title: Burkholderia cenocepacia_AU16956_2

description:
set4
a2412_ET120-2_647_pmt840_ET124-2_555_pmt760_EC_with_SNR.txt
Also_known_as_ET124.2


title: Burkholderia cenocepacia_HI4278_4

status: Public on Jul 31 2014

type: genomic

city: East Lansing

first: erick

last: cardenas

state: Michigan

address: 540 Plant and Soil Sciences Building

country: USA

institute: Michigan State University

description:
set4
a2409_ET121-4_647_pmt870_ET123-4_555_pmt770_analyzed_with_SNR.txt
Also_known_as_ET123.4

hyb_protocol: Dried DNAs from two isolates labeled with each fluorophore were resuspended together in hybridization buffer (6x SSPE, 23% formamide, and 0.05% Tween 20), heated for 5 min at 95°C, and cooled on ice for 5 min before loading onto the arrays. Coverslips were rinsed with 2% SDS, followed by water and then 100% ethanol. After two more washes with water, coverslips were overlaid on the slide to cover both arrays. Covered slides were deposited in hybridization chambers and incubated in a 48°C water bath for 16-20 h. Arrays were then sequentially washed in 6X SSPE for 2 min at 48°C and 1X SSPE for 2 min at 48°C, and then quickly dipped ten times in 0.25X SSPE at room temperature before drying by centrifugation at 2000 xg for 30 s.

scan_protocol: Arrays were scanned in an Axon 4000B scanner (Molecular Devices, Inc., Sunnyvale, CA) using the Genepix v5.1 software and a 5 μm pixel size. PMT values were customized for each channel to obtain the complete range of intensities. Images were saved in TIFF format. Before extracting data, spots were reviewed and flagged as unreadable if scratches, dust or salts precipitates were present. Data were extracted from both channels, but each channel was treated independently in the final analysis

data_processing: Global background, calculated as 5% median of the intensity of all target probes, was subtracted from each spot intensity. Arrays were then normalized using a set of 159 probes from 78 genes whose sequences were exact matches in all 5 of the genomes used for the array design.  The median spot intensity for the group of conserved probes was arbitrarily set to 10,000 and applied as a correction factor to each array. Probes with adjusted signal intensities greater than 1594 units. Data from independent hybridization reactions were consolidated to a single present/absent call for each probe, with present being defined as at least 50% of all replicate spots being called present. Finally, genes were called present if at least 50% of the probes targeted to that element were called present.

label: Alexa Dye 555

molecule: genomic DNA

organism: Burkholderia cenocepacia

source_name: Pure culture

label_protocol: Four micrograms of bacterial genomic DNA were labeled with Alexa Fluor 555 or Alexa Fluor 647 ester dyes using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen Corp., Carlsbad, CA) following the manufacturer’s specifications with two modifications. In place of ethanol precipitation, DNA was dried for 2 h under medium heat after Klenow amplification using the Savant DNA 120 vacuum centrifuge (Thermo Scientific, Asheville, NC), and DNA was completely dried after dye incorporation for 2 h by vacuum centrifugation with no heat.

extract_protocol: Bacteria were recovered from frozen stock by culturing on Mueller-Hinton (MH) agar overnight at 37 oC. Bacteria removed from agar were suspended in DNase-, RNase-free water, and genomic DNA was isolated using the Puregene system (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions with the following modifications.  Proteinase K was added to a final concentration of 200 µg/ml prior to incubating cell lysates at 80oC for 5 min, the final concentration of RNAse was increased to 25 µg/ml, and precipitated proteins were removed by course filter through a 1 ml syringe packed to the 0.2 ml demarcation with glass wool prior to the clarifying centrifugation. Pelleted DNA was resuspended in DNase-, RNase-free water, and DNA quality was assessed by A260/A280 ratios and agarose gel electrophoresis.

tag: strain

tag: group

tag: replicate


title: PFC_78

type: RNA

city: New York

first: Jun

last: Zhu

state: NY

address: One Gustave L Levy, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn Medical School at Mount Sinai

description: Dorsolateral prefrontal cortex (DLPFC)

hyb_protocol: Microarrays were incubated at 40C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays were completed as previously described (Hughes et al. Nat Biotech (2001), 19(4):342-7). Microarrays were washed to remove non-specific hybridized sample. Afterwards, microarrays were dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays were scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files were then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Homo sapiens

label_protocol: Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.

growth_protocol: Fresh-frozen post-mortem brain tissues.

extract_protocol: Qiagen RNeasy spin columns with DNase treatment.

tag: tissue

value: prefrontal cortex brain

tag: sample type

value: reference

tag: age

value: 73 yrs

tag: gender

value: male

tag: disease status

value: Alzheimer's disease


title: human HCC sample from young patient [HCC_89T.CEL]

city: Taipei

first: Jui-Yu

last: Hsieh

address: No. 155, Sec 2, Li-Nong Street

country: Taiwan

institute: National Yang-Ming University

description: elder HCC patient

hyb_protocol: cRNA were hybridized, washed and stained on U133 plus 2.0 chips according to standard Affymetrix protocol.

scan_protocol: Chips are stained on Affymetrix GCS3000 scanner (scanner type M10)

data_processing: The CEL file was loaded to R/Bioconductor software and normalized by GC-RMA with default settings.

label: biotin

source_name: human HCC sample from young patient

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

growth_protocol: The HCC samples used in this study were the original tumors obtained from the first operations of patients.

extract_protocol: Total RNA was extracted by Trizol according to the manufacturer's instructions.

treatment_protocol: Fresh HCC tissues and non-tumor counter parts that had been removed during surgery were snap frozen and kept in liquid nitrogen for RNA extraction.

value: Tumor

value: elder HCC patient


title: human HCC sample from young patient [HCC_1684T.CEL]

description: young HCC patient

value: young HCC patient


title: PFC_73

description: Dorsolateral prefrontal cortex (DLPFC)

value: 81 yrs

value: female


title: human HCC sample from elder patient [HCC_69N.CEL]

description: elder HCC patient

source_name: human HCC sample from elder patient


title: PFC_75

description: Dorsolateral prefrontal cortex (DLPFC)

value: 68 yrs


title: PFC_72

description: Dorsolateral prefrontal cortex (DLPFC)

value: 92 yrs


title: PFC_70

description: Dorsolateral prefrontal cortex (DLPFC)

value: 83 yrs


title: human HCC sample from young patient [HCC_1637T.CEL]

description: young HCC patient


title: PFC_77

description: Dorsolateral prefrontal cortex (DLPFC)

value: 84 yrs


title: Burkholderia cenocepacia_HI4278_2

description:
set4
a2420_ET123-2_647_pmt850_ET129-2_555_pmt780_EC.txt
Also_known_as_ET123.2

label: Alexa Dye 647


title: PFC_71

description: Dorsolateral prefrontal cortex (DLPFC)

value: 80 yrs


title: PFC_74

description: Dorsolateral prefrontal cortex (DLPFC)

value: 85 yrs


title: PFC_69

description: Dorsolateral prefrontal cortex (DLPFC)

value: 82 yrs


title: Burkholderia cenocepacia_AU16955_4

description:
set4
a2407_ET120-3_647_pmt880_ET122-4_555_pmt760_analyzed_with_SNR.txt
Also_known_as_ET122.4


title: human HCC sample from elder patient [HCC_523T.CEL]

description: elder HCC patient


title: PFC_68

description: Dorsolateral prefrontal cortex (DLPFC)

value: prefrontal cortex brain

value: 75 yrs


title: PFC_65

description: Dorsolateral prefrontal cortex (DLPFC)

value: reference


title: Burkholderia cenocepacia_HI4278_1

description:
set4
a2416_ET122-1_647_pmt820_ET123-1_555_pmt760_EC_with_SNR.txt
Also_known_as_ET123.1


title: human HCC sample from elder patient [HCC_40T.CEL]

description: elder HCC patient


title: PFC_59

description: Dorsolateral prefrontal cortex (DLPFC)

value: 67 yrs


title: PFC_67

description: Dorsolateral prefrontal cortex (DLPFC)

value: male

value: Alzheimer's disease


title: PFC_62

description: Dorsolateral prefrontal cortex (DLPFC)

value: 74 yrs


title: PFC_64

description: Dorsolateral prefrontal cortex (DLPFC)

value: 73 yrs


title: PFC_66

description: Dorsolateral prefrontal cortex (DLPFC)

value: 62 yrs


title: Burkholderia cenocepacia_HI4277_1

description:
set4
a2414_ET121-1_647_pmt900_ET125-1_555_pmt780_EC_wiht_SNR.txt
Also_known_as_ET121.1


title: PFC_56

description: Dorsolateral prefrontal cortex (DLPFC)

value: 77 yrs


title: PFC_63

description: Dorsolateral prefrontal cortex (DLPFC)

value: 69 yrs

value: female


title: Burkholderia cenocepacia_HI4277_4

description:
set4
a2409_ET121-4_647_pmt870_ET123-4_555_pmt770_analyzed_with_SNR.txt
Also_known_as_ET121.4


title: PFC_60

description: Dorsolateral prefrontal cortex (DLPFC)

value: 89 yrs


title: PFC_61

description: Dorsolateral prefrontal cortex (DLPFC)

value: 87 yrs


title: human HCC sample from elder patient [HCC_307T.CEL]

description: elder HCC patient

value: Tumor

value: elder HCC patient


title: Burkholderia cenocepacia_AU16955_1

description:
set4
a2416_ET122-1_647_pmt820_ET123-1_555_pmt760_EC_with_SNR.txt
Also_known_as_ET122.1


title: human HCC sample from elder patient [HCC_239T.CEL]

description: elder HCC patient


title: human HCC sample from elder patient [HCC_19T.CEL]

description: elder HCC patient


title: PFC_58

description: Dorsolateral prefrontal cortex (DLPFC)

value: 85 yrs


title: PFC_55

description: Dorsolateral prefrontal cortex (DLPFC)

value: prefrontal cortex brain

value: 83 yrs


title: PFC_57

description: Dorsolateral prefrontal cortex (DLPFC)

value: reference

value: 78 yrs


title: human HCC sample from elder patient [HCC_185T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_HI4277_2

description:
set4
a2415_ET121-2_647_pmt890_ET127-2_555_pmt790.txt
Also_known_as_ET121.2


title: Burkholderia cenocepacia_AU16955_2

description:
set4
a2418_ET127-1_647_pmt830_ET122-2_555_pmt770_EC_wiht_SNR.txt
Also_known_as_ET122.2


title: Burkholderia cenocepacia_HI2821_2

description:
set4
a2412_ET120-2_647_pmt840_ET124-2_555_pmt760_EC_with_SNR.txt
Also_known_as_ET120.2


title: human HCC sample from elder patient [HCC_463T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_HI2821_1

description:
set4
a2413_ET126-1_647_pmt840_ET120-1_555_pmt760_analyzed.txt
Also_known_as_ET120.1


title: Burkholderia cenocepacia_HI2821_3

description:
set4
a2407_ET120-3_647_pmt880_ET122-4_555_pmt760_analyzed_with_SNR.txt
Also_known_as_ET120.3


title: human HCC sample from elder patient [HCC_199T.CEL]

description: elder HCC patient


title: PFC_53

description: Dorsolateral prefrontal cortex (DLPFC)

value: 68 yrs

value: male


title: PFC_54

description: Dorsolateral prefrontal cortex (DLPFC)

value: Alzheimer's disease


title: PFC_52

description: Dorsolateral prefrontal cortex (DLPFC)


title: human HCC sample from elder patient [HCC_108T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU9722_35

description:
set4
3279_AU9722-35_647_pmt950_HI3557-35_555_pmt860.txt

value: Sporadic IIIA


title: Burkholderia cenocepacia_AU9512_2

description:
set4
2728_AU1189-1__647pmt900_AU9512-2_555pm_0620_with_SNR.txt


title: PFC_48

description: Dorsolateral prefrontal cortex (DLPFC)


title: PFC_44

description: Dorsolateral prefrontal cortex (DLPFC)

value: 84 yrs


title: Burkholderia cenocepacia_AU9722_25

description:
set4
2957-AU1529-25_647pmt1000_555_AU9722-25_pmt930.txt


title: PFC_49

description: Dorsolateral prefrontal cortex (DLPFC)

value: 92 yrs


title: PFC_51

description: Dorsolateral prefrontal cortex (DLPFC)


title: PFC_45

description: Dorsolateral prefrontal cortex (DLPFC)


title: PFC_41

description: Dorsolateral prefrontal cortex (DLPFC)

value: 90 yrs


title: human HCC sample from elder patient [HCC_91T2.CEL]

description: elder HCC patient


title: human HCC sample from elder patient [HCC_942T.CEL]

description: elder HCC patient


title: PFC_50

description: Dorsolateral prefrontal cortex (DLPFC)

value: 74 yrs

value: female


title: PFC_47

description: Dorsolateral prefrontal cortex (DLPFC)

value: 82 yrs


title: human HCC sample from elder patient [HCC_1042T.CEL]

description: elder HCC patient

value: Tumor


title: Burkholderia cenocepacia_AU9722_26

description:
set4
3281_HI3557-36_647_pmt890_AU9722-26_555_pmt790.txt


title: human HCC sample from elder patient [HCC_68T.CEL]

description: elder HCC patient

value: elder HCC patient


title: PFC_43

description: Dorsolateral prefrontal cortex (DLPFC)

value: 76 yrs


title: Burkholderia cenocepacia_AU9448_11

description:
set4
a2678_AU9448-11_647_pmt930_AU3516-15_555_pm_0610_with_SNR.txt


title: PFC_46

description: Dorsolateral prefrontal cortex (DLPFC)

value: prefrontal cortex brain

value: 75 yrs


title: Burkholderia cenocepacia_AU9512_12

description:
set4
2682_AU9512-12_647_pmt939_AU0411-11_555_pmt630.txt


title: human HCC sample from elder patient [HCC_59T.CEL]

description: elder HCC patient


title: PFC_42

description: Dorsolateral prefrontal cortex (DLPFC)

value: reference


title: PFC_38

description: Dorsolateral prefrontal cortex (DLPFC)

value: 89 yrs


title: PFC_39

description: Dorsolateral prefrontal cortex (DLPFC)

value: 85 yrs


title: Burkholderia cenocepacia_AU9448_10

description:
set4
2415_AU1480-11_647_pmt960_AU9448-10_555_pmt660.txt


title: human HCC sample from elder patient [HCC_80T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU9410_20

description:
set4
2919_AU11555-9_647_pmt770_AU9410-20_555_pmt770_with_SNR.txt


title: human HCC sample from elder patient [HCC_103T.CEL]

description: elder HCC patient


title: PFC_36

description: Dorsolateral prefrontal cortex (DLPFC)


title: human HCC sample from elder patient [HCC_107T.CEL]

description: elder HCC patient


title: PFC_37

description: Dorsolateral prefrontal cortex (DLPFC)

value: male


title: PFC_34

description: Dorsolateral prefrontal cortex (DLPFC)

value: Alzheimer's disease


title: PFC_30

description: Dorsolateral prefrontal cortex (DLPFC)

value: 55 yrs


title: human normal liver sample from elder HCC patient [HCC_89N.CEL]

description: elder HCC patient

value: Normal


title: PFC_31

description: Dorsolateral prefrontal cortex (DLPFC)

value: 77 yrs


title: Burkholderia cenocepacia_AU9410_3

description:
set4
2397_AU9410-3_647_pmt1000_HI2762-2_555_pmt830.txt


title: Burkholderia cenocepacia_AU9277_30

description:
set4
2901-AU9277-30_647pmt850-AU5757-30_0555_with_SNR.txt

value: Sporadic IIIA


title: PFC_28

description: Dorsolateral prefrontal cortex (DLPFC)

value: 65 yrs


title: PFC_33

description: Dorsolateral prefrontal cortex (DLPFC)

value: 79 yrs


title: human normal liver sample from elder HCC patient [HCC_83N.CEL]

description: elder HCC patient


title: human HCC sample from elder patient [HCC_15T.CEL]

description: elder HCC patient


title: human normal liver sample from elder HCC patient [HCC_464N.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU9307_1

description:
set4
2688_AU8831-2_647_pmt939_AU9307-1_555_pmt670_with_SNR.txt


title: PFC_27

description: Dorsolateral prefrontal cortex (DLPFC)

value: 84 yrs

value: female


title: Burkholderia cenocepacia_AU9277_31

description:
set4
2903-AU1644-30_647pmt850-AU9277-31_0555_with_SNR.txt


title: PFC_35

description: Dorsolateral prefrontal cortex (DLPFC)


title: PFC_24

description: Dorsolateral prefrontal cortex (DLPFC)


title: PFC_25

description: Dorsolateral prefrontal cortex (DLPFC)


title: human normal liver sample from elder HCC patient [HCC_76T.CEL]

description: elder HCC patient

value: elder HCC patient


title: Burkholderia cenocepacia_AU9307_30

description:
set4
2921-AU9307-30_647pmt810-AU0756-31_0555_with_SNR.txt


title: PFC_29

description: Dorsolateral prefrontal cortex (DLPFC)

value: 66 yrs


title: PFC_26

description: Dorsolateral prefrontal cortex (DLPFC)

value: prefrontal cortex brain

value: 76 yrs


title: PFC_32

description: Dorsolateral prefrontal cortex (DLPFC)

value: reference

value: 61 yrs


title: human normal liver sample from elder HCC patient [HCC_69T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU9220_2

description:
set4
3282_AU2765-25_647_pmt910_AU9220-2_555_pmt830.txt

value: PHDC


title: Burkholderia cenocepacia_AU9220_1

description:
set4
3283_AU9220-1_647_pmt990_AU8714-3_555_pmt800.txt


title: Burkholderia cenocepacia_AU8831_1

description:
set4
2689_HI2555-1_647_pmt939_AU8831-1_555_pmt650_with_SNR.txt

value: Midwest


title: PFC_19

description: Dorsolateral prefrontal cortex (DLPFC)

value: male

value: Alzheimer's disease


title: Burkholderia cenocepacia_AU8831_2


title: PFC_23

description: Dorsolateral prefrontal cortex (DLPFC)


title: Burkholderia cenocepacia_AU9096_2

description:
set4
2902-AU15723-2_647pmt870-AU9096-2_0555_with_SNR.txt


title: human normal liver sample from elder HCC patient [HCC_199N.CEL]

description: elder HCC patient

value: Normal


title: PFC_22

description: Dorsolateral prefrontal cortex (DLPFC)

value: 87 yrs


title: Burkholderia cenocepacia_AU9096_1

description:
set4
2907-AU9096-1_647pmt900-AU6699-15_0555_with_SNR.txt

value: Sporadic IIIA


title: human normal liver sample from elder HCC patient [HCC_19N.CEL]

description: elder HCC patient


title: PFC_21

description: Dorsolateral prefrontal cortex (DLPFC)

value: 91 yrs


title: PFC_13

description: Dorsolateral prefrontal cortex (DLPFC)


title: human normal liver sample from elder HCC patient [HCC_306T.CEL]

description: elder HCC patient


title: PFC_16

description: Dorsolateral prefrontal cortex (DLPFC)

value: 89 yrs


title: PFC_20

description: Dorsolateral prefrontal cortex (DLPFC)

value: 77 yrs


title: PFC_14

description: Dorsolateral prefrontal cortex (DLPFC)

value: 93 yrs


title: PFC_17

description: Dorsolateral prefrontal cortex (DLPFC)

value: 81 yrs


title: Burkholderia cenocepacia_AU8830_10

description:
set4
a2681_AU12848-1_647_pmt920_AU8830-10_555_pm_0610_with_SNR.txt


title: Burkholderia cenocepacia_AU8830_6

description:
set4
2683-HI2811-3_647-AU8830-6_0555_with_SNR.txt


title: human normal liver sample from elder HCC patient [HCC_91N.CEL]

description: elder HCC patient

value: elder HCC patient


title: PFC_15

description: Dorsolateral prefrontal cortex (DLPFC)

value: prefrontal cortex brain

value: female


title: human normal liver sample from elder HCC patient [HCC_197N.CEL]

description: elder HCC patient


title: PFC_18

description: Dorsolateral prefrontal cortex (DLPFC)

value: reference

value: 85 yrs


title: human normal liver sample from elder HCC patient [HCC_108N.CEL]

description: elder HCC patient


title: PFC_11

description: Dorsolateral prefrontal cortex (DLPFC)


title: PFC_10

description: Dorsolateral prefrontal cortex (DLPFC)

value: 64 yrs


title: PFC_9

description: Dorsolateral prefrontal cortex (DLPFC)

value: 72 yrs


title: PFC_40

description: Dorsolateral prefrontal cortex (DLPFC)

value: 67 yrs


title: PFC_12

description: Dorsolateral prefrontal cortex (DLPFC)

value: 80 yrs

value: Alzheimer's disease


title: Burkholderia cenocepacia_AU8830_3

description:
set4
2399_AU8830-3_647_pmt800_AU1189-12_555_pmt710_analyzed_with_SNR.txt

value: Midwest


title: human normal liver sample from elder HCC patient [HCC_185N.CEL]

description: elder HCC patient

value: Normal


title: human normal liver sample from elder HCC patient [HCC_80N.CEL]

description: elder HCC patient


title: human normal liver sample from elder HCC patient [HCC_79N.CEL]

description: elder HCC patient


title: PFC_7

description: Dorsolateral prefrontal cortex (DLPFC)


title: 1921-WT-L

city: St. Louis

first: Debabrata

last: Patra

state: MO

address: 425 S. Euclid Avenue

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with Illumina GUI in R.

label: Biotin

organism: Mus musculus

source_name: Wild type appendicular bones

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy kit as per manufacturer's protocol provided with kit. Quality control was performed with Agilent Bioanalyser.

tag: strain/background

tag: genotype/variation

value: wild type

value: entire appendicular skeleton elements such as femora, tibia, humeri

value: embryonic (E) 16.5


title: Burkholderia cenocepacia_AU8718_2

description:
set4
2904_AU5417-1_647_pmt770_AU8718-2_0555.txt

value: Sporadic IIIA


title: PFC_4

description: Dorsolateral prefrontal cortex (DLPFC)

value: 90 yrs


title: Burkholderia cenocepacia_AU8714_26

description:
set4
2954_AU8714-26_647_pmt1000_HI3558-25_555_pmt880_with_SNR.txt


title: PFC_8

description: Dorsolateral prefrontal cortex (DLPFC)

value: 100 yrs


title: 1926-S1Pcko-Cal

description: Replicate 1

source_name: S1Pcko calvarium

value: calvarium


title: Burkholderia cenocepacia_AU8714_3


title: 1920-S1Pcko-C

description: Replicate 1

source_name: S1Pcko chondroepiphyseal cartilage

value: chondroepiphyseal cartilage from most appendicular skeletal elements


title: PFC_5

description: Dorsolateral prefrontal cortex (DLPFC)

value: prefrontal cortex brain

value: reference

value: female


title: PFC_3

description: Dorsolateral prefrontal cortex (DLPFC)

value: 62 yrs

value: male


title: PFC_2

description: Dorsolateral prefrontal cortex (DLPFC)

value: 88 yrs


title: PFC_6

description: Dorsolateral prefrontal cortex (DLPFC)

value: 95 yrs

value: Alzheimer's disease


title: 1924-S1Pcko-L

description: Replicate 3

source_name: S1Pcko appendicular bones


title: human normal liver sample from elder HCC patient [HCC_68N_2.CEL]

description: elder HCC patient

value: Normal

value: elder HCC patient


title: 1925-WT-Cal

description: Replicate 1

source_name: Wild type calvarium

value: wild type


title: Burkholderia cenocepacia_AU8260_26

description:
set4
2958_AU8260-26_647_pmt990_AU1874-25_555_pmt1000_with_SNR.txt


title: 1929-2WT-L-amp#2

description: Replicate 4

value: entire appendicular skeleton elements such as femora, tibia, humeri

value: embryonic (E) 16.5


title: Burkholderia cenocepacia_AU8260_25

description:
set4
2958-AU0129-25_647pmt1000_AU8260-25_555pmt850.txt

value: Sporadic IIIA


title: PFC_1

description: Dorsolateral prefrontal cortex (DLPFC)

value: 67 yrs


title: 1928-S1Pcko-C-amp#2

description: Replicate 2


title: Burkholderia cenocepacia_AU8006.1_3

description:
set4
a2691_HI2617-1_555_pmt939_AU8006.1-3_647_pmt590_with_SNR.txt


title: human normal liver sample from elder HCC patient [HCC_68N_1.CEL]

description: elder HCC patient


title: human normal liver sample from elder HCC patient [HCC_378N.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU8006.1_1

description:
set4
2861_AU3018-18_647_pmt939_AU8006.1-1_555_pmt710_wiht_SNR.txt


title: human normal liver sample from elder HCC patient [HCC_59N.CEL]

description: elder HCC patient


title: human normal liver sample from elder HCC patient [HCC_364T.CEL]

description: elder HCC patient


title: human normal liver sample from elder HCC patient [HCC_351N.CEL]

description: elder HCC patient


title: 1927-WT-C-amp#2

description: Replicate 2

source_name: Wild type chondroepiphyseal cartilage


title: Burkholderia cenocepacia_AU7610_15

description:
set4
2676-AU2260-15_647pmt939-AU7610-15_0555_with_SNR.txt


title: human normal liver sample from elder HCC patient [HCC_347N.CEL]

description: elder HCC patient


title: 1923-2WT-L

description: Replicate 3


title: 1922-S1Pcko-L

description: Replicate 3


title: human HCC sample from elder patient [HCC_889T.CEL]

description: elder HCC patient

value: Tumor


title: Burkholderia cenocepacia_AU7610_11

description:
set4
2410_AU7610-11_647_pmt1000_AU11375-11_555_pmt800.txt


title: Burkholderia cenocepacia_AU7861_1

description:
set4
2903_HI2763-2_647_pmt840_AU7861-1_555_pmt680_with_SNR.txt


title: Burkholderia cenocepacia_AU7320_1

description:
set4
3285_AU7320-1_647_pmt940_AU13032-0_555_pmt790.txt


title: human normal liver sample from elder HCC patient [HCC_1245N.CEL]

description: elder HCC patient


title: 1919-WT-C

description: Replicate 1

value: chondroepiphyseal cartilage from most appendicular skeletal elements


title: human HCC sample from elder patient [HCC_377T.CEL]

description: elder HCC patient


title: 1930-S1Pcko-L-amp#2

description: Replicate 4


title: Burkholderia cenocepacia_AU7320_2

description:
set4
a2676_AU0986-1_647_pmt930_AU7320-2_555_pm_0610_with_SNR.txt


title: human normal liver sample from elder HCC patient [HCC_1009N.CEL]

description: elder HCC patient


title: human HCC sample from elder patient [HCC_351T.CEL]

description: elder HCC patient


title: human HCC sample from elder patient [HCC_364N.CEL]

description: elder HCC patient


title: CHADL knockdown, biological replicate 2

city: Lund

first: James

middle: Chin Shing

last: Ho

address: Sölvegatan 23

country: Sweden

institute: Lund University

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix MG-430 PM array strip. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Affymetrix MG-430 PM array strips were scanned using the GeneAtlas Imaging Station.

data_processing: The data were analyzed with R Bioconductor, Ingenuity Pathway Analysis and using RMA as normalization method.

source_name: ATDC5_CHADL knockdown_differentiated for 5days

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 50 ug total RNA (GeneAtlas 3' IVT Express Kit, Affymetrix).

growth_protocol: ATDC5 cells were cultured in DMEM/F12 1:1 medium with 5% fetal bovine serum (HyClone), 30 nM sodium selenite, and 10 ug/mL transferrin, under 5% CO2.

extract_protocol: RNA from these cells was isolated using Quick-RNA kit (Zymo Research).

treatment_protocol: 27-mer shRNA duplexes were purchased from Origene. The only effective knockdown was obtained from the sequence ACAAGGUAGAGAAACAAAGAGACCA. Universal scrambled negative control duplex (Origene) was used as negative control. ATDC5 cells were transfected with 30 nM shRNA using Lipofectamine 2000, according to manufacturer’s protocol. After 16 h incubation, the medium was changed to differentiation medium that was replaced every two days for the remaining course of the experiment.

tag: cell line

tag: cell type

value: chondrogenic cell line

tag: transfected with

value: shRNA specific for CHADL


title: human HCC sample from elder patient [HCC_341T.CEL]

description: elder HCC patient


title: human HCC sample from elder patient [HCC_348T.CEL]

description: elder HCC patient


title: CHADL knockdown, biological replicate 1


title: Burkholderia cenocepacia_AU7195_3

description:
set4
a2674_AU7195-3_555.txt

value: PHDC


title: Burkholderia cenocepacia_AU6888_3

description:
set4
a2404_AU6888-3_647_pmt850_AU2002-3_555_pmt820.txt


title: Burkholderia cenocepacia_AU7195_2

description:
set4
a2744_AU7195-2_647_pmt910_AU1361_555_pm_0620_with_SNR.txt


title: Burkholderia cenocepacia_AU6888_1

description:
set4
2860_AU6888-1_647_pmt939_AU1450-1_555_pmt690_with_SNR.txt


title: Control, biological replicate 1

source_name: ATDC5_control_differentiated for 5days

value: scrambled negative control shRNA


title: Burkholderia cenocepacia_AU7195_3.2

description:
set4
2721-AU2348-10_647pmt910-AU7195-3.2_555pmt580_with_SNR.txt


title: human HCC sample from elder patient [HCC_198T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU6880_30

description:
set4
2922-AU6880-30_647pmt840-AU0332-31_0555_with_SNR.txt


title: Control, biological replicate 2


title: human HCC sample from elder patient [HCC_275T.CEL]

description: elder HCC patient


title: Som.TTF.2

city: Boston

first: Robert

middle: E

last: Kingston

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: RMA package. Fold-change and statistical significance were estimated for the log2 expression values of each gene based on the data for individual replicates within each replicate set.

source_name: tail tip fibroblasts

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using TRIZOL

value: tail tip fibroblasts


title: iPSC.A5.2

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells


title: human HCC sample from elder patient [HCC_1010T.CEL]

description: elder HCC patient


title: iPSC.A5.1


title: human HCC sample from elder patient [HCC_109T.CEL]

description: elder HCC patient


title: Som.TTF.1


title: human HCC sample from elder patient [HCC_1246T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU8718_1

description:
set4
2906-AU8718-1_647pmt880-HI3521-B-1_0555.txt


title: Burkholderia cenocepacia_AU6831_15

description:
set4
2918-AU6831-15_647pmt-HI3742_17_0555_with_SNR.txt


title: Burkholderia cenocepacia_AU6791_12

description:
set4
2398_AU1054-2_647_pmt850_AU6791-12_555_pmt730_withSNR.txt


title: ESC.A5.2

source_name: embryonic stem cells

value: embryonic stem cells


title: human HCC sample from elder patient [HCC_330T.CEL]

description: elder HCC patient


title: Burkholderia cenocepacia_AU6831_16

description:
set4
2923-HI4350-11_647pmt930-AU6831-16_0555_with_SNR.txt


title: Burkholderia cenocepacia_AU6880_18

description:
set4
2924-AU6880-18_647pmt850-AU2071-11_0555.txt


title: ESC.A5.1


title: UAS-Hexim-RNAi strain, biological replicate 4

city: Orsay

first: Patricia

last: Uguen

address: Rue des Adèles

department: Biologie

country: France

institute: Université Paris Sud

description: Gene expression data from HEXIM knockdown mutant head.

hyb_protocol: Procedures followed the manufacturer's intructions. CRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned with a GeneChIP Scanner 3000.

data_processing: Data were processed with the “Robust Multi-array Average” (RMA) algorithm from Affymetrix “Expression Console”.

organism: Drosophila melanogaster

source_name: HEXIM knockdown Drosophila adult head

label_protocol: Standard Affymetrix target labeling protocol, in which mRNA  are reverse - transcribed into double stranded cDNA using an oligo- dT  primer containing the promoter sequence of the bacteriophage T7 RNA polymerase. cDNAs are transcribed into cRNAs with T7 polymerase and biotinylated ribonucleotides.

growth_protocol: Flies were reared on standard conditions at 29°C.

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

value: Head

value: HEXIM knockdown mutant

tag: developmental stage

value: adult


title: UAS-Hexim-RNAi strain, biological replicate 3


title: Burkholderia cenocepacia_AU6791_11

description:
set4
2708_AU6791-11_647pmt920-AU1189-11_555pmt620_with_SNR.txt


title: 186L

city: Merelbeke

first: Tiphanie

last: Goetstouwers

state: East Flanders

address: Heidestraat 19

department: Veterinary Medicine

country: Belgium

institute: Ghent University

hyb_protocol: As described by Dupuis et al. (2011)

scan_protocol: According to the manufacturer’s protocol of the Porcine SNP60 BeadChip (Illumina)

data_processing: Genomic DNA extracted from blood was genotyped according to the manufacturer's protocol of the Porcine SNP60 BeadChip (Illumina)

label: PicoGreen

organism: Sus scrofa

source_name: Blood

label_protocol: As described by Dupuis et al. (2011)

extract_protocol: DNA isolation from blood was performed as described by Dupuis et al. (2011)

tag: affected status f4ab/ac (1=na/2=a)

tag: gender (1=m/2=f)

tag: father id

tag: mother id

tag: breed

value: Large White

value: blood


title: UAS-Hexim-RNAi strain, biological replicate 2

tag: strain


title: Burkholderia cenocepacia_AU6699_11

description:
set4
2921-AU6699-11_647pmt760-AU15723-1_0555.txt

tag: group

tag: replicate


title: Burkholderia cenocepacia_AU6690_31

description:
set4
2920-AU0332-30_647pmt800-AU6690-31_0555_with_SNR.txt


title: 185L

tag: tissue


title: Wt strain, biological replicate 3

description: Gene expression data from wild type head.

source_name: Wt Drosophila adult head

value: wild type


title: Burkholderia cenocepacia_AU6550_3

description:
set4
a2406_AU12643-3_647_pmt880_AU6550-3_555_pmt820.txt

source_name: Pure culture

value: Sporadic IIIA


title: 182L


title: 183L


title: UAS-Hexim-RNAi strain, biological replicate 1


title: Burkholderia cenocepacia_AU6550_1

description:
set4
2861_AU0391-18_647_AU6550-1_0555_with_SNR.txt


title: Burkholderia cenocepacia_AU6690_30

description:
set4
2919_AU6690-30_647_pmt940_AU1790-26_555_pmt810_with_SNR.txt


title: Wt strain, biological replicate 1


title: Wt strain, biological replicate 2


title: Wt strain, biological replicate 4


title: human normal liver sample from elder HCC patient [HCC_1151N.CEL]

description: elder HCC patient

value: Normal

tag: age

tag: sample type

value: elder HCC patient


title: 181L


title: 180L


title: Burkholderia cenocepacia_AU6286_26

description:
set4
2954_AU5712-25_647_pmt1000_AU6286-26_555_pmt1000_with_SNR.txt


title: 179L


title: Burkholderia cenocepacia_AU6362_15

description:
set4
2725-AU6362-15_647pmt939-AU10396-1_555pmt580_with_SNR.txt


title: Burkholderia cenocepacia_AU6362_10

description:
set4
a2688_AU1551-1_647_pmt930_AU6362-10_555_pm_0610_with_SNR.txt


title: 177L


title: 178L


title: Burkholderia cenocepacia_AU6362_8

description:
set4
2681_AU6362-8_647pmt939-HI2811-8_0555_with_SNR.txt


title: 176L


title: 175L


title: Burkholderia cenocepacia_AU5951_3

description:
set4
a2674_AU5951-3_647.txt


title: Burkholderia cenocepacia_AU5951_20

description:
set4
2904_AU0787-9_647_pmt_930_AU5951-20_555_pmt700_with_SNR.txt


title: Whole_adrenal_GDX_rep1

first: Maximiliaan

last: Schillebeeckx

address: 4444 Forest Parkway

department: Genetics

institute: Washington University in St. Louis

description:
8844 - 5-GDX
Gonadectomized treatment, biological replicate 1

hyb_protocol: 750ug of each aRNA in water (5ul) was suspended in Illumina HYB buffer (10ul) and heated to 65C for five minutes, then allowed to cool to room temperature. The samples were applied to Illumina MouseWG-6 v2.0 Expression BeadChips and hybridized at 58C for 16-20 hours at high humidity. Arrays were washed according to Illumina standard protocol. Immobilized, biotinylated aRNAs were then detected by staining with Cy3 Steptavidin (1ug Cy3-SA per 1 ml of Illumina Block E1 ) for 10 minutes at room temperature. Arrays were washed and dried according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader. Laser power and PMT voltage were kept constant for Cy3 scans. Images were quantitated by Illumina Beadscan, v3. Quantitated data was imported into Illumina GenomeStudio software (version 2011). On-array spot replicates were averaged by GenomeStudio and individual spot probe was reported.

data_processing: The data were background subtracted and then normalised using quantile normalisation with IlluminaGUI in R.

source_name: Whole adrenal gland, gonadectomized

label_protocol: RNA transcripts were amplified by T7 linear amplification (MessageAmp TotalPrep amplification kit; Life Technologies). 100 ng of each total cellular RNA sample (11ul) was mixed with an oligo-dT T7 primer (1ul), 10x reaction buffer (2ul), dNTP mix (4ul), RNase Inhibitor (1ul), and Arrayscript RT enzyme (1ul). Reverse transcription was carried out for 2 hours at 42C. After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and RNase H (1ul). This cocktail was incubated at 16C for 2 hours. Following a column cleanup using Zymo DNA Clean and Concentrator 5s (Zymo Research) according to protocol, in vitro-transcription was carried out by adding 10x T7 reaction buffer (2.5ul), T7 biotin-NTP mix (2.5ul), and T7 RNA polymerase enzyme mix (2.5ul) and incubation at 37C. The IVT reaction was carried out for 14 hours. Following reaction termination with water (75ul), the amplified RNAs (aRNA) were cleaned with RNA columns provided in the MessageAmp TotalPrep kit. The aRNAs were then quantitated on a spectrophotometer, and quality determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer's recommendations.

extract_protocol: RNA was isolated from whole adrenal glands using RNeasy® Mini Kit (Qiagen, Valencia, CA) and amplified using the TotalPrep RNA amplification kit (Illumina, San Diego, CA).

tag: strain/background

tag: gender

value: female

value: 4 months

value: whole adrenal gland

tag: treatment

value: gonadectomy


title: Burkholderia cenocepacia_AU6286_25

description:
set4
2955_AU6286-25_647_pmt980_AU4116-26_555_pmt940_with_SNR.txt


title: Burkholderia cenocepacia_AU5792_12

description:
set4
2680_AU0009-12_647_pmt939_AU5792-12_555_pmt610.txt


title: Whole_adrenal_nGDX_rep1

description:
8840 - 1-nGDX
Non-gonadectomized control, biological replicate 1

source_name: Whole adrenal gland, non-gonadectomized control


title: Whole_adrenal_GDX_rep2

description:
8845 - 6-GDX
Gonadectomized treatment, biological replicate 2


title: 172L


title: Burkholderia cenocepacia_AU5792_10

description:
set4
a2692_HI2718-12_647_pmt920_AU5792-10_555_pmt630_with_SNR.txt


title: Whole_adrenal_nGDX_rep3

description:
8842 - 3-nGDX
Non-gonadectomized control, biological replicate 3


title: Whole_adrenal_nGDX_rep2

description:
8841 - 2-nGDX
Non-gonadectomized control, biological replicate 2


title: 170L


title: H3f3b HET 3975

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

description: HET litter 2

hyb_protocol: Standard Illumina hybridization protocol-Direct Hybridization

scan_protocol: Standard Illumina scanning protocol-Illumina iScan System

data_processing: The data were normalized using average normalization using genome studio software

source_name: 8 week old H3f3b HET

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

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini Prep kit. Quality control was performed with Agilent Bioanalyser.
RNA amplification: Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

tag: genotype

value: H3f3b WT/-

value: 1 of 2 mouse testes


title: Burkholderia cenocepacia_AU5792_11

description:
set4
a2680_AU5792-11_647_pmt939_HI2712-A-3_555_pm_0580_with_SNR.txt


title: Whole_adrenal_GDX_rep3

description:
8944 - 7-GDX
Gonadectomized treatment, biological replicate 3


title: H3f3b KO 3973

description: KO litter 2

source_name: 8 week old H3f3b KO


title: Burkholderia cenocepacia_AU5757_30

description:
set4
2901-AU9277-30_647pmt850-AU5757-30_0555_with_SNR.txt


title: Burkholderia cenocepacia_AU5712_26

description:
set4
2956-AU3397-25_647pmt1000_AU5712-26_555pmt950.txt


title: 171L


title: 167L


title: Burkholderia cenocepacia_AU5757_1

description:
set4
2907-AU5757-1_647pmt870-HI2809-1_0555.txt


title: 184BL

value: Belgian Landrace×Large White


title: H3f3b WT 3974

description: WT litter 2

source_name: 8 week old H3f3b WT

value: H3f3b WT/WT


title: H3f3b HET 3968

description: HET litter 1


title: 168H

value: hybrid


title: 173L


title: 169B

value: Belgian Landrace


title: 174L


title: 166B


title: Burkholderia cenocepacia_AU5712_25

description:
set4
2954_AU5712-25_647_pmt1000_AU6286-26_555_pmt1000_with_SNR.txt


title: 165H


title: Burkholderia cenocepacia_AU5417_1

description:
set4
2904_AU5417-1_647_pmt770_AU8718-2_0555.txt


title: 164H


title: EglN2 siRNA, replicate 2

city: Chapel Hill

first: Qing

last: Zhang

address: 450 West Drive

institute: University of North Carolina at Chapel Hill

description: Gene expression

hyb_protocol: Hyb protocol were followed by standard affymetrix protocol

scan_protocol: Data Chip was scanned by using a Genearray scanner

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al.,2003).

source_name: T47D breast cancer cells

label_protocol: cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: T47D cells were grown in RPMI supplmented with 10%FBS+1% Pen-strep, they were grown in 37 degree incubator with 5% CO2

extract_protocol: Total RNAs were extracted by using Rnaeasy kit from qiagen

treatment_protocol: T47D cells were transfected with either Ctrl or EglN2 siRNA (4) followed by hypoxia (1% O2) and DMOG (1 mM) treatment for 16 hours

value: Breast

tag: cell line


title: Burkholderia cenocepacia_AU5229_11

description:
set4
2720-AU5229-11_647pmt910-AU0199-12_555pmt620_with_SNR.txt


title: Burkholderia cenocepacia_AU5382_3

description:
set4
a2673_AU5382-3_647_pmt930_AU11230-2_555_pm_0640_with_SNR.txt


title: Ctrl siRNA, replicate 2

description: Gene expression


title: Burkholderia cenocepacia_AU5229_8

description:
set4
2678-AU5229-8_647pmt939-AU2260-10_0555_with_SNR.txt


title: H3f3b KO 3967

description: KO litter 1


title: EglN2 siRNA, replicate 1

description: Gene expression


title: 158LP

value: Large White×Piétran


title: 162H

value: blood


title: Ctrl siRNA, replicate 1

description: Gene expression


title: 161BL


title: 16 week old Sox17-GOF mouse pancreatic islet,dox was given,  biological rep3

city: Cincinnati

last: Wells

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Childrens Hospital Medical Center

description:
Gene expression data from pancreatic islet Sox17-GOF mice, with Dox, biological replicate 3
Mouse pancreas - Sox17 GOF 3
All mice were originally maintained on an outbred background and were then backcrossed to C57BL/6 background for at least 3 generations.

hyb_protocol: For each sample a hybridization cocktail was created that includes a total of 2.5 micrograms of fragmented cDNA. Probe arrays were filled with hybridization cocktail and placed in a GeneChip® Hybridization Oven 640 (Affymetrix) for 18 hours. Arrays were then washed and stained using the Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G. All files including .dat, .cel, and .chp files were created by the scanning and analysis software, the Genechip Operating Software (Affymetrix).

data_processing: The data were analyzed with Expression Console (Affymetrix systems).

source_name: Mouse pancreatic islet, Sox17-GOF 3, with dox

label_protocol: Assays from NuGEN were used to create biotin-labeled cDNA target. Specifically the WT- Ovation Pico RNA Amplification System Version 1.0 (Nugen) was used to prepare target cDNA.  Then the WT-Ovation Exon Module v1.0 (NuGEN) was used to create sense-strand cDNA targets. Finally the FL-Ovation cDNA Biotin Module V2 (NuGEN) chemically fragmented and labeled the sense-strand cDNA targets.

extract_protocol: total islet RNA was extracted using PureLink RNA Mini Kit (Invitrogen, cat. no. 12183-018A), performed according to the manufacturer's instructions.

treatment_protocol: In order to upregulate Sox17 expression in this gain-of-function system, doxycycline (Dox) was given in the food and water for 24 hours before mice were euthanized and sacrificed. Pancreas was dissected, islets were isolated using standard collagenase digestion followed by purification through a Ficoll gradient and islet gravity sedimentation.

value: pancreatic islet

value: 16 weeks old


title: Burkholderia cenocepacia_AU5382_2

description:
set4
a2407_AU5382-2_647_pmt950_AU1551-2_555_pmt820.txt

value: Sporadic IIIA


title: Burkholderia cenocepacia_AU5209_20

description:
set4
2907_AU5209-20_647_pmt930_AU0089-20_555_pmt820.txt

value: PHDC


title: 16 week old Sox17-GOF mouse pancreatic islet,dox was given,  biological rep1

description:
Gene expression data from pancreatic islet Sox17-GOF mice, with Dox, biological replicate 1
Mouse pancreas - Sox17 GOF 1
All mice were originally maintained on an outbred background and were then backcrossed to C57BL/6 background for at least 3 generations.

source_name: Mouse pancreatic islet, Sox17-GOF 1, with dox


title: 160LP


title: 159BL


title: 16 week old control mouse pancreatic islet,dox was given,  biological rep3

description:
Gene expression data from pancreatic islet control mice, with Dox, biological replicate 3
Mouse pancreas - Control 3
All mice were originally maintained on an outbred background and were then backcrossed to C57BL/6 background for at least 3 generations.

source_name: Mouse pancreatic islet, control 3, with dox


title: 16 week old Sox17-GOF mouse pancreatic islet,dox was given,  biological rep2

description:
Gene expression data from pancreatic islet Sox17-GOF mice, with Dox, biological replicate 2
Mouse pancreas - Sox17 GOF 2
All mice were originally maintained on an outbred background and were then backcrossed to C57BL/6 background for at least 3 generations.

source_name: Mouse pancreatic islet, Sox17-GOF 2, with dox


title: Burkholderia cenocepacia_AU5229_12

description:
set4
2684_AU14381-10_647_pmt850_AU5229-12_555_pmt590.txt


title: H3f3b WT 3966

description: WT litter 1

source_name: 8 week old H3ff3b WT


title: Burkholderia cenocepacia_AU5209_5

description:
set4
2742-AU2362-2_647pmt939-AU5209-5_0555_with_SNR.txt


title: 163L

value: Large White


title: 157H


title: Burkholderia cenocepacia_AU6791_2

description:
set4
2731_AU0304-A-2_647pmt900_AU6791-2_555pm_0620_with_SNR.txt


title: Burkholderia cenocepacia_AU4259_B21

description:
set3
2918_AU0005-1_647_pmt850_AU4259-B-21_555_pmt770_with_SNR.txt

value: Midwest


title: 156H


title: Burkholderia cenocepacia_AU4259_B20

description:
set3
2902_AU4259-B-20_647_pmt900_AU14067-21_555_pmt750_with_SNR.txt


title: Burkholderia cenocepacia_AU4116_26

description:
set3
2955_AU6286-25_647_pmt980_AU4116-26_555_pmt940_with_SNR.txt


title: 16 week old control mouse pancreatic islet,dox was given,  biological rep1

description:
Gene expression data from pancreatic islet control mice, with Dox, biological replicate 1
Mouse pancreas - Control 1
All mice were originally maintained on an outbred background and were then backcrossed to C57BL/6 background for at least 3 generations.

source_name: Mouse pancreatic islet, control 1, with dox


title: 155H


title: normal thyroid sample 7

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: NT DS #7

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: NT

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: tissue type

value: normal thyroid


title: 16 week old control mouse pancreatic islet,dox was given,  biological rep2

description:
Gene expression data from pancreatic islet control mice, with Dox, biological replicate 2
Mouse pancreas - Control 2
All mice were originally maintained on an outbred background and were then backcrossed to C57BL/6 background for at least 3 generations.

source_name: Mouse pancreatic islet, control 2, with dox


title: MC-engrafted - stroke - 2

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

institute: Stanford University

hyb_protocol: The fragmented and labeled DNA targets were hybridized to the arrays per standard protocol, which includes 16 hr (overnight) hybridization at 45 degrees C at 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: The hybridized arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450 and scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw data was normalized for batch effects using robust multiarray (RMA) preprocessing using the 'affy' package in R version 3.0.0.

source_name: dura taken at 2d post-stroke, mast cell-engrafted

label_protocol: The Ambion Whole-Transcript (WT) Expression kit was used to generate ssDNA, which was then biotin-labeled by TdT (terminal deoxynucleotidyl transferase) using the Affymetrix WT Terminal Labeling and Controls Reagent kit.

growth_protocol: Animals were housed in standard conditions.

extract_protocol: Dura were lysed using Qiagen Qiashredder and total RNA isolated using a Qiagen RNeasy Micro Kit according to the manufacturer's protocol.

treatment_protocol: Animals were anesthetized with isoflurane and transcardially perfused with ice cold PBS (0.9% NaCl) prior to removing the dura. Upon removal, dura maters were kept in RNAlater RNA Stabilization Solution (Life Technologies) for 24 hours at 4ºC, then were spun down and kept at -80ºC until used for RNA isolation.

value: male

value: dura

tag: mast cell engraftment

value: yes

value: stroke

tag: age at stroke surgery

value: 17 - 21 weeks


title: 154BL

source_name: Blood

tag: affected status f4ab/ac (1=na/2=a)

tag: gender (1=m/2=f)

tag: father id

value: Belgian Landrace×Large White


title: normal thyroid sample 5

description: NT DS #5


title: Burkholderia cenocepacia_AU4116_25

description:
set3
2957_AU4116-25_647_pmt910_AU2029-26_555_pmt910_647_ONLY.txt

source_name: Pure culture

tag: strain


title: normal thyroid sample 8

description: NT DS #8


title: Burkholderia cenocepacia_AU3820_15

description:
set3
a2683_AU1138-10_647_pmt939_AU3820-15_555_pm_0620_with_SNR.txt

tag: group


title: 152L

tag: mother id

tag: breed


title: Burkholderia cenocepacia_AU3942_10

description:
set3
a2682_AU13051-2_647_pmt939_AU3942-10_555_pm_0620_with_SNR.txt

tag: replicate


title: MC-engrafted - stroke - 3

tag: tissue


title: normal thyroid sample 6

description: NT DS #6


title: MC-deficient - stroke - 2

source_name: dura taken at 2d post-stroke, mast cell-deficient

tag: strain/background

value: no


title: MC-deficient - stroke - 3

tag: gender


title: MC-engrafted - stroke - 1

tag: treatment


title: 153H

value: hybrid


title: normal thyroid sample 4

description: NT DS #4


title: Burkholderia cenocepacia_AU3942_5

description:
set3
3284_AU3273-3_647_pmt1000_AU3942-5_555_pmt800.txt


title: 150LP

value: Large White×Piétran


title: 151LP

value: blood


title: normal thyroid sample 3

description: NT DS #3


title: 149H


title: Burkholderia cenocepacia_AU3665_1

description:
set3
2918-AU3306-1_647pmt750-AU3665-1_0555_with_SNR.txt


title: normal thyroid sample 2

description: NT DS #2


title: wild type - stroke - 3

source_name: dura taken at 2d post-stroke, WT


title: MC-deficient - stroke - 1


title: Burkholderia cenocepacia_AU3624_15

description:
set3
2680_HI4351-10_647pmt939-AU3624-15_0555_with_SNR.txt


title: 148H


title: wild type - stroke - 1


title: MC-engrafted - naïve - 2

source_name: dura, mast cell-engrafted, naive

value: naive


title: Burkholderia cenocepacia_AU3624_10

description:
set3
2679-AU3624-10_647pmt939-HI4351_0555_wiht_SNR.txt


title: thyroid tumor sample 82

description: DS #82

source_name: FTC+PDTC

value: thyroid tumor


title: 147BL


title: thyroid tumor sample 83

description: DS #83

source_name: FTC


title: MC-engrafted - naïve - 3


title: thyroid tumor sample 81

description: DS #81


title: 145L


title: 146H


title: Burkholderia cenocepacia_AU3516_15

description:
set3
a2678_AU9448-11_647_pmt930_AU3516-15_555_pm_0610_with_SNR.txt


title: normal thyroid sample 1

description: NT DS #1


title: 144H


title: thyroid tumor sample 80

description: DS #80


title: MC-engrafted - naïve - 1


title: Burkholderia cenocepacia_AU3488_10

description:
set3
2683_AU3488-10_647_pmt900_AU0199-11_555_pmt630.txt


title: Burkholderia cenocepacia_AU3516_11

description:
set3
2413_AU3516-11_647_pmt1000_AU3237-10_555_pmt730.txt


title: wild type - stroke - 2


title: 143H


title: Burkholderia cenocepacia_AU3488_2

description:
set3
2727_AU2567-3_647_pmt939_AU3488-2_555_pmt630_with_SNR.txt


title: MC-deficient - naïve - 3

source_name: dura, mast cell-deficient, naive


title: thyroid tumor sample 79

description: DS #79


title: 142BL


title: thyroid tumor sample 78

description: DS #78


title: MC-deficient - naïve - 2


title: Burkholderia cenocepacia_AU3488_1

description:
set3
2683_AU3488-1_647_pmt939_AU2205-2_555_pmt610_with_SNR.txt


title: thyroid tumor sample 77

description: DS #77


title: 141H


title: MC-deficient - naïve - 1


title: wild type - naïve - 2

source_name: dura, WT, naive


title: Burkholderia cenocepacia_AU3397_25

description:
set3
2956-AU3397-25_647pmt1000_AU5712-26_555pmt950.txt

value: Sporadic IIIA


title: Burkholderia cenocepacia_AU3397_36

description:
set3
3283_AU3397-36_647_pmt940_AU13670-2_555_pmt850.txt


title: thyroid tumor sample 76

description: DS #76


title: thyroid tumor sample 75

description: DS #75


title: thyroid tumor sample 74

description: DS #74


title: wild type - naïve - 3


title: Burkholderia cenocepacia_AU5417_30

description:
set4
2905-AU0649-30-647pmt880-AU5417-30_0555_with_SNR.txt


title: Burkholderia cenocepacia_AU3306_1


title: wild type - naïve - 1


title: Burkholderia cenocepacia_AU3397_35

description:
set3
3281_AU1874-35_647_pmt970_AU3397-35_555_pmt880.txt


title: 139H


title: 140H


title: 137BL


title: Burkholderia cenocepacia_AU3306_25

description:
set3
2924_AU2902-25_647_pmt950_AU3306-25_555_pmt780_with_SNR.txt


title: thyroid tumor sample 73

description: DS #73


title: 136H


title: thyroid tumor sample 72

description: DS #72


title: Testis_2WPM_rep4

city: Duluth

first: Jonathan

middle: Thomas

last: Haselman

state: MN

address: 6201 Congdon Blvd.

department: ORD

institute: US EPA

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Xenopus tropicalis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  All hybridization, wash and stain procedures were performed according to standard Affymetrix protocols (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: GeneChip Operating Software (GCOS) was used to automate control of the GeneChip Fluidics Station and GeneChip Scanner.

data_processing: Software: Agilent GeneSpring GX 12.6.  Summarization Algorithm: PLIER16.  Normalization: Quantile.  Baseline Transformation: median of all samples.  Statistical analysis: 2WPM ovary vs. 2WPM testis using Welch's t-test and Benjamini-Hotchberg MTC applied.

organism: Xenopus tropicalis

source_name: Two weeks post-metamorphosis testis tissue

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

growth_protocol: The in-house X. tropicalis breeders used to generate animals for this study were of the “golden strain” and the female was confirmed to have the W-linked polymorphism identified by Olmstead et al. (2010).  This sex-linked marker and a reference marker were used to determine the genetic sexes of the individual offspring following sampling (described later).  The animal care and culture conditions were the same as described by Olmstead et al. (2009b) and were as follows.  Adult breeding pairs were maintained on a 12:12 light:dark photoperiod at 25oC in 7 L glass aquaria with 50ml/min flow-through conditions and were fed 3/32′′ premium sinking frog food pellets (Xenopus Express, Plant City, FL, USA).  Water was from nearby Lake Superior (Duluth, MN, USA) and was ozone treated and filtered prior to use.  Mating of breeding pairs was induced by injections of hCG (Sigma Aldrich, St. Louis, MO, USA).  An initial injection of 20 IU hCG followed by a second injection of 100 IU hCG 5 hours later were administered to both the male and female breeder.  Following mating, the adult breeders were moved to another tank and embryos were allowed to hatch in flow-through conditions.  A single spawn was disbanded to a density of 40/tank (12:12 photoperiod, 25oC, 7L tank, 25ml/min flow) and fed a diet consisting of homogenized cooked carrot and spinach, Sera Micron (Sera North America, Toronto, Canada), and brine shrimp three times daily until removed for sampling.

extract_protocol: For a single sample, total RNA was extracted from pools of four individual homogenates using Qiagen's RNeasy micro kit according to kit instructions.

treatment_protocol: There were no treatments.  This was a developmental time-course study.  Gonad tissue collections were age (time) and stage matched at Nieukoop and Faber (NF) stage 58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-NF66 and two weeks post-NF66

tag: developmental stage

value: Two weeks post-NF66

value: testis

value: golden


title: 135L

value: Large White


title: Testis_2WPM_rep5


title: 138L


title: Burkholderia seminalis_AU3273_3

organism: Burkholderia seminalis

value: Bsem


title: thyroid tumor sample 71

description: DS #71


title: Burkholderia cenocepacia_AU3237_11

description:
set3
A2689_AU3237-11_647_pmt939_AU10137-10_555_pm_0620_with_SNR.txt


title: thyroid tumor sample 70

description: DS #70


title: Burkholderia seminalis_AU3273_2

description:
set3
3283_AU2877-1_647_pmt1000_AU3273-2_555_pmt1000.txt


title: Testis_2WPM_rep2


title: Testis_2WPM_rep3


title: 133H


title: Testis_2WPM_rep1


title: Burkholderia cenocepacia_AU3237_10


title: Burkholderia cenocepacia_AU3820_11

description:
set3
2678_AU3820-11_647_pmt870_HI2424-11_555_pmt650.txt


title: Burkholderia cenocepacia_AU3237_15

description:
set3
2726-AU3237-15_647pmt939-AU0862-1_555pmt580_with_SNR.txt


title: Ovary_2WPM_rep5

source_name: Two weeks post-metamorphosis ovary tissue

value: ovary


title: thyroid tumor sample 69

description: DS #69


title: 134L


title: thyroid tumor sample 68

description: DS #68


title: thyroid tumor sample 67

description: DS #67


title: 130L


title: 132BL


title: 131L


title: thyroid tumor sample 66

description: DS #66


title: Burkholderia cenocepacia_AU3095_18

description:
set3
2922_AU3095-18_647_pmt910_AU2902-26_555_pmt770_with_SNR.txt

value: PHDC


title: Ovary_2WPM_rep3


title: 129H


title: Ovary_2WPM_rep4


title: thyroid tumor sample 64

description: DS #64

source_name: FA


title: 128BL


title: Burkholderia cenocepacia_AU3047_B19

description:
set3
2952_AU1539-25_647_pmt910_AU3047-B-19_555_pmt690_with_SNR.txt


title: 127H


title: Burkholderia cenocepacia_AU3018_18

description:
set3
2861_AU3018-18_647_pmt939_AU8006.1-1_555_pmt710_wiht_SNR.txt


title: Burkholderia cenocepacia_AU3047_B18

description:
set3
2951_AU3047-B-18_647_pmt910_HI3543-18_555_pmt890_with_SNR.txt


title: thyroid tumor sample 63

description: DS #63


title: Burkholderia cenocepacia_AU3018_3

description:
set3
2418_AU1268-3_647_pmt920_AU3018-3_555_pmt720_with_SNR.txt


title: Ovary_2WPM_rep2


title: thyroid tumor sample 62

description: DS #62

source_name: FAh


title: Ovary_2WPM_rep1


title: Testis_1WPM_rep4

source_name: One week post-metamorphosis testis tissue

value: One week post-NF66


title: Burkholderia cenocepacia_AU2947_12

description:
set3
2401_AU2947-12_647_pmt980_AU2260-12_555_pmt1000.txt


title: 125B

value: Belgian Landrace


title: 126B


title: Burkholderia cenocepacia_AU3095_19

description:
set3
2920_AU0279-25_647_pmt830_AU3095-19_555_pmt780_with_SNR.txt


title: thyroid tumor sample 61

description: DS #61


title: thyroid tumor sample 60

description: DS #60


title: Burkholderia cenocepacia_AU2902_26

value: Midwest


title: Testis_1WPM_rep5


title: Testis_1WPM_rep2


title: Burkholderia cenocepacia_AU2902_25


title: 124B


title: Testis_1WPM_rep3


title: thyroid tumor sample 59

description: DS #59


title: 123L


title: Ovary_1WPM_rep5

source_name: One week post-metamorphosis ovary tissue


title: thyroid tumor sample 57

description: DS #57


title: Ovary_1WPM_rep4


title: 120H


title: Burkholderia seminalis_AU2877_2

description:
set3
3284_AU1751-1_647_pmt990_AU2877-2_555_pmt850.txt


title: Testis_1WPM_rep1


title: 121H


title: thyroid tumor sample 56

description: DS #56


title: 119BL

value: Belgian Landrace×Large White


title: thyroid tumor sample 58

description: DS #58


title: 122L


title: thyroid tumor sample 54

description: DS #54


title: Burkholderia cenocepacia_AU2857_2

description:
set3
a2690_AU2857-2_647_pmt220_AU14381-11_555_pm_0670_with_SNR.txt


title: Ovary_1WPM_rep3


title: Burkholderia seminalis_AU2877_1


title: thyroid tumor sample 55

description: DS #55


title: Burkholderia cenocepacia_AU2855_1

description:
set3
2906_AU2855-1_647_pmt930_AU0068-1_555_pmt710_with_SNR.txt


title: Ovary_1WPM_rep2


title: Burkholderia cenocepacia_AU2765_26

description:
set3
3282_AU1529-1_647_pmt1000_AU2765-26_555_pmt880.txt


title: Burkholderia cenocepacia_AU2765_25

description:
set3
3282_AU2765-25_647_pmt910_AU9220-2_555_pmt830.txt


title: Ovary_1WPM_rep1


title: 117B


title: Burkholderia cenocepacia_AU2857_3

description:
set3
2413_AU7320-3_BAD__647_pmt1000_AU2857-3_555_pmt780.txt


title: 116BL


title: thyroid tumor sample 53

description: DS #53


title: 118BL


title: Testis_NF66_rep5

source_name: Nieukoop and Faber stage 66 testis tissue

value: Nieukoop and Faber stage 66


title: thyroid tumor sample 52

description: DS #52


title: 115L


title: Testis_NF66_rep4


title: Testis_NF66_rep3


title: Burkholderia cenocepacia_AU2738_20

description:
set3
2901_AU0007-20_647_pmt870_AU2738-20_555_pmt810_with_SNR.txt


title: 114LP

value: Large White×Piétran


title: thyroid tumor sample 50

description: DS #50


title: Testis_NF66_rep2


title: Burkholderia cenocepacia_AU2738_1

description:
set3
2673_AU2738-1_647_pmt800_AU11360-2_555_pmt660.txt


title: Testis_NF66_rep1


title: 113L

value: blood


title: thyroid tumor sample 65

description: DS #65


title: thyroid tumor sample 51

description: DS #51


title: Burkholderia cenocepacia_AU2615_18

description:
set3
2860_AU1100-1_647_pmt939_AU2615-18_555_pmt680_with_SNR.txt


title: Burkholderia cenocepacia_AU2615_3

description:
set3
2398_AU1361-3_647_pmt1000_AU2615-3_555_pmt900_with_SNR.txt


title: 112H

value: hybrid


title: 110LP


title: thyroid tumor sample 46

description: DS #46

source_name: fvPTC

value: thyroid tumor


title: 109H

source_name: Blood


title: Burkholderia cenocepacia_AU2567_3

description:
set3
2727_AU2567-3_647_pmt939_AU3488-2_555_pmt630_with_SNR.txt

source_name: Pure culture


title: Ovary_NF66_rep3

source_name: Nieukoop and Faber stage 66 ovary tissue


title: thyroid tumor sample 47

description: DS #47


title: thyroid tumor sample 45

description: DS #45


title: Burkholderia cenocepacia_AU2480_18

description:
set3
2862_HI4352-18_647_pmt939_AU2480-18_555_pmt610_wiht_SNR.txt


title: Burkholderia cenocepacia_AU2567_1

description:
set3
2728_PC676-P2-3_647_pmt939_AU2567-1_555_pmt690_with_SNR.txt


title: Testis_NF58_rep3

description: Faulty hybridization based on hybridization controls; removed from analyses

source_name: Nieukoop and Faber stage 58 testis tissue

value: Nieukoop and Faber stage 58


title: Ovary_NF66_rep4


title: thyroid tumor sample 49

description: DS #49


title: Burkholderia cenocepacia_AU2480_4

description:
set3
a2401_AU0089-A-3_647_pmt880_AU2480-4_555_pmt710_wiht_SNR.txt


title: thyroid tumor sample 44

description: DS #44


title: 111H


title: thyroid tumor sample 41

description: DS #41

source_name: PTCc


title: Burkholderia cenocepacia_AU2367_3

description:
set3
2397_AU2367-3_647_pmt1000_HI2701-3_555_pmt900_with_SNR.txt


title: thyroid tumor sample 48

description: DS #48


title: Ovary_NF66_rep2


title: 106H


title: thyroid tumor sample 42

description: DS #42


title: Ovary_NF66_rep5


title: 105H


title: Testis_NF58_rep2


title: Burkholderia cenocepacia_AU2367_2

description:
set3
a2742_AU0116-2_647_pmt939_AU2367-2_555_pm_0630_with_SNR.txt


title: Ovary_NF66_rep1


title: thyroid tumor sample 43

description: DS #43


title: Burkholderia cenocepacia_AU2362_18

description:
set3
2862_AU2362-18_647_pmt939_AU16949-2_555_pmt710_with_SNR.txt


title: thyroid tumor sample 40

description: DS #40

source_name: tcPTC


title: Testis_NF58_rep4


title: Burkholderia cenocepacia_AU2362_2

description:
set3
2742-AU2362-2_647pmt939-AU5209-5_0555_with_SNR.txt


title: Testis_NF58_rep1


title: 102H


title: 104H


title: thyroid tumor sample 39

description: DS #39

source_name: ovPTC


title: Ovary_NF58_rep4

source_name: Nieukoop and Faber stage 58 ovary tissue


title: Burkholderia cenocepacia_AU2348_10

description:
set3
2721-AU2348-10_647pmt910-AU7195-3.2_555pmt580_with_SNR.txt


title: Ovary_NF58_rep2


title: 101BL


title: thyroid tumor sample 37

description: DS #37


title: 103H


title: Burkholderia cenocepacia_AU2348_11

description:
set3
2679_AU2348-11_647_pmt900_AU1138-12_555_pmt730.txt


title: thyroid tumor sample 35

description: DS #35


title: 100H


title: 99H


title: Burkholderia seminalis_AU2283_3

description:
set3
3278_AU0028-2_647_pmt990_AU2283-3_555_pmt980.txt


title: Ovary_NF58_rep3


title: Burkholderia cenocepacia_AU2260_15

description:
set3
2676-AU2260-15_647pmt939-AU7610-15_0555_with_SNR.txt

value: Sporadic IIIA


title: thyroid tumor sample 36

description: DS #36


title: Daoy_48h_control_rep3

city: Berlin

first: Christoph

last: Wierling

address: Ihnestr. 73

department: Department Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: replicate 3

hyb_protocol: To perform whole genome expression analysis HumanHT-12 v4 chips were incubated with biotin labeled cRNA for 18h at 58°C in a hybridization oven under humidity controlled conditions. After hybridization the Illumina® Sentrix BeadChips were washed using buffers provided by the kit. 2.5 µl (1mg/ml) of Streptavidin-Cy3 (per Chip) diluted in 2.5 ml Blocking buffer were incubated on a Chip for 10 min under gentle shaking to allow binding of cRNA to gene specific probes. After washing, Illumina® Sentrix BeadChips were dried and and scanned.

scan_protocol: Standard Illumina scanning protocol

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

source_name: 48 h, control, rep 3

label_protocol: 500 ng of total RNA in 11 µl RNase free water served as starting material for the generation of biotin-labeled cRNA with the Illumina® TotalPrepTM RNA amplification kit following supplier instructions. cRNA was cleaned up with cRNA filter cartridges before use for subsequent hybridization on Illumina® Sentrix BeadChips.

growth_protocol: Daoy cells (ATCC: HTB-186) were cultivated in Dulbecco’s modified Eagle’s medium (DMEM, Gibco/Invitrogen) with 10% (v/v) fetal bovine serum (FBS, Gibco/Invitrogen).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, 74104) according to the manufacturer's protocol. Quantity and purity of RNA were determined by measuring the optical density at 260 and 280 nm with an UV/Vis Spectrophotometer (Thermo Scientific, Nanodrop 1000) and BioAnalyzer 2100 (Agilent Technologies Deutschland GmbH).

treatment_protocol: Hyperconfluent Daoy cells were pre-starved for 24 h in serum-reduced DMEM medium containing 0.5% (v/v) FBS before adding Sonic Hedgehog conditioned medium (Shh-N) or EGF (5 ng/ml) for stimulation. Total RNA was obtained at 14 different time points 24 h after EGF stimulation.

tag: cell line

value: Daoy cells (ATCC:HTB-186)

value: control

tag: timepoint


title: thyroid tumor sample 33

description: DS #33

tag: tissue type


title: thyroid tumor sample 34

description: DS #34


title: 108L

value: Large White


title: Daoy_36h_SHH+EGF_rep3

description: replicate 3

source_name: 36 h, SHH+EGF, rep 3

value: SHH+EGF


title: Daoy_48h_SHH+EGF_rep3

description: replicate 3

source_name: 48 h, SHH+EGF, rep 3


title: thyroid tumor sample 38

description: DS #38


title: Burkholderia cenocepacia_AU2260_10

description:
set3
2678-AU5229-8_647pmt939-AU2260-10_0555_with_SNR.txt


title: Burkholderia cenocepacia_AU2260_12

description:
set3
2401_AU2947-12_647_pmt980_AU2260-12_555_pmt1000.txt


title: Ovary_NF58_rep1

value: ovary

value: golden


title: Burkholderia cenocepacia_AU2208_15

description:
set3
2675-HI3286-8_647pmt939-AU2208-15_0555_wiht_SNR.txt


title: Burkholderia seminalis_AU2283_2

description:
set3
3285_AU2283-2_647_PMT990_AU0028-3_555_PMT850.txt

value: Bsem


title: 97LP


title: 98H


title: 95H


title: 96H


title: thyroid tumor sample 32

description: DS #32


title: Daoy_36h_EGF_rep3

description: replicate 3

source_name: 36 h, EGF, rep 3

value: EGF


title: Burkholderia cenocepacia_AU2208_10

description:
set3
2406_HI2767-12_647_pmt1000_AU2208-10_555_pmt980.txt


title: thyroid tumor sample 29

description: DS #29


title: Burkholderia cenocepacia_AU2208_11

description:
set3
2674-AU2208-11_647pmt939-HI2670-7_0555_with_SNR.txt


title: Daoy_36h_SHH_rep3

description: replicate 3

source_name: 36 h, SHH, rep 3

value: SHH


title: Burkholderia cenocepacia_AU2205_2

description:
set3
2683_AU3488-1_647_pmt939_AU2205-2_555_pmt610_with_SNR.txt

value: PHDC


title: thyroid tumor sample 28

description: DS #28


title: Daoy_24h_EGF_rep3

description: replicate 3

source_name: 24 h, EGF, rep 3


title: 92H


title: thyroid tumor sample 26

description: DS #26


title: thyroid tumor sample 31

description: DS #31


title: Daoy_24h_SHH_rep3

description: replicate 3

source_name: 24 h, SHH, rep 3


title: thyroid tumor sample 25

description: DS #25


title: 90LP


title: Burkholderia cenocepacia_AU2157_3

description:
set3
2721_AU2157-3_647_pmt939_HI2631-1_555_pmt630_with_SNR.txt

value: Midwest


title: thyroid tumor sample 27

description: DS #27


title: Daoy_24h_control_rep3

description: replicate 3

source_name: 24 h, control, rep 3


title: Burkholderia cenocepacia_AU2205_1

description:
set3
2694_AU2205-1_647_pmt939_AU0280-2_555_pmt650_with_SNR.txt


title: 94H


title: thyroid tumor sample 30

description: DS #30


title: 91H


title: Burkholderia cenocepacia_AU2157_2

description:
set3
2690_HI3520-B-1_647_pmt939_AU2157-2_555_pmt670_with_SNR.txt


title: 89H


title: Daoy_18h_SHH+EGF_rep3

description: replicate 3

source_name: 18 h, SHH+EGF, rep 3


title: Burkholderia cenocepacia_AU2071_11

description:
set3
2924-AU6880-18_647pmt850-AU2071-11_0555.txt


title: Daoy_36h_control_rep3

description: replicate 3

source_name: 36 h, control, rep 3


title: Daoy_24h_SHH+EGF_rep3

description: replicate 3

source_name: 24 h, SHH+EGF, rep 3


title: 88LP

source_name: Blood

value: Large White×Piétran


title: 87BL

value: Belgian Landrace×Large White

value: blood


title: 107H

value: hybrid


title: Burkholderia cenocepacia_AU2029_25

description:
set3
2956_AU2029-25_647_pmt900_AU3397-26_555_pmt1000_647_ONLY.txt

source_name: Pure culture


title: 86LP


title: 83BL


title: thyroid tumor sample 20

description: DS #20

source_name: PTCc

value: thyroid tumor


title: thyroid tumor sample 19

description: DS #19


title: 93H


title: thyroid tumor sample 21

description: DS #21


title: Daoy_18h_EGF_rep3

description: replicate 3

source_name: 18 h, EGF, rep 3


title: thyroid tumor sample 22

description: DS #22


title: Daoy_18h_SHH_rep3

description: replicate 3

source_name: 18 h, SHH, rep 3


title: Burkholderia cenocepacia_AU1874_25

description:
set3
2958_AU8260-26_647_pmt990_AU1874-25_555_pmt1000_with_SNR.txt

value: Sporadic IIIA


title: Burkholderia cenocepacia_AU2071_15

description:
set3
2902_AU2071-15_647_pmt760_HI2708-1_555_pmt630.txt


title: Burkholderia cenocepacia_AU2002_3

description:
set3
a2404_AU6888-3_647_pmt850_AU2002-3_555_pmt820.txt


title: 85H


title: Burkholderia cenocepacia_AU1874_35

description:
set3
3281_AU1874-35_647_pmt970_AU3397-35_555_pmt880.txt


title: Daoy_12h_SHH_rep3

description: replicate 3

source_name: 12 h, SHH, rep 3

value: Daoy cells (ATCC:HTB-186)


title: thyroid tumor sample 24

description: DS #24


title: 82BL


title: Daoy_12h_EGF_rep3

description: replicate 3

source_name: 12 h, EGF, rep 3


title: Daoy_12h_control_rep3

description: replicate 3

source_name: 12 h, control, rep 3

value: control


title: 84BL


title: Burkholderia cenocepacia_AU2002_1

description:
set3
2863_AU2002-1_647_pmt939_AU1367-18_555_pmt600_use_647_only.txt


title: thyroid tumor sample 18

description: DS #18

source_name: dvPTC


title: Daoy_12h_SHH+EGF_rep3

description: replicate 3

source_name: 12 h, SHH+EGF, rep 3


title: Burkholderia cenocepacia_AU1790_26

description:
set3
2919_AU6690-30_647_pmt940_AU1790-26_555_pmt810_with_SNR.txt


title: 81H


title: 80P

value: Piétran


title: Daoy_10.5h_SHH+EGF_rep3

description: replicate 3

source_name: 10.5 h, SHH+EGF, rep 3

value: SHH+EGF


title: thyroid tumor sample 23

description: DS #23


title: thyroid tumor sample 16

description: DS #16


title: Burkholderia cenocepacia_AU2029_2

description:
set3
3278_AU13032-26_647_pmt1000_AU2029-2_555_pmt940.txt


title: thyroid tumor sample 17

description: DS #17


title: Daoy_18h_control_rep3

description: replicate 3

source_name: 18 h, control, rep 3


title: Daoy_10.5h_SHH_rep3

description: replicate 3

source_name: 10.5 h, SHH, rep 3


title: Burkholderia cenocepacia_AU1790_25

description:
set3
2923_AU1790-25_647_pmt1000_AU0279-26_555_pmt880_with_SNR.txt


title: thyroid tumor sample 15

description: DS #15


title: Burkholderia seminalis_AU1751_2

description:
set3
3282_HI2490-2_647_PMT990_AU1751-2_555_PMT850.txt


title: thyroid tumor sample 14

description: DS #14


title: 79L

value: Large White


title: Burkholderia cenocepacia_PC676-P2_2

value: Environmental


title: Daoy_10.5h_EGF_rep3

description: replicate 3

source_name: 10.5 h, EGF, rep 3


title: Burkholderia cenocepacia_PC184_


title: Daoy_10.5h_control_rep3

description: replicate 3

source_name: 10.5 h, control, rep 3


title: thyroid tumor sample 12

description: DS #12


title: Daoy_9h_SHH_rep3

description: replicate 3

source_name: 9 h, SHH, rep 3

value: 9 h


title: 76H


title: Daoy_9h_SHH+EGF_rep3

description: replicate 3

source_name: 9 h, SHH+EGF, rep 3


title: 78H

source_name: Blood


title: Burkholderia cenocepacia_PC676-P2_1

source_name: Pure culture


title: thyroid tumor sample 11

description: DS #11

source_name: PTCc


title: Burkholderia cenocepacia_HI4283_4


title: thyroid tumor sample 13

description: DS #13


title: Daoy_9h_control_rep3

description: replicate 3

source_name: 9 h, control, rep 3


title: Burkholderia cenocepacia_HI4283_3


title: 73H


title: thyroid tumor sample 10

description: DS #10


title: Daoy_9h_EGF_rep3

description: replicate 3

source_name: 9 h, EGF, rep 3

value: EGF


title: 77H


title: thyroid tumor sample 9

description: DS #9

source_name: PTC+PDTC


title: 75H


title: Burkholderia cenocepacia_HI2718_B1


title: Burkholderia cenocepacia_HI2718_2


title: 72H


title: 71H


title: 70H


title: 74H


title: Burkholderia cenocepacia_AU9512_4


title: Daoy_7.5h_SHH_rep3

description: replicate 3

source_name: 7.5 h, SHH, rep 3

value: SHH


title: Daoy_7.5h_EGF_rep3

description: replicate 3

source_name: 7.5 h, EGF, rep 3


title: Burkholderia cenocepacia_AU2947_2

value: PHDC


title: thyroid tumor sample 7

description: DS #7


title: 10 Hr vs REF

city: Madison

first: Christina

last: Hull

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry, Medical Microbiology and Immunology

institute: University of Wisconsin- Madison

hyb_protocol: Slides were incubated in pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) for 1 hour at 42ºC. cDNAs were then applied to slides in 1X formamide buffer (25% formamide, 5X SSC, 0.1% SDS) containing 10 µg each sheared salmon sperm DNA (Eppendorf, Westbury, NY) and yeast tRNA (Sigma-Aldrich, St. Louis MO). Hybridizations were incubated at 42ºC for 12 hours. Slides were washed (1x SSC, .05XSSC) and dried before scanning.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner and the data extracted using GenePix Pro 4.0 (Molecular Devices, Sunnyvale CA) at the University of Wisconsin-Madison Gene Expression Center.

data_processing: Extracted data were analyzed using the GeneSpring 10.0 software package (Agilent Technologies, Santa Clara CA). After initial background correction, data were normalized using the LOWESS (locally weighted scatter plot smoothing) algorithm (Quackenbush 2001) and assessed for statistical significance utilizing ANOVA. Genes meeting the criterion p<0.05 were considered statistically significant and used in further analyses. Significant genes meeting the fold-change threshold were clustered using Cluster 3.0 (de Hoon et al. 2004) according to a robust K-means 5 algorithm (1000 iterations)

label: Cy5, Cy3

organism: Cryptococcus deneoformans

source_name: RNA was harvested from germinating spores

label_protocol: Amplified antisense RNA was synthesized usisng the MessageAmp II RNA amplification kit (Life Technologies, Carlsbad CA). Amino allyl-UTP was added to amplification reaction, and then antisense RNA was directly coupled to Oyster dyes (Boca Scientific, Boca Raton FL).

extract_protocol: Cells were flash frozen in liquid nitrogen. RNA was harvested from frozen pellet via hot-acid phenol as described in (Ausubel, Current Protocols in Molecular Biology, 1997)

treatment_protocol: C. neoformans spores were produced by crossing JEC20 and JEC21 on V8 agar pH 7 for 4 days. Spores were isolated using a Percoll density gradient and then placed in rich medium (YPD broth) to trigger germination. Spores were germinted in rich medium at 30 degrees with shaking. Aliquots of germinating spores were removed at each time point, and frozen in liquid nitrogen prior to RNA extraction.

tag: time point

value: 10 Hr in rich medium at 30 degrees with shaking

label: Cy3, Cy5

source_name: RNA was harvested from spores at all time points

value: mixture of all time points


title: thyroid tumor sample 4

description: DS #4


title: thyroid tumor sample 3

description: DS #3


title: Burkholderia cenocepacia_AU0062_2

last: cardenas

address: 540 Plant and Soil Sciences Building

institute: Michigan State University

hyb_protocol: Dried DNAs from two isolates labeled with each fluorophore were resuspended together in hybridization buffer (6x SSPE, 23% formamide, and 0.05% Tween 20), heated for 5 min at 95°C, and cooled on ice for 5 min before loading onto the arrays. Coverslips were rinsed with 2% SDS, followed by water and then 100% ethanol. After two more washes with water, coverslips were overlaid on the slide to cover both arrays. Covered slides were deposited in hybridization chambers and incubated in a 48°C water bath for 16-20 h. Arrays were then sequentially washed in 6X SSPE for 2 min at 48°C and 1X SSPE for 2 min at 48°C, and then quickly dipped ten times in 0.25X SSPE at room temperature before drying by centrifugation at 2000 xg for 30 s.

scan_protocol: Arrays were scanned in an Axon 4000B scanner (Molecular Devices, Inc., Sunnyvale, CA) using the Genepix v5.1 software and a 5 μm pixel size. PMT values were customized for each channel to obtain the complete range of intensities. Images were saved in TIFF format. Before extracting data, spots were reviewed and flagged as unreadable if scratches, dust or salts precipitates were present. Data were extracted from both channels, but each channel was treated independently in the final analysis

data_processing: Global background, calculated as 5% median of the intensity of all target probes, was subtracted from each spot intensity. Arrays were then normalized using a set of 159 probes from 78 genes whose sequences were exact matches in all 5 of the genomes used for the array design.  The median spot intensity for the group of conserved probes was arbitrarily set to 10,000 and applied as a correction factor to each array. Probes with adjusted signal intensities greater than 1594 units. Data from independent hybridization reactions were consolidated to a single present/absent call for each probe, with present being defined as at least 50% of all replicate spots being called present. Finally, genes were called present if at least 50% of the probes targeted to that element were called present.

label_protocol: Four micrograms of bacterial genomic DNA were labeled with Alexa Fluor 555 or Alexa Fluor 647 ester dyes using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen Corp., Carlsbad, CA) following the manufacturer’s specifications with two modifications. In place of ethanol precipitation, DNA was dried for 2 h under medium heat after Klenow amplification using the Savant DNA 120 vacuum centrifuge (Thermo Scientific, Asheville, NC), and DNA was completely dried after dye incorporation for 2 h by vacuum centrifugation with no heat.

extract_protocol: Bacteria were recovered from frozen stock by culturing on Mueller-Hinton (MH) agar overnight at 37 oC. Bacteria removed from agar were suspended in DNase-, RNase-free water, and genomic DNA was isolated using the Puregene system (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions with the following modifications.  Proteinase K was added to a final concentration of 200 µg/ml prior to incubating cell lysates at 80oC for 5 min, the final concentration of RNAse was increased to 25 µg/ml, and precipitated proteins were removed by course filter through a 1 ml syringe packed to the 0.2 ml demarcation with glass wool prior to the clarifying centrifugation. Pelleted DNA was resuspended in DNase-, RNase-free water, and DNA quality was assessed by A260/A280 ratios and agarose gel electrophoresis.

value: Midwest


title: 8 Hr vs REF

growth_protocol: C. neoformans spores were produced by crossing JEC20 and JEC21 on V8 agar pH 7 for 4 days. Spores were isolated using a Percoll density gradient and then placed in rich medium (YPD broth) to trigger germination. Spores were germinted in rich medium at 30 degrees with shaking.

value: 8 Hr in rich medium at 30 degrees with shaking


title: Daoy_6h_EGF_rep3

description: replicate 3

source_name: 6 h, EGF, rep 3

value: 6 h


title: thyroid tumor sample 6

description: DS #6

value: thyroid tumor


title: thyroid tumor sample 5

description: DS #5


title: 67H

tag: affected status f4ab/ac (1=na/2=a)

value: hybrid

value: blood


title: Daoy_6h_SHH_rep3

description: replicate 3

source_name: 6 h, SHH, rep 3

value: Daoy cells (ATCC:HTB-186)


title: Daoy_6h_SHH+EGF_rep3

description: replicate 3

source_name: 6 h, SHH+EGF, rep 3


title: 6 Hr vs REF

value: 6 Hr in rich medium at 30 degrees with shaking


title: thyroid tumor sample 2

description: DS #2


title: Daoy_7.5h_control_rep3

description: replicate 3

source_name: 7.5 h, control, rep 3

value: control


title: 68H

tag: gender (1=m/2=f)


title: Daoy_6h_control_rep3

description: replicate 3

source_name: 6 h, control, rep 3


title: Hansenula polymorpha Hpmet4 Cd, rep3

city: Daejeon

first: Min Jeong

last: Sohn

address: 52 Eoeun-dong, Yuseong-gu

department: Protein therapeutics research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

hyb_protocol: Hybridization was performed using the 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) according to the manufacturer's instructions as described previously (Oh et al.).

scan_protocol: The hybridized slides were scanned with the ScanArray 5000 scanner (Axon, Foster City, CA, U.S.A.).

data_processing:
Using GenePixTM Pro 4.0 (Axon) software, spot intensity was quantified for each channel and transferred to a Microsoft Excel spreadsheet. All arrays were analyzed using Quintet, an R-based unified cDNA microarray data analysis system with GUI (Choe et al., 2005).
Choe, J.-K., T.-H. Chung, S. Park, H. G. Cho, and C.-G. Hur. 2005. An open source microarray data analysis system with GUI: Quintet. In Slezak D. et al., (Eds) RSFDGrC 2005, LNAI 3642, pp. 392-401, Springer-Verlag Berling Heidelberg.

organism: Ogataea angusta

source_name: Hpmet4, control

label_protocol: The labeling of target cDNAs was performed using the 3DNA™ Submicro® EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) as described previously (Oh et al.).

extract_protocol:
Isolation of RNA and cDNA synthesis were carried out as described in Oh et al., 2004.
Oh, K.S., Kwon, O., Oh, Y.W., Sohn, M.J., Jung, S., Kim, Y.K., Kim, M.-G., Rhee, S.K., Gellissen, G., and Kang, H.A. (2004) Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14, 1239-1248.

tag: genotype

value: Hpmet4 deletion mutant

tag: medium

value: YPD

source_name: Hpmet4, Cd

value: cadmium stress


title: Burkholderia cenocepacia_AU16957_A3

city: East Lansing

first: erick

tag: strain

tag: group


title: Burkholderia cenocepacia_AU16957_A4


title: 4 Hr vs REF

value: 4 Hr in rich medium at 30 degrees with shaking


title: 0 Hr vs REF


title: thyroid tumor sample 1

description: DS #1


title: Daoy_7.5h_SHH+EGF_rep3

description: replicate 3

source_name: 7.5 h, SHH+EGF, rep 3

value: SHH+EGF


title: Hansenula polymorpha Hpmet4 Cd, rep1


title: Hansenula polymorpha Hpmet4 Cd, rep2


title: CalhL1_liver

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided was done by data standardization of the median (JMP Genomics, V6.0).

organism: Micropterus salmoides

source_name: male liver

label_protocol: Agilent one color protocol for Cy3

extract_protocol: STAT60 protocol for total RNA

value: male

value: liver

tag: location

value: Lake Calhoun


title: Daoy_4.5h_SHH+EGF_rep3

description: replicate 3

source_name: 4.5 h, SHH+EGF, rep 3


title: Daoy_3h_SHH+EGF_rep3

description: replicate 3

source_name: 3 h, SHH+EGF, rep 3

value: 3 h


title: CalhL3_liver


title: Daoy_4.5h_control_rep3

description: replicate 3

source_name: 4.5 h, control, rep 3


title: 2 Hr vs REF

value: 2 Hr in rich medium at 30 degrees with shaking

value: mixture of all time points


title: Hansenula polymorpha DL1-L Cd, rep3

source_name: DL1-L, 0.6mM Cd

value: wild-type

source_name: DL1-L, control


title: Daoy_4.5h_EGF_rep3

description: replicate 3

source_name: 4.5 h, EGF, rep 3

value: EGF


title: ERF96OE rep3

city: Taipei

first: Jeremy

last: Catinot

state: Taipei

address: n°1 sec 4 Roosevelt road

department: Institue of plant biology

institute: National Taiwan University

description: Gene expression data from four-week old leaves

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on GeneChip ATH1 Genome Array.

scan_protocol: Gene chip were scanned with Affymetrix GeneChip® Scanner 3000

data_processing: The data were analyzed using Gene Spring GX11 software using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana leaves

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

growth_protocol: Plants were grown on soil plus perlite for four weeks on a daily 8h light/ 16h dark photoperiod at 22°C.

extract_protocol: RNA of leaves was extracted using Trizol according to manufacturer's instructions

value: leaf

tag: age

value: four weeks


title: STL2_liver

tag: tissue

value: Steiger Lake


title: Daoy_4.5h_SHH_rep3

description: replicate 3

source_name: 4.5 h, SHH, rep 3

value: Daoy cells (ATCC:HTB-186)

value: SHH


title: TwinL2_liver

value: Twin Lake


title: ERF96OE rep2


title: STL3_liver


title: Hansenula polymorpha DL1-L Cd, rep4

value: control

value: YPD

source_name: DL1-L, Cd

value: cadmium stress


title: ERF96OE rep1


title: Daoy_3h_SHH_rep3

description: replicate 3

source_name: 3 h, SHH, rep 3


title: Daoy_3h_EGF_rep3

description: replicate 3

source_name: 3 h, EGF, rep 3


title: CalhL2_liver

value: male


title: Hansenula polymorpha DL1-L Cd, rep1


title: WT rep3

tag: cultivar


title: Hansenula polymorpha Hpmet4 sulfur starvation, rep4

value: Hpmet4 deletion mutant

source_name: Hpmet4, sulfur starvation

value: sulfur starvation

value: B


title: WT rep2


title: TwinL1_liver

tag: gender

value: liver


title: Hansenula polymorpha Hpmet4 sulfur starvation, rep3

tag: treatment


title: Daoy_3h_control_rep3

description: replicate 3

source_name: 3 h, control, rep 3

value: 3 h


title: 69H

source_name: Blood

tag: father id

tag: mother id

tag: breed

value: hybrid

value: blood


title: STL1_liver


title: Hansenula polymorpha Hpmet4 sulfur starvation, rep2

source_name: Hpmet4, control


title: thyroid tumor sample 8

description: DS #8

source_name: PTCc

tag: tissue type

value: thyroid tumor


title: TwinL5_liver

source_name: male liver


title: Hansenula polymorpha Hpmet4 sulfur starvation, rep1

description: Transcriptome profiling of H. polymorpha in the sulfur starvation condition.


title: Hansenula polymorpha DL1-L sulfur starvation, rep3

description: Transcriptome profiling of H. polymorpha in the sulfur starvation condition (repeat).

source_name: DL1-L, sulfur starvation

value: wild-type


title: Daoy_1.5h_EGF_rep3

description: replicate 3

source_name: 1.5 h, EGF, rep 3

tag: cell line

value: EGF

tag: timepoint


title: Daoy_1.5h_SHH+EGF_rep3

description: replicate 3

source_name: 1.5 h, SHH+EGF, rep 3

value: Daoy cells (ATCC:HTB-186)

value: SHH+EGF


title: CalhL4_liver

value: Lake Calhoun


title: STL5_liver

value: Steiger Lake


title: Daoy_1.5h_SHH_rep3

description: replicate 3

source_name: 1.5 h, SHH, rep 3

value: SHH


title: WT rep1

value: leaf

value: four weeks


title: Daoy_1h_SHH+EGF_rep3

description: replicate 3

source_name: 1 h, SHH+EGF, rep 3

value: 1 h


title: Hansenula polymorpha DL1-L sulfur starvation, rep2

description: Transcriptome profiling of H. polymorpha in the sulfur starvation condition (dye swap).

source_name: DL1-L, control

value: control

value: YPD

value: sulfur starvation


title: Hansenula polymorpha DL1-L sulfur starvation, rep4

value: B


title: Daoy_1.5h_control_rep3

description: replicate 3

source_name: 1.5 h, control, rep 3


title: CalhL5_liver

value: male

value: liver


title: Hansenula polymorpha DL1-L sulfur starvation, rep1

description: Transcriptome profiling of H. polymorpha DL1-L in the sulfur starvation condition.


title: Daoy_1h_EGF_rep3

description: replicate 3

source_name: 1 h, EGF, rep 3


title: CalhL8_liver


title: TwinL8_liver

value: Twin Lake


title: Daoy_1h_control_rep3

description: replicate 3

source_name: 1 h, control, rep 3


title: TwinL7_liver


title: Rat hypothalamus Saline vs T3 replicate 3

city: Aberdeen

first: Perry

last: Barrett

address: Greenburn Road, Bucksburn

department: Rowett Institute for Nutrition and Health

country: United Kingdom

institute: University of Aberdeen

hyb_protocol: Equal volume of Aglient's 2X GEx hybridization buffer was added to the targets. Hybridization was performed at 65C for 17h in an Aglient rotating hybridzation oven. Slides were sequential washed in Agilent's Gene Expression Wash Buffer 1 then buffer 2.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: The data were loess normalized in R 3.02 using the Bioconductor library  limma 3.18.9. Duplicated Ids were averaged after normalisaton.

organism: Rattus norvegicus

source_name: hypothalamus Bregma -2.12 to -4.52 under Saline treatment

label_protocol: Two step amplification procedure using the Agilent labelling kit incorporating either Cy-3 or Cy-5 dye

growth_protocol: Seven week old Sprague Dawley rats on 12:12 light:dark cycle fed on chow (8 rats)

extract_protocol: Blocks of hypothalamic tissue removed from brain. RNA extracted with with Trizol.

treatment_protocol: Rats rendered hypothyroid by adding 0.025% MMI to the drinking water for 22 days. On day 21 4 rats received either saline or T3 injections (25ug/100g). Rats killed 24h later

value: hypothalamus Bregma -2.12 to -4.52

value: saline

value: Sprague Dawley

value: 10 wk

source_name: hypothalamus Bregma -2.12 to -4.52 under T3 treatment


title: Daoy_1h_SHH_rep3

description: replicate 3

source_name: 1 h, SHH, rep 3

value: Daoy cells (ATCC:HTB-186)


title: TwinL6_liver


title: STL8_liver

value: Steiger Lake


title: CalhL7_liver

value: Lake Calhoun


title: Rat hypothalamus Saline vs T3 replicate 2


title: Daoy_0.5h_SHH+EGF_rep3

description: replicate 3

source_name: 0.5 h, SHH+EGF, rep 3

value: SHH+EGF


title: TwinL4_liver


title: Hsf1 null fibroblasts, Rep A

city: Cambridge

first: Marc

last: Mendillo

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Gene Expression after 72 hours in the presence or absence of coculture

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hsf1 null fibroblasts, Rep A

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: In vitro cultured in DMEM with 10% FCS

extract_protocol: Qiagen RNeasy kit

treatment_protocol: For profiling of cancer cells, MEFs were treated with 10 μg/ml mitomycin C for 2h before co-culture.

tag: cell type

value: Mouse Embryonic Fibroblasts


title: Rat hypothalamus Saline vs T3 replicate 1


title: Daoy_0.5h_EGF_rep3

description: replicate 3

source_name: 0.5 h, EGF, rep 3

value: EGF


title: Hsf1 null fibroblasts, Rep B

source_name: Hsf1 null fibroblasts, Rep B

tag: genotype


title: CalhL6_liver

source_name: male liver


title: Daoy_0.5h_SHH_rep3

description: replicate 3

source_name: 0.5 h, SHH, rep 3

value: SHH


title: STL7_liver


title: Hsf1 null fibroblasts from co-culture with tumor cells, Rep B


title: Daoy_0.5h_control_rep3

description: replicate 3

source_name: 0.5 h, control, rep 3

value: control


title: WT fibroblasts, Rep B

source_name: WT fibroblasts, Rep B


title: Daoy_0.25h_SHH+EGF_rep3

description: replicate 3

source_name: 0.25 h, SHH+EGF, rep 3


title: Rat hypothalamus Saline vs T3 replicate 4


title: STL6_liver