v) Fetal Bovine Serum (FBS) and 1% (v/v) antibiotic-antimycotic (AA) solution in a humidified 37°C incubator with 5% CO2.

extract_protocol: Total RNA was isolated using Trizol reagent.

treatment_protocol: One day prior to and during ligand treatments, cells were cultured in the same media containing 10% 3X charcoal stripped FBS to deplete them of steroid exposure.

tag: treatment

tag: cell line

tag: cell type

value: breast cancer


title: V5 seminal root, biological replicate 2


title: V5 stalk below tassel, biological replicate 3


title: Muscle wild type age 70 days rep6

description:
MUSW070N06
replicate 6


title: Muscle wild type age 70 days rep5

description:
MUSW070N05
replicate 5


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 20 nM endoxifen, 24 h, rep 2

description:
Replicate 2
Sample name: 74


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 20 nM endoxifen, 24 h, rep 1

description:
Replicate 1
Sample name: 73


title: Muscle wild type age 70 days rep4

description:
MUSW070N04
replicate 4


title: V5 seminal root, biological replicate 1


title: V2 leaf, biological replicate 3

source_name: V2 leaf


title: Muscle wild type age 70 days rep2

description:
MUSW070N02
replicate 2


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 100 nM endoxifen, 24 h, rep 3

description:
Replicate 3
Sample name: 69


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 100 nM endoxifen, 24 h, rep 2

description:
Replicate 2
Sample name: 68


title: Muscle G93A-SOD1 age 100 days rep5

description:
MUST100N05
replicate 5


title: V2 leaf, biological replicate 1


title: Muscle wild type age 70 days rep1

description:
MUSW070N01
replicate 1


title: Muscle G93A-SOD1 age 100 days rep7

description:
MUST100N07
replicate 7


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 1000 nM endoxifen, 24 h, rep 3

description:
Replicate 3
Sample name: 66


title: Muscle G93A-SOD1 age 100 days rep2

description:
MUST100N02
replicate 2


title: Muscle G93A-SOD1 age 100 days rep3

description:
MUST100N03
replicate 3


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 100 nM endoxifen, 24 h, rep 1

description:
Replicate 1
Sample name: 67


title: Muscle G93A-SOD1 age 70 days rep7

description:
MUST070N07
replicate 7


title: Muscle G93A-SOD1 age 100 days rep1

description:
MUST100N01
replicate 1


title: V2 leaf, biological replicate 2


title: V2 stalk, biological replicate 3

source_name: V2 stalk

value: stalk


title: V2 stalk, biological replicate 1


title: Muscle G93A-SOD1 age 100 days rep6

description:
MUST100N06
replicate 6


title: V2 stalk, biological replicate 2


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen, 24 h, rep 3

description:
Replicate 3
Sample name: 63


title: Muscle wild type age 70 days rep3

description:
MUSW070N03
replicate 3


title: V2 nodal root, biological replicate 3

source_name: V2 nodal root


title: Muscle G93A-SOD1 age 70 days rep5

description:
MUST070N05
replicate 5


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 1000 nM endoxifen, 24 h, rep 2

description:
Replicate 2
Sample name: 65


title: Muscle G93A-SOD1 age 70 days rep6

description:
MUST070N06
replicate 6


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen + 1000 nM endoxifen, 24 h, rep 1

description:
Replicate 1
Sample name: 64


title: V2 nodal root, biological replicate 2


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen, 24 h, rep 1

description:
Replicate 1
Sample name: 61


title: Muscle G93A-SOD1 age 70 days rep3

description:
MUST070N03
replicate 3


title: Muscle G93A-SOD1 age 70 days rep1

description:
MUST070N01
replicate 1


title: Muscle G93A-SOD1 age 70 days rep2

description:
MUST070N02
replicate 2


title: V2 seminal root, biological replicate 1

source_name: V2 seminal root


title: Blood wild type age 100 days rep7

description:
BLDW100N07
replicate 7

source_name: Mouse Whole blood

value: Whole blood


title: Muscle G93A-SOD1 age 70 days rep8

description:
MUST070N08
replicate 8


title: MCF7, 10 nM estradiol + 300 nM tamoxifen + 7 nM 4HT + 700 nM N-desmethyl-tamoxifen, 24 h, rep 2

description:
Replicate 2
Sample name: 62


title: V2 nodal root, biological replicate 1


title: Blood wild type age 100 days rep5

description:
BLDW100N05
replicate 5


title: Muscle G93A-SOD1 age 100 days rep4

description:
MUST100N04
replicate 4


title: Blood wild type age 100 days rep3

description:
BLDW100N03
replicate 3


title: Muscle G93A-SOD1 age 70 days rep4

description:
MUST070N04
replicate 4


title: MCF7, 10 nM estradiol + 100 nM ICI, 24 h, rep 2

description:
Replicate 2
Sample name: 44

value: 10 nM estradiol + 100 nM ICI


title: MCF7, 10 nM estradiol + 100 nM ICI, 24 h, rep 3

description:
Replicate 3
Sample name: 45


title: Blood wild type age 100 days rep6

description:
BLDW100N06
replicate 6


title: MCF7, 10 nM estradiol + 100 nM ICI, 24 h, rep 1

description:
Replicate 1
Sample name: 43


title: Blood wild type age 100 days rep4

description:
BLDW100N04
replicate 4


title: Blood wild type age 100 days rep1

description:
BLDW100N01
replicate 1


title: MCF7, 10 nM estradiol + 100 nM endoxifen, 24 h, rep 2

description:
Replicate 2
Sample name: 41

value: 10 nM estradiol + 100 nM endoxifen


title: Blood wild type age 70 days rep5

description:
BLDW070N05
replicate 5


title: V2 seminal root, biological replicate 2


title: Blood wild type age 100 days rep2

description:
BLDW100N02
replicate 2


title: MCF7, 10 nM estradiol + 100 nM 4HT, 24 h, rep 3

description:
Replicate 3
Sample name: 39

value: 10 nM estradiol + 100 nM 4HT


title: V1 leaf, biological replicate 3

source_name: V1 leaf


title: Blood G93A-SOD1 age 100 days rep6

description:
BLDT100N06
replicate 6


title: MCF7, 10 nM estradiol + 100 nM 4HT, 24 h, rep 1

description:
Replicate 1
Sample name: 37


title: V2 seminal root, biological replicate 3


title: MCF7, 10 nM estradiol, 24 h, rep 3

description:
Replicate 3
Sample name: 36

value: 10 nM estradiol


title: MCF7, 10 nM estradiol + 100 nM endoxifen, 24 h, rep 3

description:
Replicate 3
Sample name: 42


title: V1 leaf, biological replicate 2


title: Blood wild type age 70 days rep6

description:
BLDW070N06
replicate 6

value: 70 days


title: MCF7, 10 nM estradiol + 100 nM endoxifen, 24 h, rep 1

description:
Replicate 1
Sample name: 40


title: Blood wild type age 70 days rep4

description:
BLDW070N04
replicate 4


title: V1 root, biological replicate 2

source_name: V1 root

value: root


title: Blood wild type age 70 days rep8

description:
BLDW070N08
replicate 8


title: Blood G93A-SOD1 age 100 days rep5

description:
BLDT100N05
replicate 5


title: Blood wild type age 70 days rep2

description:
BLDW070N02
replicate 2


title: Blood wild type age 70 days rep7

description:
BLDW070N07
replicate 7


title: Blood wild type age 70 days rep3

description:
BLDW070N03
replicate 3


title: Blood G93A-SOD1 age 100 days rep7

description:
BLDT100N07
replicate 7


title: Blood wild type age 70 days rep1

description:
BLDW070N01
replicate 1


title: Blood G93A-SOD1 age 100 days rep8

description:
BLDT100N08
replicate 8


title: MCF7, 10 nM estradiol + 100 nM 4HT, 24 h, rep 2

description:
Replicate 2
Sample name: 38


title: V1 root, biological replicate 3


title: V1 root, biological replicate 1


title: VE root, biological replicate 3

source_name: VE root

value: VE (germination and emergence)


title: MCF7, 10 nM estradiol, 24 h, rep 2

description:
Replicate 2
Sample name: 35


title: VE root, biological replicate 2


title: Blood G93A-SOD1 age 100 days rep2

description:
BLDT100N02
replicate 2


title: Blood G93A-SOD1 age 100 days rep3

description:
BLDT100N03
replicate 3


title: VE root, biological replicate 1


title: Blood G93A-SOD1 age 100 days rep4

description:
BLDT100N04
replicate 4


title: VE leaf, biological replicate 3

source_name: VE leaf


title: V1 leaf, biological replicate 1


title: MCF7, vehicle, 24 h, rep 6

description:
Replicate 3
Sample name: 33

value: ethanol vehicle


title: Blood G93A-SOD1 age 70 days rep8

description:
BLDT070N08
replicate 8


title: Blood G93A-SOD1 age 100 days rep1

description:
BLDT100N01
replicate 1

value: 100 days


title: MCF7, 10 nM estradiol, 24 h, rep 1

description:
Replicate 1
Sample name: 34


title: VE leaf, biological replicate 2

value: leaf


title: Blood G93A-SOD1 age 70 days rep6

description:
BLDT070N06
replicate 6


title: Blood G93A-SOD1 age 70 days rep5

description:
BLDT070N05
replicate 5


title: Blood G93A-SOD1 age 70 days rep2

description:
BLDT070N02
replicate 2


title: Blood G93A-SOD1 age 70 days rep1

description:
BLDT070N01
replicate 1


title: Blood G93A-SOD1 age 70 days rep3

description:
BLDT070N03
replicate 3


title: MCF7, vehicle, 24 h, rep 5

description:
Replicate 2
Sample name: 32


title: MCF7, vehicle, 24 h, rep 4

description:
Replicate 1
Sample name: 31


title: MCF7, 100 nM ICI, 24 h, rep 1

description:
Replicate 1
Sample name: 16

value: 100 nM ICI


title: VE leaf, biological replicate 1


title: Blood G93A-SOD1 age 70 days rep7

description:
BLDT070N07
replicate 7


title: MCF7, 100 nM ICI, 24 h, rep 2

description:
Replicate 2
Sample name: 17


title: MCF7, 100 nM endoxifen, 24 h, rep 3

description:
Replicate 3
Sample name: 15

value: 100 nM endoxifen


title: MCF7, 100 nM 4HT, 24 h, rep 3

description:
Replicate 3
Sample name: 9

value: 100 nM 4HT


title: MCF7, 100 nM 4HT, 24 h, rep 2

description:
Replicate 2
Sample name: 8


title: MCF7, 100 nM 4HT, 24 h, rep 1

description:
Replicate 1
Sample name: 7


title: Human-bioETV1

type: genomic

city: Boston

first: Esther

last: Baena

state: MA

address: 300 Longwood Avenue

department: Hematology/Oncology

institute: Childrens Hospital Boston

hyb_protocol: According to standard Affymetrix protocols.

data_processing: MAT (Johnson et al., 2006) was used to process the raw CEL files. The following settings; Bandwith = 300, MaxGap = 300, MinProbe = 10 were used. BAR and BED files were generated by using Mm_PromPR_v02-1_NCBIv36.NR.bpmap.

molecule: genomic DNA

source_name: bioETV1 ChIP DNA from human prostate cancer cell, LNCaP

label_protocol: Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.

growth_protocol: Normal LNCaP and VCaP growth conditions

extract_protocol: For biotin-mediated ChIP, approximately, 5 × 107 human LNCaP cells expressing both BirA and biotinylated ETV1 were used. Briefly, cells were cross-linked by addition of final 1% formaldehyde for 7 min at room temperature. Cross-linking was terminated by adding final 125 mM glycine and cells were washed with cold phosphate-buffered saline (PBS) containing PMSF, scraped off the plates, collected by centrifugation and washed again. Collected cell pellet was resuspended in SDS ChIP buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, and protease inhibitors). Cells were sonicated and fragmented DNA was visualized on an agarose gel (average size 0.5-1 kb). The sample was centrifuged at 12000 rpm at 4°C for 10 min and supernatant was collected. Sample was incubated with streptavidin beads (Dynabeads® MyOne™ Streptavidin T1) at 4°C overnight. For reference sample, LNCaP cells expressing BirA enzyme without biotinylated protein were used. Immunoprecipitated complexes were successively washed with buffer I (2% SDS), buffer II (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), buffer III (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). All washes were for 8 min at room temperature. SDS elution buffer was added and incubated at 65°C overnight to reverse crosslink protein-DNA complexes. The sample was treated with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet was resuspended in 25μl of water.        Conventional ChIP reaction was performed as described above but sonicated samples were pre-cleared with protein A-beads () for 1h at 4°C and then incubated with 1:1000 dilution of ERG (C17X, Santa Cruz) antibody at 4°C  overnight. For the mock IP, the antibody was left out. Pre-washed protein A-beads  (Preotein A Dynabeads®) were added and protein-DNA complexes were recoveres after a 3 hour incubation at 4°C. Immunoprecipitated complexes were successively washed with buffer low salt wash buffer (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 150 mM NaCl), buffer II (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), buffer III (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). The rest is as described above.

treatment_protocol: Normal LNCaP and VCaP growth conditions

value: LNCaP cells

tag: fraction

value: ChIP

tag: target

tag: expression

value: BirA and biotinylated ETV1

value: BirA

source_name: Mock biotin ChIP DNA from LNCaP cells expressing BirA

value: reference (mock ChIP)


title: Human-ERG

scan_protocol: According to standard Affymetrix protocols.

source_name: ERG ChIP DNA from human prostate cancer cell, VCaP

value: VCaP cells

value: ERG

tag: antibody

tag: vendor/catalog#

value: Santa Cruz C17X

source_name: Mock ChIP DNA from VCaP cells


title: MCF7, vehicle, 24 h, rep 2

description:
Replicate 2
Sample name: 2

value: breast cancer


title: MCF7, 100 nM endoxifen, 24 h, rep 2

description:
Replicate 2
Sample name: 14


title: MCF7, vehicle, 24 h, rep 3

description:
Replicate 3
Sample name: 3


title: Blood G93A-SOD1 age 70 days rep4

description:
BLDT070N04
replicate 4

value: 70 days

value: Whole blood


title: H1299 Ago2 clone #1

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

country: China

institute: Nanjing Agricultural University

description: replicate 1

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

source_name: H1299 Ago2 clone #1

extract_protocol: RNA was extracted with Trizol reagent

value: lung adenocarcinoma


title: H1299 Lin-28B clone #2

description: replicate 2

source_name: H1299 Lin-28B clone #2


title: H1299 control for Lin-28B

description: replicate 1

source_name: H1299 control for Lin-28B


title: H1299 Ago2 clone #2

description: replicate 2

source_name: H1299 Ago2 clone #2


title: H1299 control for Ago2

description: replicate 1

source_name: H1299 control for Ago2


title: MCF7, vehicle, 24 h, rep 1

description:
Replicate 1
Sample name: 1

source_name: Parental MCF7 cells

value: ethanol vehicle


title: Treatment C Population 7 Colony b replica 1

city: Groningen

first: Pilar

middle: E

last: Puentes-Téllez

address: Nijenborgh 7

department: Microbial Ecology

institute: University of Groningen

hyb_protocol: Hybridization in a dye-swap design was performed using the Agilent Gene Expression Hybridization Kit (Agilent technologies CA, USA) at 65°C for 17 h to genome-wide multi-strain E. coli (8x15K) microarrays of 60-mer oligonucleotides (Agilent Technologies, CA, USA). Two microarrays in the slides were used per evolved colony type (two biological replicas). Each replica was labeled with a different dye (cy3 or cy5)  and hybridazed to the ancestors labeled with the oposite dye.

scan_protocol: Scanning was performed using GenePix autoloader 4200AL confocal laser scanner (Molecular devices Ltd.) according to the provider's protocol. http://www.moleculardevices.com

data_processing: Statistical analysis was performed using R Limma package (Linear Models for Microarrays Data)  (Smyth 2004), where the two microarrays per sample were normalized using lowess normalization method. Multiple-gene probes results were merged and normalized using the MA table conversion tool available on the MOLGEN Bioinformatics Server (http://server.molgenrug.nl/ - Molecular genetics, university of Groningen, the Netherlands).

organism: Escherichia coli

source_name: Pure culture in LB

label_protocol: High quality RNA samples were reverse-transcribed into cDNA with the Superscript III reverse transcriptase kit (Invitrogen, Carlsbad, USA) and labeled with Dylight Amine-Reactive Dyes Cy3 and Cy5 (Thermo Scientific, Rockford, USA).

growth_protocol: Growth curves of all selected evolved colony types and the ancestor were obtained by growing them under their evolved environmental conditions in LB medium until Log-phase. For this, optical density was recorded at 600nm at a value of 0.6 to 0.7.

extract_protocol: Cells of each evolved colony type were collected by centrifugation at 13,000 × g for 1 min at 4°C and were immediately used for total RNA isolation with NucleoSpin RNA II isolation kit (Macherey – Nagel, Biokè, Leiden, the Netherlands).

tag: oxygen regime

value: transfers in constant static conditions

tag: population

tag: morphology

value: b

tag: culture type

value: evolved

value: Ancestor


title: Treatment C Population 7 Colony c replica 2

value: c


title: Head and neck squamous cell carcinoma HN124 Agilent 4x44K

city: Chapel Hill

first: Vonn

last: Walter

state: NC

address: CB#7295, School of Medicine

institute: Lineberger Comprehensive Cancer Center

description: Stratagene Human Universal RNA Reference

hyb_protocol: Hybridization was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

scan_protocol: Scanned on an Agilent High Resolution Model B scanner that has been upgraded to Model C. Images were quantified using Agilent Feature Extraction software.

data_processing: The normexp background correction and loess normalization procedures were applied to the probe-level data using the limma R package. Normalized log2 ratios (test/reference) were then computed.

label_protocol: Labeling was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

treatment_protocol: Not applicable

value: Tumor

tag: race

value: African American

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Moderate

tag: tumor site

value: Hypopharynx

tag: Stage

value: II

tag: tumor status

tag: node status

value: Radiation Alone

tag: hpv status

value: HPV-

tag: reference


title: Treatment C Population 7 Colony b replica 2

tag: strain


title: Head and neck squamous cell carcinoma HN117 Agilent 4x44K

tag: tissue

tag: age

value: Caucasian

value: Female

value: Oral Cavity

value: IVa

tag: treatment

value: Surgery and Radiation

value: Unknown

source_name: Stratagene Human Universal RNA Reference


title: Treatment C Population 7 Colony c replica 1

tag: oxygen regime

value: transfers in constant static conditions

tag: population

tag: morphology

value: evolved

value: Ancestor


title: Head and neck squamous cell carcinoma HN121 Agilent 4x44K

value: Tumor

tag: race

tag: gender

value: Larynx

value: Concurrent Chemoradiation

value: HPV+

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN114 Agilent 4x44K

value: African American

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

value: Moderate

value: Hypopharynx


title: H1299 Lin-28B clone #1

description: replicate 1

source_name: H1299 Lin-28B clone #1

tag: cell line

value: lung adenocarcinoma


title: Head and neck squamous cell carcinoma HN123 Agilent 4x44K

value: Caucasian

value: Female

value: Heavy

tag: differentiation

value: Well

tag: tumor site

tag: Stage

value: II

value: Radiation Alone


title: Treatment C Population 6 Colony b replica 1

value: transfers in constant static conditions

value: b

tag: culture type

value: evolved

value: Ancestor


title: Head and neck squamous cell carcinoma HN118 Agilent 4x44K

value: Tumor

value: Larynx

value: IVa

tag: tumor status

tag: node status

value: Concurrent Chemoradiation

tag: hpv status

value: HPV-

tag: reference

value: Stratagene Human Universal RNA Reference


title: Treatment C Population 6 Colony c replica 1

tag: strain

value: c


title: Head and neck squamous cell carcinoma HN120 Agilent 4x44K

tag: tissue

tag: age

value: Caucasian

value: Male

value: None or Light/Moderate

value: Moderate

value: Other

value: III

tag: treatment

value: Surgery and Radiation


title: Treatment C Population 6 Colony c replica 2

tag: oxygen regime

value: transfers in constant static conditions

tag: population

tag: morphology


title: Head and neck squamous cell carcinoma HN116 Agilent 4x44K

tag: race

value: African American

tag: gender

tag: smoking packyears

tag: alcohol use

value: Well

value: Oral Cavity

value: Surgery and Concurrent Chemoradiation


title: Treatment B Population 5 Colony b replica 2

value: daily shift between shaking and static (no shaking) conditions

value: b

value: evolved

value: Ancestor


title: Treatment C Population 6 Colony b replica 2


title: Treatment B Population 5 Colony b replica 1


title: MCF7, 100 nM ICI, 24 h, rep 3

description:
Replicate 3
Sample name: 18

value: 100 nM ICI

tag: cell line

tag: cell type

value: breast cancer


title: Treatment B Population 5 Colony a replica 2

value: a

tag: culture type


title: Head and neck squamous cell carcinoma HN122 Agilent 4x44K

value: Tumor

value: Female

value: None or Light/Moderate

tag: differentiation

tag: tumor site

tag: Stage

value: IVa

tag: tumor status

tag: node status

value: HPV-

value: Stratagene Human Universal RNA Reference


title: Treatment B Population 5 Colony c replica 1

tag: strain

value: c


title: Head and neck squamous cell carcinoma HN119 Agilent 4x44K

tag: tissue

tag: age

value: Caucasian

value: Male

value: Well

value: Other

value: III

tag: treatment

value: Surgery and Radiation

tag: hpv status

tag: reference


title: Head and neck squamous cell carcinoma HN115 Agilent 4x44K

tag: race

value: African American

tag: gender

value: Moderate

value: Oral Cavity

value: Concurrent Chemoradiation


title: Treatment B Population 5 Colony a replica 1

tag: oxygen regime

value: daily shift between shaking and static (no shaking) conditions

tag: population

tag: morphology

value: a

value: evolved

value: Ancestor


title: Head and neck squamous cell carcinoma HN112 Agilent 4x44K

value: Tumor

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

value: Larynx

value: IVa

value: HPV-


title: Treatment B Population 4 Colony c replica 2

value: c

tag: culture type


title: Treatment B Population 5 Colony c replica 2


title: Head and neck squamous cell carcinoma HN110 Agilent 4x44K

value: Male

value: Heavy

tag: differentiation

value: Poor

tag: tumor site

value: Other

tag: Stage

value: I

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN111 Agilent 4x44K

value: Caucasian

value: Well

value: Oral Cavity

tag: tumor status

tag: node status

value: Surgery and Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN108 Agilent 4x44K

tag: tissue

tag: age

value: Female

value: Oropharynx

value: Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN109 Agilent 4x44K

value: Tumor

value: None or Light/Moderate

tag: treatment

tag: hpv status

value: HPV+


title: Treatment B Population 4 Colony b replica 1

tag: strain

value: daily shift between shaking and static (no shaking) conditions

value: b

value: evolved

value: Ancestor


title: Treatment B Population 4 Colony b replica 2


title: Head and neck squamous cell carcinoma HN107 Agilent 4x44K

tag: race

tag: gender

value: Larynx

value: II

value: Surgery Alone

value: HPV-

tag: reference


title: Treatment B Population 4 Colony c replica 1

tag: oxygen regime

tag: population

tag: morphology

value: c


title: Treatment B Population 3 Colony c replica 2

tag: culture type


title: Head and neck squamous cell carcinoma HN105 Agilent 4x44K

value: African American

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderate

value: Oral Cavity

value: IVa

value: Surgery and Radiation

value: Stratagene Human Universal RNA Reference


title: mcf10erbb2 miRB-1

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

description: 3-D cell culture 7 days

hyb_protocol: Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99C for 2 min. and then 45C for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000

data_processing: Raw intensity files from the Affymetrix Human Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.   Gene-level expression measurements were computed using the iterPLIER algorithm on the “core” probesets and exported with annotation release 32, dated June 23rd, 2011.

source_name: mcf10erbb2 miRB-1

label_protocol: Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

growth_protocol: DMEM/F12 supplemented with 2% horse serum, 10μg/ml insulin 1ng/ml cholera toxin, 100μg/ml hydrocortisone, 100 U/ml penicillin/streptomycin and 2mM L-glutamine

extract_protocol: RNA extraction was perfomed Following steps were followed according to manufacturer’s instructions from RNA-STAT-60 (Tel-Test, Friendswood, TX, USA)

treatment_protocol: Media was aspirated from 8well chamber-slides and added 250ul of RNA-STAT-60 (Tel-Test, Friendswood, TX, USA) to each well. Immediately the mixture of cells and matrigel was resuspened several times and collected in an eppendorf tube.

tag: cell line

tag: cell type

value: RB-deficient


title: Head and neck squamous cell carcinoma HN098 Agilent 4x44K

tag: tissue

value: Tumor

value: Caucasian

value: Heavy

tag: tumor site

tag: Stage

value: III

tag: tumor status

tag: node status

value: Concurrent Chemoradiation


title: mcf10erbb2 miRB-2

description: 3-D cell culture 7 days

source_name: mcf10erbb2 miRB-2


title: Treatment B Population 3 Colony c replica 1

tag: strain

value: daily shift between shaking and static (no shaking) conditions

value: evolved

value: Ancestor


title: Treatment B Population 3 Colony b replica 1

value: b


title: Treatment B Population 4 Colony a replica 1

value: a


title: mcf10erbb2 miRB-3

description: 3-D cell culture 7 days

source_name: mcf10erbb2 miRB-3


title: Head and neck squamous cell carcinoma HN097 Agilent 4x44K

tag: age

tag: race

tag: gender

value: Female

value: None or Light/Moderate

tag: treatment

tag: hpv status

value: HPV-


title: Treatment B Population 3 Colony b replica 2

tag: oxygen regime

tag: population

tag: morphology

tag: culture type


title: Treatment B Population 4 Colony a replica 2


title: Treatment B Population 3 Colony a replica 2


title: Head and neck squamous cell carcinoma HN093 Agilent 4x44K

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderate

value: Oropharynx

value: IVa

value: Surgery and Concurrent Chemoradiation

value: HPV+

tag: reference


title: mcf10erbb2 miNS-2

description: 3-D cell culture 7 days

source_name: mcf10erbb2 miNS-2

tag: cell line

tag: cell type

value: RB-proficient


title: Head and neck squamous cell carcinoma HN094 Agilent 4x44K

tag: tissue

value: Tumor

value: Caucasian

value: Heavy

tag: tumor site

tag: Stage

tag: tumor status

tag: node status

value: Stratagene Human Universal RNA Reference


title: Normal mouse liver 2

city: Kolkata

first: Suvendra

middle: Nath

last: Bhattacharyya

state: West Bengal

address: 4, Raja S.C.Mullick Road

department: Molecular and Human Genetics

country: India

institute: Indian Institute of Chemical Biology

data_processing: The data were normalised using Average normalisation with IlluminaGUI in Bead Studio Software

label: Biotin

source_name: Normal liver

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

treatment_protocol: 4-6 weeks Balb/c mice were infected with 107 2nd passage stationary phase Ag83 strain of Leishmania donovani and mice were scarificed at 2 months post infection alongwith uninfected mice and liver samples are dissected out ,snap freezed in liquid nitrogen and stored at -80°C

tag: infection

tag: strain

value: Balb/c

tag: age

value: 3-3.5 month

value: liver


title: Head and neck squamous cell carcinoma HN103 Agilent 4x44K

tag: race

tag: gender

value: Female

value: Well

value: Oral Cavity

value: I

tag: treatment

value: Surgery Alone

tag: hpv status


title: Head and neck squamous cell carcinoma HN104 Agilent 4x44K

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

value: Moderate

value: Oropharynx

value: Concurrent Chemoradiation

value: HPV-


title: Head and neck squamous cell carcinoma HN095 Agilent 4x44K

value: Tumor

value: Caucasian

tag: differentiation

value: Poor

value: IVa

value: HPV+

tag: reference


title: Treatment B Population 3 Colony a replica 1

tag: oxygen regime

value: daily shift between shaking and static (no shaking) conditions

tag: population

tag: morphology

value: a

tag: culture type

value: evolved

value: Ancestor


title: Normal mouse liver 3

value: Balb/c

value: 3-3.5 month

tag: tissue

value: liver


title: mcf10erbb2 miNS-3

description: 3-D cell culture 7 days

source_name: mcf10erbb2 miNS-3

tag: cell line

tag: cell type

value: RB-proficient


title: Treatment A Population 2 Colony c replica 2

tag: strain

value: transfers under constant shaking (200rpm)

value: c


title: Normal mouse liver 1

tag: infection

tag: age


title: Leishmania donovani Infected mouse liver 2

source_name: 60 days infected liver

value: Leishmania donovani Ag83


title: Head and neck squamous cell carcinoma HN091 Agilent 4x44K

tag: race

tag: gender

value: Male

value: None or Light/Moderate

value: Moderate

tag: tumor site

value: Oral Cavity

tag: Stage

tag: tumor status

tag: node status

value: Surgery Alone

value: HPV-

value: Stratagene Human Universal RNA Reference


title: Treatment A Population 2 Colony c replica 1


title: Treatment A Population 2 Colony b replica 2

value: b


title: Head and neck squamous cell carcinoma HN089 Agilent 4x44K

value: Tumor

value: Caucasian

value: Female

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Poor

value: Larynx

value: IVa

tag: treatment

value: Surgery and Concurrent Chemoradiation

tag: hpv status

tag: reference


title: Head and neck squamous cell carcinoma HN092 Agilent 4x44K

tag: tissue

value: African American

value: Heavy

value: Well

value: Hypopharynx

value: IVb

value: Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN090 Agilent 4x44K

value: Moderate


title: Treatment A Population 2 Colony b replica 1

tag: oxygen regime

value: transfers under constant shaking (200rpm)

tag: population

tag: morphology

tag: culture type

value: evolved

value: Ancestor


title: CHIR_2

city: Cambridge

first: Xiaoxiao

last: Zhang

address: 7 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University

hyb_protocol: 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on mouse genechip 1.0 st arrays. Arrays  were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Data were analyzed by RMA in R.

source_name: 2i-adapted mouse embryonic stem cells, CHIR99021(3 μM), PD0325901 and LIF are withdrawn for 24 hours

label_protocol: 300 ng of total RNA were labeled for each sample using the GeneChip WT cDNA Synthesis and Amplification Kit and WT Terminal Labeling Kit (Affymetrix, 900673 and 900671).

growth_protocol: 2i culture of ESCs was performed as described using CHIR99021 (3 μM , Stemgent, 04-0004) and PD0325901 (1 μM ; Stemgent, 04-0006) (Ying QL et al. 2008 Nature)

extract_protocol: Total RNA was isolated using TRIZOL Reagent (Invitrogen, 15596-026) and purified by RNeasy Mini Kit (QIAGEN, 74104).

treatment_protocol: CHIR99021, PD0325901 and/or LIF were withdrawn from cell culture for 24 hours before subjected to RNA extraction.

tag: cell line

value: 2i-adapated Ctnnb1-Biotin-3xFLAG knock-in ESC line (Ctnnb1-BioFLneo;BirA ESC)


title: DMSO_3

source_name: 2i-adapted mouse embryonic stem cells, DMSO, CHIR99021, PD0325901 and LIF are withdrawn for 24 hours

value: DMSO


title: Head and neck squamous cell carcinoma HN087 Agilent 4x44K

value: Tumor

tag: age

tag: race

value: Caucasian

tag: gender

value: Male

value: None or Light/Moderate

value: Oropharynx

value: IVc

value: HPV-

value: Stratagene Human Universal RNA Reference


title: CHIR_3


title: Leishmania donovani Infected mouse liver 1

tag: infection

value: Leishmania donovani Ag83

tag: strain

value: Balb/c

value: 3-3.5 month

value: liver


title: DMSO_2


title: Treatment A Population 2 Colony a replica 2

value: transfers under constant shaking (200rpm)

value: a


title: PD03_2

source_name: 2i-adapted mouse embryonic stem cells, PD0325901(1 μM), CHIR99021 and LIF are withdrawn for 24 hours


title: PD03_1


title: Head and neck squamous cell carcinoma HN086 Agilent 4x44K

value: African American

tag: smoking packyears

value: Heavy

value: Well

tag: tumor site

value: Oral Cavity

tag: Stage

value: I

tag: tumor status

tag: node status

value: Surgery Alone


title: DMSO_1

tag: treatment

value: DMSO

value: 2i-adapated Ctnnb1-Biotin-3xFLAG knock-in ESC line (Ctnnb1-BioFLneo;BirA ESC)


title: Treatment A Population 2 Colony a replica 1

value: evolved

value: Ancestor


title: Head and neck squamous cell carcinoma HN085 Agilent 4x44K

tag: tissue

value: Tumor

value: Caucasian

value: Male

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Poor

value: III

value: Concurrent Chemoradiation

tag: hpv status

value: HPV-

tag: reference

value: Stratagene Human Universal RNA Reference


title: PD03_3

tag: cell line


title: Head and neck squamous cell carcinoma HN088 Agilent 4x44K

tag: age

value: Moderate

value: Oropharynx

value: IVa

value: Surgery and Concurrent Chemoradiation

value: HPV+


title: 2i_2

source_name: 2i-adapted mouse embryonic stem cells, CHIR99021(3 μM)+PD0325901(1 μM), LIF is withdrawn for 24 hours

value: 2i-adapated Ctnnb1-Biotin-3xFLAG knock-in ESC line (Ctnnb1-BioFLneo;BirA ESC)


title: 2iLIF_3

source_name: 2i-adapted mouse embryonic stem cells, CHIR99021(3 μM)+PD0325901(1 μM)+LIF, long term culture


title: Treatment A Population 1 Colony c replica 2

tag: oxygen regime

value: transfers under constant shaking (200rpm)

tag: population

tag: morphology

value: c

tag: culture type

value: evolved


title: CHIR_1


title: 2i_3


title: 2i_1


title: 2iLIF_2


title: Treatment A Population 1 Colony b replica 2

tag: strain

value: b

value: Ancestor


title: Treatment A Population 1 Colony c replica 1


title: Treatment A Population 1 Colony a replica 1

value: a


title: Head and neck squamous cell carcinoma HN084 Agilent 4x44K

value: Tumor

tag: race

value: Caucasian

tag: gender

value: Male

tag: smoking packyears

value: None or Light/Moderate

tag: tumor site

value: Hypopharynx


title: mESC_XAV_rep2

hyb_protocol: 10 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on mouse genechip 1.0 st arrays. Arrays  were washed and stained in the Affymetrix Fluidics Station 450.

source_name: mouse embryonic stem cells, serum+LIF culture, XAV939 (3 μM), 24 hours

growth_protocol: All ESCs were maintained in complete ES media (15% fetal bovine serum, 0.1 mM non-essential amino acids, 0.1 mM b-mercaptoethanol, 2 mM L-glutamine, 10^3 units/ml LIF, and 1X nucleotide mix in DMEM high glucose) with feeder cells isolated from DR4 mice

treatment_protocol: Cells were treated for 24 hours with CHIR99021 (3μM) or XAV939 (1 μM)

tag: treatment

value: XAV939 (3 μM), 24 hours

value: Ctnnb1-Biotin-3xFLAG knock-in V6.5 ESC line (Ctnnb1-BioFLneo;BirA ESC)


title: Head and neck squamous cell carcinoma HN081 Agilent 4x44K

tag: tissue

value: Well

value: Oral Cavity

tag: Stage

value: IVa

tag: tumor status

tag: node status

value: Surgery and Radiation

value: HPV-

value: Stratagene Human Universal RNA Reference


title: mESC_CHIR_rep1

source_name: mouse embryonic stem cells, serum+LIF culture, CHIR99021 (3 μM), 24 hours

value: CHIR99021 (3 μM), 24 hours


title: Treatment A Population 1 Colony a replica 2

source_name: Pure culture in LB

value: transfers under constant shaking (200rpm)

value: evolved


title: mESC_XAV_rep3


title: Head and neck squamous cell carcinoma HN080 Agilent 4x44K

value: Female

tag: alcohol use

tag: differentiation

value: Moderate

value: Oropharynx

value: III

value: Concurrent Chemoradiation

tag: hpv status

source_name: Stratagene Human Universal RNA Reference

tag: reference


title: Head and neck squamous cell carcinoma HN082 Agilent 4x44K

value: Tumor

tag: age

value: Caucasian

value: Male

value: None or Light/Moderate

value: HPV+


title: mESC_CHIR_rep2

tag: cell line

value: Ctnnb1-Biotin-3xFLAG knock-in V6.5 ESC line (Ctnnb1-BioFLneo;BirA ESC)


title: mESC_XAV_rep1

value: XAV939 (3 μM), 24 hours


title: Treatment A Population 1 Colony b replica 1

tag: oxygen regime

tag: population

tag: morphology

value: b

tag: culture type

value: Ancestor


title: kidney_IR_26min_vehicle_rep2

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: Gene expression data from kidneys at day 1.5 following IR-induced injury and vehicle treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned in an Affymetrix 7G plus scanner using AGCC v. 1.1

data_processing: The data were analyzed with Affymetrix Expression Console v. 1.1 using an RMA normalization algorithm producing log base 2 results.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Using phenol based reagent, RNA-Bee, extraction of total RNA was performed and followed by clean-up with RNeasy according to the manufacturer's instructions.

treatment_protocol: 26 ischemia with non-traumatic clamp followed by reperfusion on a heating pad at 37C were performed. Mice were treated either with vehicle, 20% of 2-(Hydroxypropyl)-b-cyclodextrin in water or with 100mg/kg b.w m4PTB

value: kidney

tag: background strain

value: Balb/c

value: 10-12 weeks


title: Head and neck squamous cell carcinoma HN083 Agilent 4x44K

tag: race

tag: gender

tag: smoking packyears

tag: tumor site

value: IVa

value: Stratagene Human Universal RNA Reference


title: 2iLIF_1

tag: treatment

value: 2i-adapated Ctnnb1-Biotin-3xFLAG knock-in ESC line (Ctnnb1-BioFLneo;BirA ESC)


title: kidney_IR_26min_m4PTB_rep2

description: Gene expression data from kidneys at day 1.5 following IR-induced injury and m4PTB treatment

tag: tissue


title: kidney_IR_26min_vehicle_rep3


title: kidney_IR_26min_m4PTB_rep3


title: kidney_IR_26min_m4PTB_rep1


title: mix6 rep2

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

description: fmol of spiked oligos per 1mg of total RNA

hyb_protocol: Samples were hybridized to a GeneChip miRNA 2.0 Array (Affymetrix) at 48°C and 60 rpm for 16 hours, then washed and stained on Fluidics Station 450 (Fluidics script FS450_0003)

scan_protocol: Chips were scanned on a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data were analyzed with Affymetrix miRNA QC tool and normalized using default parameters, and  batch  corrected  using Partek default, human probes were selected.

source_name: placenta

label_protocol: 500 ng RNA was labeled using Flashtag RNA labeling kit (Genisphere #HSR10FTA). Briefly, RNA underwent a PolyA tailing reaction using 2.5 mM MnCl2, ATP and PolyA Polymerase, followed by ligation of the biotinylated 3DNA signal molecule to the RNA sample

growth_protocol: RNA purchased (see extract protocol).

extract_protocol: Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005.

treatment_protocol: Oligos representing mature, modified and precursor miRNA were artificially introduced to native RNA

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: Head and neck squamous cell carcinoma HN079 Agilent 4x44K

tag: age

tag: race

tag: gender

value: Female

tag: alcohol use

tag: differentiation

value: Moderate

value: Oropharynx

tag: Stage

tag: tumor status

tag: node status

tag: hpv status

tag: reference


title: Cox6a2 KO diaphragm, biological replicate 3

city: Leuven

first: Katleen

last: Lemaire

address: Herestraat 49, bus 901

country: Belgium

hyb_protocol: Labeled DNA was hybridized to the array during 16h at 45°C

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All image files were generated using the Affymetrix GeneChip command console (AGCC). The raw data were analyzed with RMA sketch using the standard settings for Gene 1.0 ST arrays of Expression Console in the AGCC software (affymetrix).

source_name: Mouse diaphragm

label_protocol: according to manufacturer’s manual 701880Rev4 (Affymetrix, Santa Clara, CA). Briefly, in the first cycle, double stranded cDNA was prepared with random hexamers tagged with a T7 promoter sequence followed by the generation of cRNA using the GeneChip WT Synthesis and Amplification kit (Affymetrix). cRNA concentration after cleanup was measured with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW). In the second cycle, sense oriented single-stranded DNA containing dUTP is generated and the concentration is, after cleanup, measured using the nanodrop. The cRNA is hydrolysed and the single stranded DNA is fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) (GeneChip WT terminal Labeling kit, Affymetrix). The quality of fragmentation (fragments should be between 40 and 70 nucleotides) is checked on the bioanalyzer (Agilent, Waldbronn, Germany). The fragmented DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix).

extract_protocol: Total RNA was extracted using TRIzol Reagent according to the manufacturer's protocol (Gibco BRL, Carlsbad, CA), followed by a cleanup procedure with RNeasy columns (Qiagen, Cologne, Germany).The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

tag: strain

tag: genotype/variation

value: Cox6a2 KO

tag: tissue

value: diaphragm

value: male mice

value: 10-12 weeks old


title: Cox6a2 KO gastrocnimius, biological replicate 1

source_name: Mouse gastrocnimius

value: gastrocnimius


title: Cox6a2 KO diaphragm, biological replicate 2


title: mix5 rep2

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p


title: Cox6a2 KO gastrocnimius, biological replicate 3

tag: gender

tag: age


title: mESC_CHIR_rep3

tag: treatment

value: CHIR99021 (3 μM), 24 hours

tag: cell line

value: Ctnnb1-Biotin-3xFLAG knock-in V6.5 ESC line (Ctnnb1-BioFLneo;BirA ESC)


title: Head and neck squamous cell carcinoma HN072 Agilent 4x44K

value: Tumor

tag: race

value: Caucasian

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Well

tag: tumor site

value: Oral Cavity

tag: Stage

tag: tumor status

tag: node status

value: Surgery Alone

tag: hpv status

tag: reference


title: Head and neck squamous cell carcinoma HN077 Agilent 4x44K

tag: tissue

value: Larynx

value: III

value: Stratagene Human Universal RNA Reference


title: kidney_IR_26min_vehicle_rep1

value: kidney

tag: background strain

value: Balb/c

value: 10-12 weeks


title: WT gastrocnimius, biological replicate 2

tag: strain

tag: genotype/variation

value: wild type

value: male mice

value: 10-12 weeks old


title: WT gastrocnimius, biological replicate 3

value: gastrocnimius

tag: gender

tag: age


title: Head and neck squamous cell carcinoma HN078 Agilent 4x44K

value: Tumor

value: Heavy

value: Poor

value: IVa

tag: treatment

value: Concurrent Chemoradiation


title: mix7 rep2

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: mix4 rep2


title: Cox6a2 KO gastrocnimius, biological replicate 2

tag: strain

value: Cox6a2 KO

tag: tissue


title: Cox6a2 KO diaphragm, biological replicate 1

tag: genotype/variation

value: diaphragm

tag: gender


title: WT diaphragm, biological replicate 3

tag: age


title: WT gastrocnimius, biological replicate 1


title: mix3 rep2

tag: spike-in hsa-mir-147


title: mix1 rep2

tag: spike-in hsa-mir-211


title: mix2 rep2

tag: spike-in hsa-mir-219-5p


title: mcf10erbb2 miNS-1

description: 3-D cell culture 7 days

source_name: mcf10erbb2 miNS-1

tag: cell line

tag: cell type

value: RB-proficient


title: Head and neck squamous cell carcinoma HN076 Agilent 4x44K

tag: race

value: Caucasian

value: Female

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

tag: tumor site

value: Hypopharynx

tag: Stage

tag: tumor status

tag: node status

tag: treatment

tag: hpv status

tag: reference


title: WT diaphragm, biological replicate 2

tag: strain

tag: genotype/variation

tag: tissue

tag: gender

tag: age


title: WT diaphragm, biological replicate 1


title: mix7 rep1

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: Head and neck squamous cell carcinoma HN068 Agilent 4x44K

tag: race

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Moderate

tag: tumor site

value: Oral Cavity

tag: Stage

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Concurrent Chemoradiation

tag: hpv status

value: HPV-

tag: reference

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN075 Agilent 4x44K

tag: tissue

value: Tumor

tag: age

tag: gender

value: Oropharynx

value: III

value: Surgery and Radiation

value: HPV+


title: Head and neck squamous cell carcinoma HN070 Agilent 4x44K

value: African American

value: Heavy

value: II

value: Unknown


title: mix6 rep1

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p


title: Ly-6C- Naive CD4 T cells purified from Foxp3-GFP mouse, Biological Rep3

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Gene expression data from Ly-6C- Naive CD4 T cells

hyb_protocol: These 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were RMA normalized (RMA) and analysed with Partek Genomic Suite.

source_name: CD4+ CD8- TCRβ+ CD44lo CD25- Foxp3- Ly-6C- cells

label_protocol: 50 ng of total RNAs were amplified with Ovation Pico WTA System kit and 5 µg of generated cDNA were labeled with Encore Biotin Module kit according to the manufacturer (Nugen) instructions.

extract_protocol: Total RNA was extracted using the Rneasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: T cells were isolated by magnetic bead enrichment followed by fluorescence activated cell sorting.

value: Peripheral lymph nodes

tag: strain

value: C57BL/6 Foxp3-GFP

value: 6 weeks


title: mix3 rep1

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: Head and neck squamous cell carcinoma HN067 Agilent 4x44K

tag: race

value: Caucasian

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Poor

tag: tumor site

tag: Stage

tag: tumor status

tag: node status

tag: treatment

tag: hpv status

tag: reference


title: mix5 rep1

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211


title: Head and neck squamous cell carcinoma HN065 Agilent 4x44K

tag: tissue

tag: age

tag: race

tag: gender

tag: smoking packyears

tag: alcohol use

value: Well

value: Oral Cavity

value: IVa

value: Concurrent Chemoradiation

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN074 Agilent 4x44K

value: Tumor

tag: differentiation

tag: tumor site

value: Hypopharynx

tag: Stage

tag: tumor status

tag: node status

tag: treatment

value: Surgery Alone

value: HPV-


title: Ly-6C- Naive CD4 T cells purified from Foxp3-GFP mouse, Biological Rep1

tag: strain


title: Ly-6C+ Naive CD4 T cells purified from Foxp3-GFP mouse, Biological Rep3

description: Gene expression data from Ly-6C+ Naive CD4 T cells

source_name: CD4+ CD8- TCRβ+ CD44lo CD25- Foxp3- Ly-6C+ cells


title: Ly-6C+ Naive CD4 T cells purified from Foxp3-GFP mouse, Biological Rep2


title: mix4 rep1

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: Head and neck squamous cell carcinoma HN064 Agilent 4x44K

tag: tissue

tag: age

tag: race

tag: gender

value: Female

tag: smoking packyears

tag: alcohol use

value: Moderate

value: Oropharynx

tag: hpv status

value: HPV+

tag: reference


title: Head and neck squamous cell carcinoma HN066 Agilent 4x44K

value: Caucasian

tag: differentiation

tag: tumor site

tag: Stage

value: II

tag: tumor status

tag: node status

tag: treatment


title: Ly-6C+ Naive CD4 T cells purified from Foxp3-GFP mouse, Biological Rep1

value: Peripheral lymph nodes

tag: strain

value: C57BL/6 Foxp3-GFP

value: 6 weeks


title: Pca_vpa_3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Undifferentiated Embryonal stem cells Stra8  Biological Replicate 3

hyb_protocol: Following fragmentation, 5.5 mg of biotinilated RNA were hybridized for 16 hr at 45C into individual Affymetrix Gene Mouse Arrays 1.0 ST. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) according to GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual (Affymetrix) instructions.

scan_protocol: Microarrays were scanned in a GeneChip® Scanner 3000 7G (Affymetrix) and quality control was evaluated by Affymetrix software (Expression ConsoleTM).

data_processing: The data where preprocessed (RMA) using the Expression Console TM from Affymetrix.

label_protocol: Labeling protocol was carried out with 300 ng of purified RNA, with biotin, accord to Affymetrix Gene Mouse Arrays 1.0 ST protocol.

extract_protocol: Trizol (Invitrogen) isolation according to the manufactures standard protocol, Subsequent DNase I treatment

tag: cell type

value: undifferentiated stem cells


title: Pca_control_3

description: Differentiated Embryonal stem cells 129SV Biological Replicate 3

value: differentiated stem cells


title: Ly-6C- Naive CD4 T cells purified from Foxp3-GFP mouse, Biological Rep2


title: Pca_vpa_2

description: Undifferentiated Embryonal stem cells Stra8  Biological Replicate 2


title: mix2 rep1

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p

tag: precursor spike-in hsa-mir-383

tag: o-methyl spike-in hsa-mir-429


title: Head and neck squamous cell carcinoma HN063 Agilent 4x44K

tag: tissue

tag: age

tag: race

tag: gender

value: Male

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Poor

tag: tumor site

value: Oral Cavity

tag: Stage

value: III

tag: tumor status

value: Concurrent Chemoradiation

tag: hpv status

tag: reference


title: Pca_control_2

description: Differentiated Embryonal stem cells 129SV Biological Replicate 2

tag: strain

tag: cell type


title: Pca_control_1

description: Differentiated Embryonal stem cells 129SV Biological Replicate 1


title: mix1 rep1

tag: spike-in hsa-mir-147

tag: spike-in hsa-mir-211

tag: spike-in hsa-mir-219-5p

tag: spike-in hsa-mir-338-3p

tag: spike-in hsa-mir-383

tag: spike-in hsa-mir-429

tag: precursor spike-in hsa-mir-147

tag: o-methyl spike-in hsa-mir-211

tag: o-methyl spike-in hsa-mir-219-5p

tag: precursor spike-in hsa-mir-338-3p


title: Head and neck squamous cell carcinoma HN062 Agilent 4x44K

tag: tissue

value: Tumor

tag: age

tag: race

tag: gender

value: Female

tag: smoking packyears

tag: alcohol use

tag: differentiation

tag: tumor site

tag: node status

tag: treatment

value: Surgery and Radiation

value: HPV-

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN057 Agilent 4x44K

value: African American

value: Heavy

value: Moderate

value: Oropharynx

tag: Stage

value: IVa

tag: tumor status

tag: hpv status

tag: reference


title: Head and neck squamous cell carcinoma HN059 Agilent 4x44K

value: Caucasian

value: I

value: Surgery Alone


title: Head and neck squamous cell carcinoma HN060 Agilent 4x44K

value: Male

value: None or Light/Moderate


title: Control Muscle Fibers

city: Edmonton

first: Allen

last: Herbst

state: AB

address: 114C BARB

institute: University of Alberta

hyb_protocol: Equal amounts of amplified cRNA, 7ug, from normal and abnormal muscle fibers was chemically fragmented and hybridized to the Affymetrix rat genome 230 2.0 high-density oligonuclotide arrays according to the manufacturers instructions (Affymetrix).

scan_protocol: Chips were scanned on an Affymetrix model 3000 array scanner

data_processing: GCOS v 1.40.036 was used to anaylyze the data. Genes that are called present/marginal from the ETS abnormal or control chips are considered specific to the population of cells from which they came and differentially expressed unless they are detected in both ETS and control samples. Additionally, genes whose expression is greater than a “two fold-change” are also considered to be differentially-regulated. Gene expression levels are not considered quantitative due to the inherent lack of normality derived from the small sample size and resulting amplification bias. Data was analyzed qualitatively. Genes detected from a given sample are considered differentially regulated as a result of their detection.

organism: Rattus norvegicus

source_name: Laser Capture microdissected muscle fibers from F344xBN F1 hybrid rat 36 month old

label_protocol: Total RNA was eluted into 1st strand cDNA synthesis reaction primed with an anchored polyT-T7 promoter primer (5uM) Improm II cDNA synthesis system (Promega). First cycle second strand cDNA synthesis was performed and the entire reaction was used as template for T7 based RNA transcription using the T7 MegaScript High Yield Transcription kit (Ambion). The transcribed RNA was purified using the RNeasy mini kit (Qiagen). The nascent cRNA was subsequently subjected to a second cycle of first and second strand cDNA synthesis using random hexamer primers. The cDNA was cleaned up using the Wizard SV Gel and PCR cleanup kit (Promega) and the sample subjected to a second cycle of T7 RNA polymerase based amplification. In this final round of T7 based RNA transcription, biotinylated 14-CTP (Invitrogen) and 16-UTP (Roche) were incorporated into the transcription/labeling reaction. The labeled amplified cRNA was purified using the RNeasy mini kit and subsequently ethanol precipitated prior to A260 quantification and fragmentation.

extract_protocol:
cell isolation:  Target Cells were isolated using an Arcturus PixCell II laser capture microscope. Captured cells and transfer film were further resected from LCM caps to minimize contamination
RNA was isolated by using MagneSil total RNA mini-isolation kit, 30uL of Paramagnetic particles, 300ul Lysis buffer, DNASE I treatment

tag: electron transport chain phenotype

value: Cytochrome C Oxidase Positive, Succinate dehydrogenase Normal Muscle Fibers-Normal, Control

value: Vastus lateralis skeletal muscle

tag: strain

value: F344 x BN F1 Hybrid rat

value: 36 month old


title: Head and neck squamous cell carcinoma HN056 Agilent 4x44K

value: Tumor

value: Larynx

value: Surgery and Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN054 Agilent 4x44K

value: African American

value: III

value: Stratagene Human Universal RNA Reference


title: Endometrium_Chlamydia trachomatis infection_unique_individual 11

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

hyb_protocol: Hybridization, washing and staining were performed as specified in  the GeneChip Expresson Analysis Technical Manual (P/N 702232, Rev. 3,  Affymetrix Inc. Santa Clara, CA )

scan_protocol: Stained microarrays were scanned with a GeneChip Scanner 3000 using GCOS v 1.4 software (Affymetrix Inc)

data_processing: Data were processed using the MAS 5.0 algorithm in GCOS v 1.4 with software defaults (scaling using 2% trimmed mean) and a scaling value of 500.

source_name: Trans-cervical endometrial biopsy from C. trachomatis  infected source

label_protocol: Extracted RNA was amplified using the Ovation FFPE WTA system and biotinylated using the Encore Biotin Module  (Nugen Technologies Inc. San Carlos CA)

extract_protocol: Endometrial tissue was dissociated into single-cell suspensions.Total RNA extraction using Qiagen RNeasy Mini Kits. RNA integrity determined by Agilent Bioanalyzer 2100. RIN values 5.0 - 8.0

treatment_protocol: Trans-cervical endometrial biopsy specimens were collected from 10 women with no identified upper or lower genital tract infection and 12 women with C. trachomatis endometrial infection. Endometrial tissue was dissociated into single-cell suspensions

value: Female

value: trans-cervical endometrial samples

tag: infection

value: yes


title: ETS Abnormal muscle fibers

value: Cytochrome C Oxidase negative, Succinate Dehydrogenase hyperreactive - ragged red

tag: tissue


title: WKY NTS 5

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the nucleus of tractus solitarius from 5 WKY animals

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: MessageAmpII aRNA Amplification kit (Ambion)

source_name: WKY nucleus of tractus solitarius

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

tag: Strain

value: WKY

tag: Gender

tag: Age

value: 10-13 weeks

tag: Tissue

value: Nucleus of tractus solitarius


title: WKY NTS 2

value: Male


title: WKY NTS 3


title: Endometrium_Chlamydia trachomatis infection_unique_individual 12

tag: gender


title: WKY NTS


title: Endometrium_Chlamydia trachomatis infection_unique_individual 9


title: Endometrium_Chlamydia trachomatis infection_unique_individual 8


title: WKY NTS 4


title: Head and neck squamous cell carcinoma HN053 Agilent 4x44K

tag: age

tag: race

value: Caucasian

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Well

value: Oral Cavity

value: IVa

value: Surgery Alone

value: HPV-


title: Head and neck squamous cell carcinoma HN055 Agilent 4x44K

value: Tumor

value: African American

value: Heavy

value: Moderate

tag: tumor site

value: Larynx

tag: Stage

tag: tumor status

tag: node status

tag: treatment

value: Concurrent Chemoradiation

value: HPV+


title: SHR NTS 4

description: Sample represents the nucleus of tractus solitarius from 5 SHR animals

source_name: SHR nucleus of tractus solitarius

value: SHR

value: 10-13 weeks


title: SHR NTS 5

value: Male

value: Nucleus of tractus solitarius


title: Endometrium_Chlamydia trachomatis infection_unique_individual 10

value: Female

value: trans-cervical endometrial samples

tag: infection

value: yes


title: Endometrium_Chlamydia trachomatis infection_unique_individual 3

tag: tissue


title: Endometrium_Chlamydia trachomatis infection_unique_individual 7


title: Head and neck squamous cell carcinoma HN051 Agilent 4x44K

value: Caucasian

value: None or Light/Moderate

value: Oral Cavity

value: I

tag: hpv status

tag: reference

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN050 Agilent 4x44K

value: Tumor

value: African American

value: Well

value: II


title: SHR NTS 3

tag: Strain

tag: Gender

tag: Age


title: Endometrium_Chlamydia trachomatis infection_unique_individual 6

tag: gender


title: SHR NTS 2

tag: Tissue


title: Endometrium_Chlamydia trachomatis infection_unique_individual 4


title: SHR NTS


title: Endometrium_Chlamydia trachomatis infection_unique_individual 5


title: Endometrium_Chlamydia trachomatis infection_unique_individual 2


title: Endometrium_Chlamydia trachomatis infection_unique_individual 1


title: Head and neck squamous cell carcinoma HN049 Agilent 4x44K

tag: age

tag: race

tag: smoking packyears

value: Heavy

value: Moderate

value: Oropharynx

value: Surgery Alone

value: HPV-


title: Endometrium_uninfected_unique_individual 7

source_name: Trans-cervical endometrial biopsy from uninfected source

value: Female

value: no


title: Endometrium_uninfected_unique_individual 8

value: trans-cervical endometrial samples


title: Head and neck squamous cell carcinoma HN045 Agilent 4x44K

value: Caucasian

value: Male

tag: alcohol use

tag: differentiation

tag: tumor site

value: Larynx

value: III

value: Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN046 Agilent 4x44K

value: Tumor

value: None or Light/Moderate

value: Oral Cavity

tag: Stage

value: IVa

tag: tumor status

tag: node status

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN041 Agilent 4x44K

tag: tissue

value: African American

value: Heavy

value: Moderate

tag: treatment

value: Surgery and Concurrent Chemoradiation


title: Endometrium_uninfected_unique_individual 1

value: Female

tag: infection


title: Head and neck squamous cell carcinoma HN043 Agilent 4x44K

value: Poor

value: Hypopharynx

tag: hpv status

value: HPV-

tag: reference


title: Endometrium_uninfected_unique_individual 4

value: trans-cervical endometrial samples

value: no


title: Endometrium_uninfected_unique_individual 5


title: Head and neck squamous cell carcinoma HN047 Agilent 4x44K

value: Male


title: Endometrium_uninfected_unique_individual 2


title: Endometrium_uninfected_unique_individual 9


title: Head and neck squamous cell carcinoma HN037 Agilent 4x44K

value: Surgery and Radiation


title: Head and neck squamous cell carcinoma HN044 Agilent 4x44K

value: Tumor

value: Caucasian


title: Head and neck squamous cell carcinoma HN039 Agilent 4x44K

value: None or Light/Moderate

value: Oropharynx

value: Concurrent Chemoradiation


title: Endometrium_uninfected_unique_individual 6


title: Cells incubated with IL-8

first: Idit

last: Shachar

address: 2 Hersel st

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Geneschips were scanned ccording to the manufacturer's instructions.

data_processing: The data were analyzed using Affymetrix deafault analysis settins and global scaling as normalization method. The trimmed mean tarteg intensity of each array was arbitrarily set to 100.

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

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

tag: diagnosis

value: Chronic lymphocytic leukemia (CLL)


title: Whole peripheral blood_Tempus Tube, Sample 189

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression Module)

data_processing:
The raw log2 transformed 14,343 probes that are expressed in the CHDWB study were normalized by ANOVA fitting technical effects of date of hybridization and RNA quality using JMP Genomics 5.0 (SAS Institute, Cary NC) and mean centered.
log2 transformed 14,343 probes expressed in CHDWB study, DATE and RIN3 effects removed, and mean-centered signal

source_name: Whole peripheral blood

label_protocol: Illumina's BeadArray protocol

extract_protocol: Total RNA was extracted from Whole peripheral blood using Tempus Spin RNA Isolation kit. Quality control was performed using Agilent's Bioanalyzer.

tag: gender

value: FEM

tag: percentage of body fat

tag: ethnicity

value: AFR

tag: zip code

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: I


title: Cells incubated with MIF

source_name: IS25 (+MIF)


title: Head and neck squamous cell carcinoma HN036 Agilent 4x44K

tag: age

tag: race

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Moderate

tag: tumor site

value: Oral Cavity

value: IVa

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN040 Agilent 4x44K

tag: tissue

tag: Stage

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Concurrent Chemoradiation

value: HPV-


title: Cells incubated with PBS

source_name: IS24 (+PBS)

tag: diagnosis


title: Whole peripheral blood_Tempus Tube, Sample 187

tag: gender

tag: percentage of body fat

tag: ethnicity

value: CAU

value: G


title: Whole peripheral blood_Tempus Tube, Sample 186

tag: zip code

tag: rna integrity score

tag: batch effect_date

value: F


title: Whole peripheral blood_Tempus Tube, Sample 183

value: MAL

tag: age

tag: plate id

value: C


title: Whole peripheral blood_Tempus Tube, Sample 184

value: D


title: Whole peripheral blood_Tempus Tube, Sample 185

value: E


title: Whole peripheral blood_Tempus Tube, Sample 178

value: FEM

value: L


title: Endometrium_uninfected_unique_individual 3

value: Female

value: trans-cervical endometrial samples

tag: infection

value: no


title: Whole peripheral blood_Tempus Tube, Sample 188

value: H


title: Endometrium_uninfected_unique_individual 10


title: Head and neck squamous cell carcinoma HN032 Agilent 4x44K

value: Tumor

tag: race

value: Caucasian

value: Male

tag: smoking packyears

tag: alcohol use

value: Unknown

tag: differentiation

value: Moderate

value: Hypopharynx

value: II

value: Surgery Alone

tag: hpv status

tag: reference


title: Whole peripheral blood_Tempus Tube, Sample 182

value: MAL

value: CAU

value: B


title: Pca_vpa_1

description: Undifferentiated Embryonal stem cells Stra8  Biological Replicate 1

tag: strain

tag: cell type

value: undifferentiated stem cells


title: Head and neck squamous cell carcinoma HN034 Agilent 4x44K

tag: tissue

tag: gender

value: None or Light/Moderate

tag: tumor site

value: Larynx

tag: Stage

value: IVa

tag: tumor status

tag: node status

tag: treatment

value: Surgery and Radiation

value: HPV+

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 174

value: FEM

tag: age

tag: percentage of body fat

tag: ethnicity

tag: zip code

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: K


title: Whole peripheral blood_Tempus Tube, Sample 175


title: Head and neck squamous cell carcinoma HN035 Agilent 4x44K

value: Tumor

tag: race

value: Caucasian

value: Male

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Well

value: Concurrent Chemoradiation

tag: hpv status

value: HPV-

tag: reference


title: Whole peripheral blood_Tempus Tube, Sample 180

tag: gender

value: CAU

value: L


title: Whole peripheral blood_Tempus Tube, Sample 177

value: F


title: Whole peripheral blood_Tempus Tube, Sample 181

value: A


title: Whole peripheral blood_Tempus Tube, Sample 179

value: J


title: Head and neck squamous cell carcinoma HN033 Agilent 4x44K

tag: tissue

value: None or Light/Moderate

value: Poor

tag: tumor site

value: Oropharynx

tag: Stage

value: IVa

tag: tumor status


title: Whole peripheral blood_Tempus Tube, Sample 176

value: MAL

tag: age

tag: percentage of body fat

value: D


title: Whole peripheral blood_Tempus Tube, Sample 172

tag: ethnicity

value: ASN

tag: zip code

value: G


title: Head and neck squamous cell carcinoma HN031 Agilent 4x44K

value: Tumor

value: Caucasian

value: Female

value: Moderate

value: Larynx

value: I

tag: node status

tag: treatment

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN030 Agilent 4x44K

tag: race

value: African American

value: Male

value: Heavy

value: Concurrent Chemoradiation

value: HPV-


title: Whole peripheral blood_Tempus Tube, Sample 169

value: FEM

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: A


title: Whole peripheral blood_Tempus Tube, Sample 171

value: CAU

value: E


title: Whole peripheral blood_Tempus Tube, Sample 159


title: Whole peripheral blood_Tempus Tube, Sample 170

value: MAL

value: C


title: Whole peripheral blood_Tempus Tube, Sample 160

value: G


title: Whole peripheral blood_Tempus Tube, Sample 161


title: Whole peripheral blood_Tempus Tube, Sample 168

value: AFR

value: L


title: Whole peripheral blood_Tempus Tube, Sample 162

value: K


title: Whole peripheral blood_Tempus Tube, Sample 165

value: F


title: Whole peripheral blood_Tempus Tube, Sample 156


title: Whole peripheral blood_Tempus Tube, Sample 166

value: H


title: Head and neck squamous cell carcinoma HN052 Agilent 4x44K

value: Tumor

value: Caucasian

value: Female

tag: smoking packyears

tag: alcohol use

value: None or Light/Moderate

tag: differentiation

value: Moderate

value: Other

value: IVb

value: Surgery Alone

tag: hpv status

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 155

tag: gender

value: FEM

value: CAU

value: J


title: Whole peripheral blood_Tempus Tube, Sample 164

value: D


title: Whole peripheral blood_Tempus Tube, Sample 153

value: AFR


title: Head and neck squamous cell carcinoma HN023 Agilent 4x44K

tag: tissue

value: Male

value: Poor

tag: tumor site

value: Oral Cavity

tag: Stage

value: IVa

value: Surgery and Concurrent Chemoradiation

value: HPV-

tag: reference


title: Head and neck squamous cell carcinoma HN028 Agilent 4x44K

value: Tumor

tag: age

value: Unknown

value: None or Light/Moderate

value: Larynx

tag: tumor status

value: Concurrent Chemoradiation


title: Head and neck squamous cell carcinoma HN027 Agilent 4x44K

value: Caucasian

value: Female

value: Well

value: Oropharynx

tag: node status

value: Surgery Alone

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN026 Agilent 4x44K

value: African American

value: Heavy

value: I

tag: treatment


title: Whole peripheral blood_Tempus Tube, Sample 163

value: MAL

tag: percentage of body fat

tag: ethnicity

value: CAU

tag: zip code

value: B


title: Whole peripheral blood_Tempus Tube, Sample 173

value: FEM

tag: rna integrity score

tag: batch effect_date

tag: plate id


title: Whole peripheral blood_Tempus Tube, Sample 157

value: A


title: Head and neck squamous cell carcinoma HN024 Agilent 4x44K

value: Tumor

tag: race

value: Male

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Poor

value: Oral Cavity

value: IVa

value: Surgery and Radiation

value: HPV-


title: Head and neck squamous cell carcinoma HN020 Agilent 4x44K

tag: tissue

value: Caucasian

tag: gender

value: Moderate

tag: tumor site

value: Larynx

value: II

value: Radiation Alone

tag: hpv status


title: Head and neck squamous cell carcinoma HN025 Agilent 4x44K

tag: age

value: African American

value: Heavy

value: Oropharynx

tag: Stage

tag: tumor status

value: Concurrent Chemoradiation

tag: reference

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 158

value: FEM

tag: percentage of body fat

tag: ethnicity

value: AFR

value: C


title: Whole peripheral blood_Tempus Tube, Sample 154

value: CAU

tag: zip code

tag: rna integrity score

value: H


title: Head and neck squamous cell carcinoma HN029 Agilent 4x44K

value: Tumor

value: Male

value: Hypopharynx

value: IVb

tag: node status

tag: treatment


title: Head and neck squamous cell carcinoma HN021 Agilent 4x44K

tag: race

tag: smoking packyears

value: None or Light/Moderate

value: Moderate

value: Larynx

value: III

value: Surgery Alone


title: Whole peripheral blood_Tempus Tube, Sample 167

tag: batch effect_date

tag: plate id

value: J


title: Head and neck squamous cell carcinoma HN022 Agilent 4x44K

tag: tissue

value: Caucasian

tag: gender

value: Female

tag: alcohol use

tag: differentiation

value: Poor

value: Oral Cavity

value: I

value: Surgery and Radiation


title: Whole peripheral blood_Tempus Tube, Sample 152

value: FEM

tag: age

value: CAU

value: D


title: Whole peripheral blood_Tempus Tube, Sample 151

value: AFR

value: B


title: Whole peripheral blood_Tempus Tube, Sample 149


title: Head and neck squamous cell carcinoma HN019 Agilent 4x44K

value: Tumor

value: Male

value: Heavy

tag: tumor site

value: Hypopharynx

tag: Stage

value: IVb

tag: tumor status

value: Surgery and Concurrent Chemoradiation

tag: hpv status

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 150

tag: percentage of body fat

tag: ethnicity

tag: zip code

value: K


title: Whole peripheral blood_Tempus Tube, Sample 148

tag: rna integrity score

value: G


title: Whole peripheral blood_Tempus Tube, Sample 143

value: J


title: Whole peripheral blood_Tempus Tube, Sample 146

value: MAL

value: C


title: Whole peripheral blood_Tempus Tube, Sample 147

value: E


title: Whole peripheral blood_Tempus Tube, Sample 140

value: FEM

value: CAU


title: Whole peripheral blood_Tempus Tube, Sample 144

value: L


title: Head and neck squamous cell carcinoma HN010 Agilent 4x44K

tag: race

value: African American

value: None or Light/Moderate

value: Moderate

value: Oral Cavity

value: IVa

tag: node status

tag: treatment

value: Surgery and Radiation

value: HPV-

tag: reference


title: Whole peripheral blood_Tempus Tube, Sample 142

tag: batch effect_date

tag: plate id

value: H


title: Whole peripheral blood_Tempus Tube, Sample 145

tag: gender

value: AFR

value: A


title: Whole peripheral blood_Tempus Tube, Sample 139

value: B


title: Head and neck squamous cell carcinoma HN018 Agilent 4x44K

tag: tissue

value: Tumor

value: Caucasian

value: Female

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN015 Agilent 4x44K

tag: age

value: Heavy

tag: tumor site

tag: Stage

tag: tumor status


title: Whole peripheral blood_Tempus Tube, Sample 141

value: FEM

tag: percentage of body fat

tag: ethnicity

tag: zip code

value: F


title: Whole peripheral blood_Tempus Tube, Sample 135

value: CAU

tag: rna integrity score

value: E


title: Head and neck squamous cell carcinoma HN012 Agilent 4x44K

tag: race

value: Male

value: None or Light/Moderate

value: Moderate

value: Oral Cavity

tag: node status

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status


title: Whole peripheral blood_Tempus Tube, Sample 138

tag: gender

value: MAL

tag: batch effect_date

tag: plate id


title: Whole peripheral blood_Tempus Tube, Sample 134

value: C


title: Whole peripheral blood_Tempus Tube, Sample 133

value: A


title: Whole peripheral blood_Tempus Tube, Sample 137

value: I


title: Whole peripheral blood_Tempus Tube, Sample 136

value: G


title: Head and neck squamous cell carcinoma HN006 Agilent 4x44K

tag: tissue

value: Tumor

value: Caucasian

value: Female

tag: smoking packyears

tag: alcohol use

value: Oropharynx

value: IVa

tag: reference


title: Head and neck squamous cell carcinoma HN009 Agilent 4x44K

tag: age

tag: differentiation

tag: tumor site

tag: Stage

value: III

value: Surgery and Radiation

value: HPV-

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 132

value: FEM

tag: percentage of body fat

tag: ethnicity

value: AFR

tag: zip code

value: L


title: Head and neck squamous cell carcinoma HN008 Agilent 4x44K

tag: race

value: None or Light/Moderate

value: Moderate

value: Oral Cavity

value: II

tag: tumor status

tag: node status

value: Surgery Alone


title: Head and neck squamous cell carcinoma HN007 Agilent 4x44K

value: Tumor

tag: gender

value: Male

value: Heavy

tag: treatment

value: Chemotherapy Alone - Palliative

tag: hpv status


title: Head and neck squamous cell carcinoma HN004 Agilent 4x44K

tag: tissue

value: Caucasian

value: Oropharynx


title: Whole peripheral blood_Tempus Tube, Sample 131

value: MAL

value: CAU

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: J


title: Whole peripheral blood_Tempus Tube, Sample 129

tag: age

value: AMI

value: F


title: Whole peripheral blood_Tempus Tube, Sample 130

value: FEM

value: H


title: Whole peripheral blood_Tempus Tube, Sample 125

value: I


title: Whole peripheral blood_Tempus Tube, Sample 124

value: G


title: Head and neck squamous cell carcinoma HN005 Agilent 4x44K

tag: smoking packyears

tag: alcohol use

tag: differentiation

value: Well

value: III

value: Surgery and Radiation

tag: reference

value: Stratagene Human Universal RNA Reference


title: Whole peripheral blood_Tempus Tube, Sample 127

tag: percentage of body fat

tag: ethnicity

value: B


title: Whole peripheral blood_Tempus Tube, Sample 126

value: AFR

tag: zip code

value: K


title: Head and neck squamous cell carcinoma HN003 Agilent 4x44K

value: Tumor

tag: race

value: Caucasian

value: Male

value: Heavy

value: Moderate

tag: tumor site

value: Larynx

tag: Stage

tag: tumor status

value: Surgery Alone


title: Whole peripheral blood_Tempus Tube, Sample 123

tag: gender

value: FEM

value: ASN

value: E


title: Whole peripheral blood_Tempus Tube, Sample 120

value: L


title: Whole peripheral blood_Tempus Tube, Sample 128

value: D


title: Whole peripheral blood_Tempus Tube, Sample 121

value: MAL

value: CAU

value: A


title: Whole peripheral blood_Tempus Tube, Sample 116


title: Whole peripheral blood_Tempus Tube, Sample 122

value: C


title: Whole peripheral blood_Tempus Tube, Sample 112

value: G


title: Malignant Breast Cell Line:BT483

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

description:
BT483
0=negative; 1=positive

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan with Illumina scanner settings for the Infinium chip.

data_processing: GenomeStudio V2011.1. Beta=M/(M+U).

label: Cy5 and Cy3

source_name: Malignant breast cell line, Lu

label_protocol: Standard Illumina Protocol for Infinium Methylation27 BeadChip.

extract_protocol: DNA was extracted with TNES/PK (Tris/NaCl/EDTA/SDS/proteinase K) lysis buffer prior to sodium bisulfite conversion using the Zymo Research EZ DNA Methylation Kit.

tag: cell line

tag: cell type

value: malignant breast cell line

tag: expression subtype

value: Lu

tag: er

tag: pr


title: Whole peripheral blood_Tempus Tube, Sample 114

tag: age

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: K


title: Whole peripheral blood_Tempus Tube, Sample 119

tag: percentage of body fat

value: J


title: Malignant Breast Cell Line:SUM52

description:
SUM52
0=negative; 1=positive


title: Head and neck squamous cell carcinoma HN001 Agilent 4x44K

tag: tissue

value: Tumor

value: African American

value: Male

tag: smoking packyears

tag: alcohol use

value: Heavy

tag: differentiation

value: Moderate

value: Oropharynx

value: IVa

tag: node status

tag: treatment

value: Concurrent Chemoradiation

tag: hpv status

tag: reference

value: Stratagene Human Universal RNA Reference


title: Head and neck squamous cell carcinoma HN002 Agilent 4x44K

tag: race

value: Caucasian

tag: gender

value: Female

value: None or Light/Moderate

tag: tumor site

tag: Stage

value: III

tag: tumor status


title: Malignant Breast Cell Line:SUM149PT

description:
SUM149PT
0=negative; 1=positive

source_name: Malignant breast cell line, BaB/CLDNlow

tag: cell line

tag: cell type

value: malignant breast cell line

tag: expression subtype

value: BaB/CLDNlow

tag: er

tag: pr


title: Malignant Breast Cell Line:SUM185

description:
SUM185
0=negative; 1=positive

value: Lu


title: Malignant Breast Cell Line:SUM44

description:
SUM44
0=negative; 1=positive

source_name: Malignant breast cell line


title: Malignant Breast Cell Line:SUM159PT

description:
SUM159PT
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 117

value: FEM

tag: age

tag: percentage of body fat

tag: ethnicity

value: CAU

tag: zip code

tag: rna integrity score

tag: batch effect_date

tag: plate id

value: F


title: Whole peripheral blood_Tempus Tube, Sample 111

value: AFR

value: E


title: Whole peripheral blood_Tempus Tube, Sample 118

value: MAL

value: H


title: Whole peripheral blood_Tempus Tube, Sample 109

value: A


title: Whole peripheral blood_Tempus Tube, Sample 108

value: L


title: Whole peripheral blood_Tempus Tube, Sample 107

value: J


title: Whole peripheral blood_Tempus Tube, Sample 110

value: C


title: Whole peripheral blood_Tempus Tube, Sample 113

value: ASN

value: I


title: Malignant Breast Cell Line:SUM190PT

description:
SUM190PT
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 99


title: Whole peripheral blood_Tempus Tube, Sample 100

value: G


title: Malignant Breast Cell Line:SUM225

description:
SUM225
0=negative; 1=positive

source_name: Malignant breast cell line, BaA

value: malignant breast cell line

value: BaA


title: Whole peripheral blood_Tempus Tube, Sample 106


title: Whole peripheral blood_Tempus Tube, Sample 101


title: Whole peripheral blood_Tempus Tube, Sample 98


title: Malignant Breast Cell Line:SUM1315

description:
SUM1315
0=negative; 1=positive

value: BaB/CLDNlow


title: Malignant Breast Cell Line:MDAMB361

description:
MDAMB361
0=negative; 1=positive

value: Lu


title: Whole peripheral blood_Tempus Tube, Sample 104

value: FEM

value: CAU

value: D


title: Whole peripheral blood_Tempus Tube, Sample 103

value: B


title: Whole peripheral blood_Tempus Tube, Sample 102

value: K


title: Malignant Breast Cell Line:MDAMB175

description:
MDAMB175
0=negative; 1=positive


title: Malignant Breast Cell Line:MDAMB468

description:
MDAMB468
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 97

value: AFR


title: Malignant Breast Cell Line:MDAMB157

description:
MDAMB157
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 95


title: Whole peripheral blood_Tempus Tube, Sample 93

value: F


title: Whole peripheral blood_Tempus Tube, Sample 105


title: Whole peripheral blood_Tempus Tube, Sample 94

value: H


title: Malignant Breast Cell Line:HCC1569

description:
HCC1569
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 91

value: MAL


title: Malignant Breast Cell Line:ZR75B

description:
ZR75B
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 115


title: Whole peripheral blood_Tempus Tube, Sample 96

value: L


title: Whole peripheral blood_Tempus Tube, Sample 90


title: Non-Malignant Breast Cell Line:MCF10A

description:
MCF10A
0=negative; 1=positive

source_name: Non-malignant breast cell line, BaB/CLDNlow

value: non-malignant breast cell line


title: Malignant Breast Cell Line:MDAMB436

description:
MDAMB436
0=negative; 1=positive


title: Malignant Breast Cell Line:UACC812

description:
UACC812
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 92


title: Whole peripheral blood_Tempus Tube, Sample 87

value: E


title: Whole peripheral blood_Tempus Tube, Sample 85

value: A


title: Malignant Breast Cell Line:ZR751

description:
ZR751
0=negative; 1=positive

value: malignant breast cell line


title: Malignant Breast Cell Line:HCC1419

description:
HCC1419
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 82


title: Whole peripheral blood_Tempus Tube, Sample 81


title: Whole peripheral blood_Tempus Tube, Sample 88

value: G


title: Malignant Breast Cell Line:MDAMB231

description:
MDAMB231
0=negative; 1=positive

value: BaB/CLDNlow


title: Whole peripheral blood_Tempus Tube, Sample 86

value: C


title: Whole peripheral blood_Tempus Tube, Sample 84

value: FEM


title: Whole peripheral blood_Tempus Tube, Sample 83

value: CAU

value: J


title: Whole peripheral blood_Tempus Tube, Sample 75


title: Whole peripheral blood_Tempus Tube, Sample 76


title: Malignant Breast Cell Line:ZR7530

description:
ZR7530
0=negative; 1=positive

value: Lu


title: Whole peripheral blood_Tempus Tube, Sample 79

value: B


title: Whole peripheral blood_Tempus Tube, Sample 80

value: ASN

value: D


title: Malignant Breast Cell Line:HCC2218

description:
HCC2218
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 77

value: I


title: Whole peripheral blood_Tempus Tube, Sample 78

value: MAL

value: K


title: Malignant Breast Cell Line:SKBR3

description:
SKBR3
0=negative; 1=positive


title: Malignant Breast Cell Line:MCF12A

description:
MCF12A
0=negative; 1=positive

value: BaA


title: Whole peripheral blood_Tempus Tube, Sample 71


title: Whole peripheral blood_Tempus Tube, Sample 72

value: L


title: Whole peripheral blood_Tempus Tube, Sample 89


title: Whole peripheral blood_Tempus Tube, Sample 69

value: AFR

value: F


title: Whole peripheral blood_Tempus Tube, Sample 73

value: A


title: Whole peripheral blood_Tempus Tube, Sample 70

value: H


title: Malignant Breast Cell Line:T47D

description:
T47D
0=negative; 1=positive

value: malignant breast cell line


title: Whole peripheral blood_Tempus Tube, Sample 67


title: Whole peripheral blood_Tempus Tube, Sample 74

value: FEM

value: C


title: Malignant Breast Cell Line:HCC1954

description:
HCC1954
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 59

value: CAU

value: J


title: Whole peripheral blood_Tempus Tube, Sample 54


title: Whole peripheral blood_Tempus Tube, Sample 55

value: B


title: Malignant Breast Cell Line:MDAMB453

description:
MDAMB453
0=negative; 1=positive

value: Lu


title: Whole peripheral blood_Tempus Tube, Sample 65


title: Whole peripheral blood_Tempus Tube, Sample 60


title: Malignant Breast Cell Line:HCC70

description:
HCC70
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 56

value: ASN

value: D


title: Whole peripheral blood_Tempus Tube, Sample 62

value: MAL


title: Whole peripheral blood_Tempus Tube, Sample 63

value: E


title: Whole peripheral blood_Tempus Tube, Sample 64

value: G


title: Malignant Breast Cell Line:DU4475

description:
DU4475
0=negative; 1=positive


title: Malignant Breast Cell Line:HCC1937

description:
HCC1937
0=negative; 1=positive

value: BaA


title: Malignant Breast Cell Line:HCC1806

description:
HCC1806
0=negative; 1=positive


title: Malignant Breast Cell Line:MDAMB415

description:
MDAMB415
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 52


title: Whole peripheral blood_Tempus Tube, Sample 58

value: AFR


title: Whole peripheral blood_Tempus Tube, Sample 53

value: I


title: Whole peripheral blood_Tempus Tube, Sample 61

value: A


title: Whole peripheral blood_Tempus Tube, Sample 51


title: Malignant Breast Cell Line:HCC1143

description:
HCC1143
0=negative; 1=positive


title: Malignant Breast Cell Line:LY2

description:
LY2
0=negative; 1=positive


title: Whole peripheral blood_Tempus Tube, Sample 66

value: K