title: ZR-75-30

city: LA

first: Richard

middle: S

last: Finn

state: CA

address: 10833 Le Conte, 11-934 Factor Building

department: Medicine-Hem/Onc

institute: UCLA

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to Agilent Human version 2 microarray slides enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization at 64C for 17hr, slides were washed sequentially in SSPE solutions, dried and scanned.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5.1.1).

data_processing:
Agilent Feature Extraction Software Version: 7.5
SpotFinder_Version: Version A.7.5.1   Jun  1 2004 09:41:20
CornerMethod: Auto Find Corners
CalcSpotStats_Version: Version A.7.5.1   Jun  1 2004 09:41:37
CalcSpotStats_SpotStatsMethod: Cookie Cutter Method
CalcSpotStats_RejectMethod: Interquartile Range Based
CalcSpotStats_CalculateSpotSize: Off
OutlierFlagger_Version: Version A.7.5.1   Jun  1 2004 09:44:12
OutlierFlagger_NonUnifOLOn: Nonuniformity Outlier Flag On
OutlierFlagger_PopnOLOn: Population Outlier Flagging turned On
BGSubtractor_Version: Version A.7.5.1   Jun  1 2004 09:42:46
BGSubtractor_BGSubMethod: Local background coresponding to each feature for background subtraction (local method)
BGSubtractor_BackgroundCorrectionOn: Globally adjust background turned off
BGSubtractor_SpatialDetrendOn: Spatial detrend turned off
DyeNorm_Version: Version A.7.5.1   Jun  1 2004 09:43:13
DyeNorm_SelectMethod: Rank Consistency Filter
DyeNorm_IsBGPopnOLOn: OFF
DyeNorm_CorrMethod: Linear & Lowess
Ratio_Version: Version A.7.5.1   Jun  1 2004 09:43:43
Ratio_ErrorModel: Hybrid Model
Ratio_UseSurrogates: Use of surrogates turned on
Ratio_AutoEstimateAddErrorRed: Auto-estimation turned off
Ratio_AutoEstimateAddErrorGreen: Auto-estimation turned off
FeatureExtractor_Version: Version A.7.5.1   Jun  1 2004 09:45:57

source_name: breast cell line

label_protocol: 750 ng of total RNA were primed with T7 primer at 65C for 10 min, then reverse transcribed at 42C for 2 hr in the presence of MMLV reverse transcriptase (15 units/ul) and and 50 uM each dATP, dGTP, dCTP and dTTP .  After incubation, the reaction was heated at 65C for 15 min to inactivate the MMLV RT.  Transcription buffer, DTT, NTP mix, PEG, RNaseOut, inorganic pyrophosphorylase, and T7 polymerase were added as per Agilent Low RNA Input Amplification Kit, along with 1.2 ul of 100nmol Cy5-CTP or Cy3-CTP.  The transcription mix was incubated 40C for

growth_protocol: Cells were grown in respective media to 70% confluence under standard growth conditions

extract_protocol: Total RNA extracted using Rneasy Kit (Qiagen) per manufactures instructions

source_name: pooled breast cell line reference

value: pooled breast cell lines


title: Picea_F3_D2_bark_phloem

status: Public on Oct 10 2009

type: RNA

city: Vancouver

first: Dr. Kermit

last: Ritland

state: BC

address: 2424 Main Mall

department: Forest Sciences

country: Canada

institute: University of British Columbia

description: Picea_F3_D2_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 28, 07).

hyb_protocol: The slide was pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip. First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water together with 2 ug of salmon testes DNA (Invitrogen). The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation. Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water. Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird.  Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F3_D2_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

molecule: total RNA

organism: Picea jezoensis

source_name: F3: Third biological replicate of jezo spruce

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol:  40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy5/Alexa Fluor 647 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).

extract_protocol:
Total RNA extraction used the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824.
The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.

treatment_protocol: Specimen (bark/phloem sources of tissue) pooled from various shoots of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

tag: species

value: jezo spruce

tag: tissue

value: Bark and the attached phloem were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC, Canada (collection established 1977).

organism: Picea mariana

source_name: D2: Second biological replicate of black spruce

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol:  40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy3/Alexa Fluor 546 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).

treatment_protocol: Bark/phloem sources of tissue pooled from various shoots of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

value: black spruce


title: Picea_C1_G3_bark_phloem

description: Picea_C1_G3_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 28, 07).

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird.  Fluorescent intensity data were quantified using the ImaGene 5.5 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C1_G3_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

organism: Picea abies

source_name: C1: First biological replicate of Norway spruce

value: Norway spruce

organism: Picea glauca

source_name: G3: Third biological replicate of white spruce

value: white spruce


title: mES BPA-100pM

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

description: Expose 100pM bisphenol A for 48hours

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

organism: Mus musculus

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

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

treatment_protocol: Chemicals were treated into the culture media at the iniciated stage after removing LIF.

tag: genetic background

tag: cell type

value: embryonic stem cell


title: Picea_E3_C2_needle

description: Picea_E3_C2_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 14, 07).

hyb_protocol: The slide was pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip. First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water together with 2 ug of salmon tests DNA (Invitrogen). The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation. Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water. Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird .  Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E3_C2_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

organism: Picea omorika

source_name: E3: Third biological replicate of Serbian spruce

extract_protocol:
Total RNA extraction used the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824.
The extracted RNA was quantified using spectrophotometry and quality checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) in respect to the distinct peaks of electropherogram and gel profile.

treatment_protocol: Needles pooled from various shoots of the individual tree were flash-frozen on the field by liquid nitrogen on Apr. 24, 07, and kept in -80 ºC freezer until extraction.

value: Serbian spruce

value: Fresh current-year needles were sampled from mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC, Canada (collection established 1977).

source_name: C2: Second biological replicate of Norway spruce


title: ZR-75-1

country: USA

organism: Homo sapiens

tag: cell line

tag: sample type


title: mES E2-10nM

description: Expose 10nM estradiol for 48hours


title: Picea_C2_G1_needle

description: Picea_C2_G1_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 14, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C2_G1_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: Second biological replicate of Norway spruce

source_name: F1: First biological replicate of white spruce


title: Picea_D2_C1_bark_phloem

description: Picea_D2_C1_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 28, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D2_C1_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: mES DMSO

description: Expose 0.1% dimethyl sulfoxide for 48hours

source_name: DMSO


title: Picea_F2_E1_bark_phloem

description: Picea_F2_E1_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 30, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F2_E1_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: F2: Second biological replicate of jezo spruce

source_name: E1: First biological replicate of Serbian spruce


title: UACC-893


title: UACC-812


title: Picea_C2_G1_bark_phloem

description: Picea_C2_G1_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 18, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C2_G1_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: G1: First biological replicate of white spruce


title: Picea_G2_F1_bark_phloem

description: Picea_G2_F1_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 21, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G2_F1_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: G2: Second biological replicate of white spruce

source_name: F1: First biological replicate of jezo spruce


title: UACC-732


title: Picea_E1_D3_bark_phloem

description: Picea_E1_D3_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 30, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E1_D3_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: D3: Third biological replicate of black spruce


title: Picea_C3_F2_bark_phloem

description: Picea_C3_F2_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 25, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C3_F2_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: C3: Third biological replicate of Norway spruce


title: Picea_E3_C2_bark_phloem

description: Picea_E3_C2_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 25, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E3_C2_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: mES DHT-1M

description: Expose 1nM dehydrotestosterone for 48hours


title: SUM-225

source_name: breast cell line

source_name: pooled breast cell line reference


title: T-47D


title: SUM-190


title: SK-BR-3


title: MDA-MB-468


title: Picea_G3_E2_bark_phloem

description: Picea_G3_E2_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 30, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G3_E2_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: E2: Second biological replicate of Serbian spruce


title: Picea_F1_E3_bark_phloem

description: Picea_F1_E3_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 25, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F1_E3_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

value: Bark and the attached phloem  were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC, Canada (collection established 1977).


title: Picea_D3_G2_bark_phloem

description: Picea_D3_G2_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 28, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D3_G2_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: Picea_E2_D1_bark_phloem

description: Picea_E2_D1_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 30, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E2_D1_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

value: Bark and the attached phloem  were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC (collection established 1977).

source_name: D1: First biological replicate of black spruce


title: MDA-MB-453

data_processing:
Agilent Feature Extraction Software Version: 7.5
SpotFinder_Version: Version A.7.5.1   Jun  1 2004 09:41:20
CornerMethod: Auto Find Corners
CalcSpotStats_Version: Version A.7.5.1   Jun  1 2004 09:41:37
CalcSpotStats_SpotStatsMethod: Cookie Cutter Method
CalcSpotStats_RejectMethod: Interquartile Range Based
CalcSpotStats_CalculateSpotSize: Off
OutlierFlagger_Version: Version A.7.5.1   Jun  1 2004 09:44:12
OutlierFlagger_NonUnifOLOn: Nonuniformity Outlier Flag On
OutlierFlagger_PopnOLOn: Population Outlier Flagging turned On
BGSubtractor_Version: Version A.7.5.1   Jun  1 2004 09:42:46
BGSubtractor_BGSubMethod: Local background coresponding to each feature for background subtraction (local method)
BGSubtractor_BackgroundCorrectionOn: Globally adjust background turned off
BGSubtractor_SpatialDetrendOn: Spatial detrend turned off
DyeNorm_Version: Version A.7.5.1   Jun  1 2004 09:43:13
DyeNorm_SelectMethod: Rank Consistency Filter
DyeNorm_IsBGPopnOLOn: OFF
DyeNorm_CorrMethod: Linear & Lowess
Ratio_Version: Version A.7.5.1   Jun  1 2004 09:43:43
Ratio_ErrorModel: Hybrid Model
Ratio_UseSurrogates: Use of surrogates turned on
Ratio_AutoEstimateAddErrorRed: Auto-estimation turned off
Ratio_AutoEstimateAddErrorGreen: Auto-estimation turned off
FeatureExtractor_Version: Version A.7.5.1   Jun  1 2004 09:45:57


title: MDA-MB-436


title: MDA-MB-435


title: Picea_G3_E2_xylem

description: Picea_G3_E2_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Aug. 28, 08).

hyb_protocol: The slide was pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip. First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array900 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water. The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation. Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array900 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water. Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 74 % for Cy3 channel, and 74% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G3_E2_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: G3: Third biological replicate of white spruce

label_protocol: Used Genisphere Array900 kit (Genisphere, Hatfield, USA) following the manufacturer protocol:  25 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 1.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546/Oyster-550 or Cy5/Alexa Fluor 647/Oyster-650; Cy5/Alexa Fluor 647/Oyster-650 dye-labeled; hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 10 min; and neutralized in 2 M Tris-HCl (pH 7.5).

extract_protocol:
Total RNA extraction used a modified version of the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824.
The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.

treatment_protocol: Scraped xylem pooled from various shoots of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

value: white spruce (P. glauca)

value: Xylem tissue sampled from the shoots of mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC (collection established 1977).

label_protocol: Used Genisphere Array900 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 25 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 1.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546/Oyster-550 or Cy5/Alexa Fluor 647/Oyster-650; Cy3/Alexa Fluor 546/Oyster-550 dye-labeled; hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 10 min; and neutralized in 2 M Tris-HCl (pH 7.5).

value: Serbian spruce (P. omorika)


title: Picea_F2_E1_xylem

description: Picea_F2_E1_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 4, 08).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F2_E1_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

value: jezo spruce (P. jezoensis)

extract_protocol:
Kolosova et al. (2004) Biotechniques 36: 821-824.
The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.


title: Picea_D1_C3_bark_phloem

description: Picea_D1_C3_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 25, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D1_C3_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

value: Bark and the attached phloem were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC (collection established 1977).


title: mES E2-1nM

description: Expose 1nM estradiol for 48hours

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


title: MCF-7


title: MDA-MB-134


title: Picea_F1_E3_xylem

description: Picea_F1_E3_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 2, 08).

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 75 % for Cy3 channel, and 75% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F1_E3_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: E3: Third biological replicate of Serbian spruce


title: MDA-MB-157


title: Picea_F3_D2_xylem

description: Picea_F3_D2_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 4, 08).

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 76 % for Cy3 channel, and 72% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F3_D2_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: F3: Third biological replicate of jezo spruce

source_name: D2: Second biological replicate of black spruce

value: black spruce (P. mariana)


title: MDA-MB-231

value: pooled breast cell lines


title: Picea_C1_G3_xylem

description: Picea_C1_G3_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Aug. 28, 08).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C1_G3_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: C1: First biological replicate of Norway spruce

value: Norway spruce (P. abies)


title: MDA-MB-361


title: MDA-MB-330


title: Picea_D3_G2_xylem

description: Picea_D3_G2_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 4, 08).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D3_G2_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: MDA-MB-175


title: MCF-12A


title: Picea_E3_C2_xylem

description: Picea_E3_C2_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 4, 08).

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 76 % for Cy3 channel, and 78% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E3_C2_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: C2: Second biological replicate of Norway spruce


title: Picea_E2_D1_xylem

description: Picea_E2_D1_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 4, 08).

hyb_protocol: The slide was pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip. First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array900 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water. The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array900 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water. Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E2_D1_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: MCF-10A


title: HMEC

value: HMEC


title: Picea_C2_G1_xylem

description: Picea_C2_G1_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Aug. 28, 08).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C2_G1_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: Picea_G1_F3_xylem

description: Picea_G1_F3_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 4, 08).

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 72 % for Cy3 channel, and 76% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G1_F3_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: Picea_G2_F1_xylem

description: Picea_G2_F1_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 4, 08).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G2_F1_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

label_protocol: Used Genisphere Array900 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 25 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 1.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546/Oyster-550 or Cy5/Alexa Flour 647/Oyster-650; Cy3/Alexa Fluor 546/Oyster-550 dye-labeled; hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 10 min; and neutralized in 2 M Tris-HCl (pH 7.5).


title: MDA-MB-415


title: HCC70


title: HCC2218


title: KPL-1


title: HCC202


title: HCC1599


title: HCC2157


title: Picea_D2_C1_xylem

description: Picea_D2_C1_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Aug. 26,08).

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 73 % for Cy3 channel, and 76% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D2_C1_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: HCC38


title: HCC1937


title: Bursal cells (control), biological rep 3

city: East Lansing

first: Weifeng

last: Mao

state: MI

address: 3606 E. Mount Hope Rd. USDA-ARS

department: Genetics Program

institute: Michigan State University

description: Three week old Line 0 chicken

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

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

data_processing: The .CEL files were provided and normalized at the probe level using robust multichip average method implemented into the Affymetrix Expression ConsleTM software.

label: Biotin

organism: Gallus gallus

source_name: Bursa cells (control)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: 2,000,000 bursal cells were spread on the monolayers of SCA2Flag-DF1 cells or control Vector-DF1 cells in triplicate.  After growth in the mixture of Liebovitz’s L-15 and McCoy 5A media (1:1) supplemented with 4% FBS, penicillin, and streptomycin for overnight at 37 ºC in 5% CO2, the bursal cells were recovered by washes (DF1 cells are adhesive) followed by gentle centrifugation at 1000×g for 10 min.

extract_protocol: The bursal cells were recovered by washes (DF1 cells are adhesive) followed by gentle centrifugation at 1000×g for 10 min. Total RNA was isolated using the absolutely RNA microprep kit

treatment_protocol: Growth in the mixture of Liebovitz’s L-15 and McCoy 5A media (1:1) supplemented with 4% FBS, penicillin, and streptomycin for overnight at 37 ºC in 5% CO2

value: bursal cell


title: Bursal cells induced by SCA2, biological rep 2

description: Three week old Line 0 chicken

source_name: Bursa cells induced by SCA2


title: HCC1954


title: Bursal cells induced by SCA2, biological rep 3

description: Three week old Line 0 chicken


title: Bursal cells induced by SCA2, biological rep 1

description: Three week old Line 0 chicken


title: HCC1500


title: Picea_D1_C3_xylem

description: Picea_D1_C3_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept. 2, 08).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D1_C3_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: Picea_E1_D3_xylem

description: Picea_E1_D3_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (hybridization date: Sept.2, 08).

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 76 % for Cy3 channel, and 74% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E1_D3_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: E1: First biological replicate of Serbian spruce

label_protocol: Used Genisphere Array900 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 25 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 1.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546/Oyster-550 or Cy5/Alexa Fluor 647/Oyster-650; Cy5/Alexa Fluor 647/Oyster-650 dye-labeled;hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 10 min; and neutralized in 2 M Tris-HCl (pH 7.5).


title: Bursal cells (control), biological rep 2

description: Three week old Line 0 chicken


title: Bursal cells (control), biological rep 1

description: Three week old Line 0 chicken


title: HCC1187

data_processing:
Agilent Feature Extraction Software Version: 7.5
SpotFinder_Version: Version A.7.5.1   Jun  1 2004 09:41:20
CornerMethod: Auto Find Corners
CalcSpotStats_Version: Version A.7.5.1   Jun  1 2004 09:41:37
CalcSpotStats_SpotStatsMethod: Cookie Cutter Method
CalcSpotStats_RejectMethod: Interquartile Range Based
CalcSpotStats_CalculateSpotSize: Off
OutlierFlagger_Version: Version A.7.5.1   Jun  1 2004 09:44:12
OutlierFlagger_NonUnifOLOn: Nonuniformity Outlier Flag On
OutlierFlagger_PopnOLOn: Population Outlier Flagging turned On
BGSubtractor_Version: Version A.7.5.1   Jun  1 2004 09:42:46
BGSubtractor_BGSubMethod: Local background coresponding to each feature for background subtraction (local method)
BGSubtractor_BackgroundCorrectionOn: Globally adjust background turned off
BGSubtractor_SpatialDetrendOn: Spatial detrend turned off
DyeNorm_Version: Version A.7.5.1   Jun  1 2004 09:43:13
DyeNorm_SelectMethod: Rank Consistency Filter
DyeNorm_IsBGPopnOLOn: OFF
DyeNorm_CorrMethod: Linear & Lowess
Ratio_Version: Version A.7.5.1   Jun  1 2004 09:43:43
Ratio_ErrorModel: Hybrid Model
Ratio_UseSurrogates: Use of surrogates turned on
Ratio_AutoEstimateAddErrorRed: Auto-estimation turned off
Ratio_AutoEstimateAddErrorGreen: Auto-estimation turned off
FeatureExtractor_Version: Version A.7.5.1   Jun  1 2004 09:45:57


title: HCC1569


title: EFM-19


title: HCC1143


title: EFM-192A


title: HCC1806


title: HCC1419


title: HCC1395


title: COLO-824


title: CAMA-1


title: DU4475


title: CAL-51

description: fluor reversal experiment, experiments were combined in Matrix data under CAL-51. For JC_16011521015000_S01_Red_A01.txt, Cy5 is the pooled reference.


title: Wild-type vs. mutant rep4

city: Oslo

first: Reidunn

middle: B.

last: Aalen

address: P.O.Box 1066 Blindern

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Each slide has been scanned at high and low intensity. In addition the technical replicas has been dyeswaped. This means that each replica has 4 associated gpr files

hyb_protocol: Hybridizations were performed in a Tecan , and the slides were washed according  to the manufacturers’ descriptions (Genisphere and Advalytix).

scan_protocol: Packard Bioscience  Scanarray Express HT laserscanner. The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).

data_processing: The data sets were normalized using variance stabilization and normalization (vsn)  and differentially expressed genes identified using the limma software package.

label: Cy5, Cy3

organism: Arabidopsis thaliana

source_name: AG1-76 inflorescences from wt (Colombia ecotype); AG1-77 inflorescences from mutant ashh2-1/sdg8-1

label_protocol: Total RNA (15 mg) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction.  Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.

growth_protocol: Seeds were sown out on soil and grown under the following conditions; 22oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 μmol/m2/sek in light intensity

extract_protocol: Total RNA was extracted using RNeasy midi kit (Qiagen).

treatment_protocol: Untreated

tag: genotype

value: ashh2/sdg8 mutant

value: inflorescence

source_name: AG1-76 inflorescences from mutant ashh2-1/sdg8-1; AG1-77 inflorescences from wt (Colombia ecotype)

value: wild type


title: 184B5


title: Wild-type vs. mutant rep5

source_name: AG1-78 inflorescences from wt (Colombia ecotype); AG1-79 inflorescences from mutant ashh2-1/sdg8-1

source_name: AG1-78 inflorescences from mutant ashh2-1/sdg8-1; AG1-79 inflorescences from wt (Colombia ecotype)


title: Wild-type vs. mutant rep3

source_name: AG1-74 inflorescences from wt (Colombia ecotype); AG1-75 inflorescences from mutant ashh2-1/sdg8-1

source_name: AG1-74 inflorescences from mutant ashh2-1/sdg8-1; AG1-75 inflorescences from wt (Colombia ecotype)


title: Monocyte_LVL_062

status: Public on Oct 09 2009

city: San Francisco

first: Bing

last: Sun

address: B1, R103, 4150 Clement St

institute: San Francisco VA Medical Center

hyb_protocol: Fragment 10ug labeled cRNA in 20ul by adding 5ul 5x Fragmentation Buffer and incubate for 20C at 94C. Add 78ul BufferA, 130ul BufferB 27ul water and incubate for 5min at 90C to denature cRNA. Load reaction to bioarray chamber. Incubate for 22h at 37C on a 300rmp rotating platform. Wash slides using 0.75x TNT for 1hr at 46C. Stain slides using 2ug/ml Alexa Fluor 647-streptavidin in TNB buffer at room temprature for 30 min in dark. Then wash the slides 4 times using 1x TNT for 5min each time. Wasing slides using 0.1x SSC/ 0.05% Tw20 for 30sec. Dry slides at 2000rpm for 3min.

scan_protocol: Axon Genepix Pro 4100B scanner and GenePixPro 3.0 software, using wavelength 635nm, PTM 600V, 100% laser power, 5um pixel size, focus at 0um.

data_processing: Discovery spots were loess normalized in R/BioConductor, then imported into GeneSpring GX 7.3.1 and normalized to 50th percentile per chip and median per gene, less than 0.01 set to 0.01.

source_name: monocytes, LVL

label_protocol: 0.5 ug total RNA, 2.5 ul 1:1000 - 1:2^10 bacterial mRNA controls, 1ul T7 Oligo(dT) primer, add water to 12ul. Incubate for 10min at 70C. Add 2ul 10x First Strand Buffer, 4ul 5mM dNTP, 1ul RNase Inhibitor, 1ul ArrayScript to reaction. Incubate for 2h at 42C. Add 63ul water, 10ul 10x Second Starnd Buffer, 4ul 5mM dNTP Mix, 2ul DNA polymerase, 1ul RNaseH. Incubate for 2h at 16C. Purify the cNDA using column by adding 250ul cDNA Binding Buffer, spin at 10000g for 1min. Add 500ul Washing Buffer to column followed by spin at 10000g for 1 min. Spin dry the column. Add 12ul 50C water for disolving cDNA for 2min. Spin at 10000g for 1.5min. Repeat the elute step once. For labelling, add 12ul Biotin-NTP Mix, 4ul 10x T7 Reaction Buffer, 4ul 10x T7 Enzyme Mix to reaction. Incubate for 14h at 37C. Recover cRNA by columns. Add 60ul water and 350ul cRNA Binding Buffer to reaction. Transfer to column, spin and add 250ul 100% Ethanol and spin again. Add 650ul Washing Buffer, spin. Then spin dry the column. Add 100ul 50C water to disolve the cRNA.

extract_protocol: Total RNA extracted with Qiagen Rneasy Micro kit

tag: viral load

tag: age


title: BT-549

source_name: breast cell line

source_name: pooled breast cell line reference


title: Wild-type vs. mutant rep2

source_name: AG1-72 inflorescences from wt (Colombia ecotype); AG1-73 inflorescences from mutant ashh2-1/sdg8-1

source_name: AG1-72 inflorescences from mutant ashh2-1/sdg8-1; AG1-73 inflorescences from wt (Colombia ecotype)


title: BT-20


title: Monocyte_LVL_060


title: Monocyte_HVL_058

source_name: monocytes, HVL


title: Monocyte_LVL_059


title: Wild-type vs. mutant rep1

source_name: AG1-71 inflorescences from mutant ashh2-1/sdg8-1; AG1-80 inflorescences from wt (Colombia ecotype)

source_name: AG1-71 inflorescences from wt (Colombia ecotype); AG1-80 inflorescences from mutant ashh2-1/sdg8-1


title: BT-474


title: HS578T


title: Monocyte_LVL_057


title: Monocyte_C_061

source_name: monocytes, Control


title: Monocyte_HVL_056


title: Monocyte_LVL_049


title: Monocyte_LVL_050


title: Monocyte_C_044


title: Monocyte_LVL_066


title: Monocyte_HVL_054


title: Monocyte_LVL_051


title: Monocyte_HVL_053


title: Monocyte_C_063


title: Monocyte_LVL_067


title: Monocyte_LVL_048


title: Monocyte_LVL_043


title: Monocyte_C_042


title: Monocyte_C_031


title: Monocyte_HVL_039


title: Monocyte_C_035


title: Monocyte_C_037


title: Monocyte_HVL_040


title: Monocyte_HVL_041


title: Monocyte_LVL_046


title: Monocyte_HVL_036


title: Monocyte_C_029


title: Monocyte_HVL_026


title: Monocyte_C_027


title: Monocyte_LVL_030


title: Monocyte_HVL_034


title: Monocyte_HVL_022


title: Monocyte_LVL_021


title: Monocyte_LVL_028


title: Monocyte_C_038


title: Monocyte_HVL_025


title: Monocyte_HVL_017


title: Monocyte_HVL_016


title: Monocyte_LVL_032


title: Monocyte_LVL_007


title: Monocyte_LVL_013


title: Monocyte_HVL_014


title: RNAPII_WT_rep1

type: genomic

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

institute: Institut de recherches cliniques de Montréal (IRCM)

description: Biological replicate 1 of 3. RNAPII occupancy measured by the IP/Input ratio in WT cells.

hyb_protocol: Resuspend Cy5 labeled IP in 4ul of water and combine with corresponding Cy3 labeled sample. Mix to 450ul of the hybridization buffer for each slide (45ul 0.5M Mes NaOH (pH 6.9), 135ul Formamide, 58.5ul 5M NaCl, 45ul 5% N-Lauroylsarcosine (FLUKA), 1ul 250 ug/ml Salmon Sperm DNA, 10ul 8 mg/ml yeast tRNA, 5.4ul 0.5 M EDTA, 150.1ul mQH2O). Boil samples for 3 minutes in 100ºC heat block. Transfer to 40ºC heat block for another 10 minutes. Follow standard Agilent chamber hybridization protocols. Incubate overnight at 40C in hybridization oven. Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.    Stripping is done in 1 L of 5 mM Potassium phosphate buffer pH 6.6. 1. Use a 2L beaker, which can fit a slide rack. Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly while stirring with a stir bar until the liquid boils with big bubbles. Do not overboil it. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 2.5 ml of this 1M solution in 500 ml Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Axon GenePix 4000B scanner and the GenePix Pro extraction software were used. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0um. Adjust PMTs so that approximately 1-2% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 when looking at intensity values greater than or equal to 3000 on the Intensity / Frequence histogram. Images were quantified using Axon GenePix (version 6.1.0.4).

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.     Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.     Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness. Phosphate Wash Buffer (100mL): 0.5mL 1M KPO4, pH 8.5 15.25mL ddH2O 84.25mL 95% EtOH Solution will be cloudy upon mixing. Phosphate Elution Buffer (10mL): 0.04mL 1M KPO4, pH 8.5 9.96mL ddH2O 1M KPO4, pH 8.5 (10mL): 9.5mL 1M K2HPO4 0.5mL 1M KH2PO4 1M Sodium Carbonate Buffer, pH 9.0 (100mL): 10.8g Na2CO3 80mL ddH2O pH to 9.0 with concentrated HCl Adjust volume to 100mL with ddH2O DILUTE 1:10 WHEN USING! Solution will change composition over time. Use only if less than a month old. Reference: Drouin S., Robert F. Methods (in press).

growth_protocol: 50mL of YEP+2% Glucose were inoculated and incubated at 26ºC to OD600 0.8-1.0. The cells were crosslinked at the indicated time by adding the formaldehyde to a final concentration of 1 %. The cross-linking reaction is terminated by adding 2.5M glycine to a final concentration of 125mM.

extract_protocol: Crosslinked cells are washed twice with 50mL ice cold TBS and quickly frozen by immersion in liquid nitrogen. Subsequently, they are thawed on ice, resuspended in 400uL breaking buffer and 500uL of acid-washed glass beads are added to the mixture. Then, cells are lysed using bead-beater for 45min at 40c). The whole cell extract is mixed with 500ul of FA-lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% IGEPAL-CA630 0.1% Na-deoxycholate 1mM PMSF and centrifuged at 14000rpm for 1 minute. Then, the pellet is resuspended in 1 ml of FA-lysis buffer. This step is repeated. The resulting extract is sonicated (3X15sec) using Diagenode sonicator and subsequently centrifuged at 14000rpm for 30 minutes. The supernatant containing the sonicated chromatin is transferred to a new tube.    For the immunoprecipitation, 50ul of chromatin were added to 350ul of FA-lysis buffer. After adding the antibody at the below indicated concentration, the mixture is incubated for 2hr at 4 ºC on wheel. Remove 30 ul as Input DNA to a new tube , add 170ul of TE-SDS 1% buffer and Incubate at 650c Overnight. Subsequently 50ul of protein G sepharose beads are added and the incubation is continued for 1 hour. The beads are then washed twice with 1mL ice cold FA-lysis Buffer, twice with 1mL ice cold FA-lysis Buffer (500mM NaCl), twice with ice cold ChIP wash buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA) and once with ice cold TE. The bound proteins are eluted by incubating the beads at 65ºC for 20 minutes in 100ul of TE-SDS1%. To reverse the crosslinks the eluted material is incubated overnight at 65ºC.  The 8WG16 anti-CTD of Rpb1 antibody (Covance) was used with 5 ul per immunoprecipitation.    To clean-up the DNA, co-purified RNA is degraded by digestion in 200ul of TE and 10ug Rnase A incubated for 1hr at 370C.  The proteins are digested by adding 3.5ul of TE, 1.5ul of glycogen (20mg/ml) and 5ul Proteinase K (10mg/ml) and incubated for 6 hours to overnight at 37ºC. The samples are then extracted with 400uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA is then precipitated with 1/10 volume of 3M  Potassium acetate (pH5.2) and 3 volumes of ETOH 100% After an overnight incubated at -20ºC, the samples are centrifuged at maximum velocity for 20min at 4ºC. The supernatant is discarded and the pellet is resuspended in 100ul of water.

tag: strain

tag: genotype/variation

value: RNT1 wildtype

tag: antibody

value: 8WG16 anti-CTD of Rpb1 (Covance)


title: RNAPII_dRnt1_rep2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/Input ratio in rnt1Δ cells.

value: RNT1 mutant


title: Monocyte_C_015


title: RNAPII_WT_rep3

description: Biological replicate 3 of 3. RNAPII occupancy measured by the IP/Input ratio in WT cells.


title: RNAPII_dRnt1_rep1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/Input ratio in rnt1Δ cells.


title: Grd, 24_hours, rep2

city: Cambridge

first: Tal

last: Shay

state: MA

institute: Broad Institute

hyb_protocol: Standard Affymetrix protocols for mouse ht arrays

data_processing: RMA - All values lower than 20 were replaced by 20. All probesets whose values in all samples are equal or below 20 were removed.

source_name: Grd, 24_hours

growth_protocol: mouse primary BMDCs (Amit et al. 2009)

extract_protocol: miRNEASY  (QIAGEN) as recommended by manufactor

value: primary bone marrow dendritic cell


title: RNAPII_WT_rep2

description: Biological replicate 2 of 3. RNAPII occupancy measured by the IP/Input ratio in WT cells.


title: Control, 8_hours, rep1

scan_protocol: Standard Affymetrix protocols for mouse ht arrays

source_name: Control, 8_hours


title: Monocyte_HVL_009


title: Grd, 16_hours, rep2

source_name: Grd, 16_hours

label_protocol: Standard Affymetrix protocols for mouse ht arrays


title: Grd, 4_hours, rep2

source_name: Grd, 4_hours


title: Monocyte_LVL_005


title: Monocyte_HVL_012


title: Grd, 12_hours, rep2

source_name: Grd, 12_hours


title: Monocyte_LVL_002


title: Monocyte_HVL_020


title: Monocyte_LVL_006


title: Monocyte_HVL_003


title: Grd, 2_hours, rep2

source_name: Grd, 2_hours


title: Grd, 8_hours, rep2

source_name: Grd, 8_hours


title: Monocyte_LVL_004


title: Control, 1_hours, rep1

source_name: Control, 1_hours


title: Grd, 6_hours, rep2

source_name: Grd, 6_hours


title: Grd, 1_hours, rep2

source_name: Grd, 1_hours


title: Grd, 0.5_hours, rep2

source_name: Grd, 0.5_hours


title: Control, 12_hours, rep1

source_name: Control, 12_hours


title: Grd, 24_hours, rep1


title: Control, 4_hours, rep1

source_name: Control, 4_hours


title: Control, 0_hours, rep1

source_name: Control, 0_hours


title: Grd, 2_hours, rep1


title: Monocyte_HVL_019

source_name: monocytes, HVL


title: Grd, 8_hours, rep1


title: Monocyte_HVL_008


title: Grd, 1_hours, rep1


title: Grd, 6_hours, rep1


title: Grd, 4_hours, rep1


title: Grd, 12_hours, rep1


title: Cpg, 24_hours, rep1

source_name: Cpg, 24_hours


title: Grd, 16_hours, rep1


title: Pam, 0.5_hours, rep2

source_name: Pam, 0.5_hours


title: Cpg, 16_hours, rep1

source_name: Cpg, 16_hours


title: Pam, 16_hours, rep2

source_name: Pam, 16_hours


title: Pam, 12_hours, rep2

source_name: Pam, 12_hours


title: Pam, 24_hours, rep2

source_name: Pam, 24_hours


title: Pam, 1_hours, rep2

source_name: Pam, 1_hours


title: Grd, 0.5_hours, rep1


title: Pam, 4_hours, rep2

source_name: Pam, 4_hours


title: Pam, 8_hours, rep2

source_name: Pam, 8_hours


title: Pam, 2_hours, rep2

source_name: Pam, 2_hours


title: Control, 6_hours, rep1

source_name: Control, 6_hours


title: Pam, 6_hours, rep2

source_name: Pam, 6_hours


title: Pam, 16_hours, rep1


title: Cpg, 12_hours, rep1

source_name: Cpg, 12_hours


title: Pam, 6_hours, rep1


title: Pam, 8_hours, rep1


title: Control, 24_hours, rep1

source_name: Control, 24_hours


title: Control, 2_hours, rep1

source_name: Control, 2_hours


title: Pam, 12_hours, rep1


title: Pam, 24_hours, rep1


title: Pam, 2_hours, rep1


title: Cpg, 4_hours, rep2

source_name: Cpg, 4_hours


title: Pam, 4_hours, rep1


title: MB231 hypoxia (0.5%O2) treatment 12h, biological rep2

city: Boston

first: Xiaobo

last: Xia

address: 44 Binney St, Mayer 649

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Accordinging to standard Affymetrix protocol at DFCI Microarray Core.

data_processing: We used GcRMA module on Bioconductor with most updated custom CDF (CDF: Hs133P_Hs_REFSEQ_10) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm) to normalize the microarrays, and MAS5 to get present/absent calls. LIMMA was used to identify probe sets whose expression levels were significantly changed after 4, 8, or 12 hours of hypoxia relative to the normoxic signal. The MAS5 present/absent calls were assigned values of absent=0, marginal=0.5, or present=1. For each probe set, the sum of triplicate samples was partitioned into “present” if sum≥2, and “absent” if sum<2.

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

treatment_protocol: HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells were collected under normoxic conditions (~19% O2, 0 hours) and after 4, 8 and 12 hours of hypoxia treatment (0.5% O2).

value: MDA-MB231 breast cancer

tag: stress

value: hypoxia

tag: time


title: Cpg, 6_hours, rep2

source_name: Cpg, 6_hours


title: MB231 hypoxia (0.5%O2) treatment 8h, biological rep2

scan_protocol: Accordinging to standard Affymetrix protocol at DFCI Microarray Core.


title: Pam, 1_hours, rep1


title: Pic, 12_hours, rep2

source_name: Pic, 12_hours


title: MB231 hypoxia (0.5%O2) treatment 12h, biological rep1

label_protocol: Accordinging to standard Affymetrix protocol at DFCI Microarray Core.


title: Pam, 0.5_hours, rep1

source_name: Pam, 0.5_hours


title: Pic, 24_hours, rep2

source_name: Pic, 24_hours


title: MB231 hypoxia (0.5%O2) treatment 12h, biological rep3


title: MB231 hypoxia (0.5%O2) treatment 8h, biological rep1


title: Cpg, 8_hours, rep2

source_name: Cpg, 8_hours


title: MB231 hypoxia (0.5%O2) treatment 4h, biological rep1


title: Pic, 8_hours, rep2

source_name: Pic, 8_hours


title: MB231 hypoxia (0.5%O2) treatment 4h, biological rep2


title: MB231 hypoxia (0.5%O2) treatment 0h, biological rep3

value: normoxia

value: control


title: MB231 hypoxia (0.5%O2) treatment 8h, biological rep3


title: MB231 hypoxia (0.5%O2) treatment 0h, biological rep1


title: MB231 hypoxia (0.5%O2) treatment 4h, biological rep3


title: Monocyte_HVL_001

source_name: monocytes, HVL


title: Pic, 6_hours, rep2

source_name: Pic, 6_hours


title: Pic, 2_hours, rep2

source_name: Pic, 2_hours


title: Pic, 4_hours, rep2

source_name: Pic, 4_hours


title: Pic, 1_hours, rep2

source_name: Pic, 1_hours


title: U87 hypoxia (0.5%O2) treatment 12h, biological rep3

value: U87 glioma


title: Pic, 16_hours, rep2

source_name: Pic, 16_hours


title: MB231 hypoxia (0.5%O2) treatment 0h, biological rep2


title: U87 hypoxia (0.5%O2) treatment 12h, biological rep2


title: U87 hypoxia (0.5%O2) treatment 12h, biological rep1


title: Pic, 0.5_hours, rep2

source_name: Pic, 0.5_hours


title: Cpg, 8_hours, rep1


title: U87 hypoxia (0.5%O2) treatment 8h, biological rep3


title: U87 hypoxia (0.5%O2) treatment 8h, biological rep2


title: Pic, 16_hours, rep1


title: Cpg, 6_hours, rep1


title: Pic, 24_hours, rep1


title: U87 hypoxia (0.5%O2) treatment 4h, biological rep3


title: Cpg, 4_hours, rep1


title: Pic, 12_hours, rep1


title: U87 hypoxia (0.5%O2) treatment 4h, biological rep1


title: U87 hypoxia (0.5%O2) treatment 4h, biological rep2


title: Pic, 8_hours, rep1


title: U87 hypoxia (0.5%O2) treatment 0h, biological rep1


title: U87 hypoxia (0.5%O2) treatment 0h, biological rep3


title: Pic, 4_hours, rep1


title: Pic, 2_hours, rep1


title: U87 hypoxia (0.5%O2) treatment 0h, biological rep2


title: U87 hypoxia (0.5%O2) treatment 8h, biological rep1


title: Pic, 6_hours, rep1


title: Cpg, 2_hours, rep2

source_name: Cpg, 2_hours


title: HepG2 hypoxia (0.5%O2) treatment 12h, biological rep1

value: HepG2 hepatoma


title: HepG2 hypoxia (0.5%O2) treatment 12h, biological rep2


title: HepG2 hypoxia (0.5%O2) treatment 12h, biological rep3


title: Cpg, 1_hours, rep2

source_name: Cpg, 1_hours


title: HepG2 hypoxia (0.5%O2) treatment 8h, biological rep3


title: HepG2 hypoxia (0.5%O2) treatment 8h, biological rep2


title: Cpg, 0.5_hours, rep2

source_name: Cpg, 0.5_hours


title: HepG2 hypoxia (0.5%O2) treatment 8h, biological rep1


title: Pic, 0.5_hours, rep1


title: HepG2 hypoxia (0.5%O2) treatment 4h, biological rep1


title: Lps, 16_hours, rep2

source_name: Lps, 16_hours


title: Lps, 8_hours, rep2

source_name: Lps, 8_hours


title: Lps, 1_hours, rep2

source_name: Lps, 1_hours


title: HepG2 hypoxia (0.5%O2) treatment 0h, biological rep2


title: HepG2 hypoxia (0.5%O2) treatment 4h, biological rep3


title: Cpg, 12_hours, rep2

source_name: Cpg, 12_hours


title: HepG2-H3K4me3 ChIP-chip

description:
HepG2 H3K4me3 ChIP Normoxia Biological Rep 1-3 v.s. Inputs, Affymetrix Human Promoter 1.0R Array
test CEL file: HepG2_K4C1.CEL
test CEL file: HepG2_K4C2.CEL
test CEL file: HepG2_K4C3.CEL
control CEL file: HepG2_NI1.CEL
control CEL file: HepG2_NI2.CEL
control CEL file: HepG2_NI3.CEL

hyb_protocol: Approximately 3ug of DNA was hybridzed per array.

scan_protocol: Both hybridization and scan were performed by Microarray Core at Dana-Farber Cancer Institute.

data_processing: The Model-based Analysis of Tiling-array (MAT) algorithm was used to identify regions enriched by ChIP-chip (ChIP hits). For the U87 HIF-1 ChIP, the triplicate hypoxic U87 HIF-1 ChIP samples were compared directly to triplicate normoxic samples; MAT was run with parameters of bandwidth = 200, maximum gap = 400, minimum probes = 10, and p-value cutoff = 1x10-5. For H3K4me3, H3K27me3, and RNA Pol II ChIP, normoxic ChIP samples were compared to matched input samples; the MAT parameters were increased to account for broader peaks: bandwidth = 500, maximum gap = 400, minimum probes = 20, and p-value cutoff = 1x10-5. The MAT library and mapping files were based on the March 2006 Human Genome Assembly (HG18). Hits flagged by MAT as mapping to repeat regions were excluded from consideration in all cases.

source_name: HepG2 H3K4me3 ChIP Normoxia

label_protocol: Amplified ChIP and Input samples were fragmented with DNase to 50~100bp size and labeled using the Terminal transferase (TdT, Promega) to add biotinylated-ddATP to the ends of the fragments

extract_protocol: Cells were fixed with 1% formaldehyde (37°C, 10 min) and lysed with 0.5% SDS lysis buffer. Chromatin was then sonicated to 500-1000bp fragments and immunoprecipitation carried out with HIF-1α pAb (Novus Biologicals, NB 100-134). RNA polymerase II and H3K4me3 ChIP were carried out using normoxic U87 or HepG2 cell samples with RNA polymerase II mAb (Abcam, ab5408) and H3K4me3 pAb (Abcam, ab8580). A small aliquot for each biological sample are reserved for an input control. Both Chiped DNA and Input samples were amplified by LM-PCR.

treatment_protocol: U87 cells were cultured for 4 hours under normoxic or hypoxic (0.5%O2) conditions.

value: H3K4me3 pAb (Abcam, ab8580)

value: HepG2 cells

value: normoxic (ambient) conditions

source_name: HepG2 H3K4me3 input Normoxia


title: U87-RNApolII ChIP-chip

description:
U87 RNA polII ChIP Normoxia Biological Rep 1-3 v.s. Inputs, Affymetrix Human Promoter 1.0R Array
test CEL file: U87_PolII_C1.CEL
test CEL file: U87_PolII_C2.CEL
test CEL file: U87_PolII_C3.CEL
control CEL file: U87-NI1.CEL
control CEL file: U87-NI2.CEL
control CEL file: U87-NI3.CEL

source_name: U87 RNA polII ChIP Normoxia

value: RNA polymerase II mAb (Abcam, ab5408)

value: U87 cells

source_name: U87 RNA polII input Normoxia


title: HepG2-RNApolII ChIP-chip

description:
HepG2 RNA polII ChIP Normoxia Biological Rep 1-3 v.s. Inputs, Affymetrix Human Promoter 1.0R Array
test CEL file: HepG2_PolII_C1.CEL
test CEL file: HepG2_PolII_C2.CEL
test CEL file: HepG2_PolII_C3.CEL
control CEL file: HepG2_NI1.CEL
control CEL file: HepG2_NI2.CEL
control CEL file: HepG2_NI3.CEL

source_name: HepG2 RNA polII ChIP Normoxia

source_name: HepG2 RNA polII input Normoxia


title: Lps, 24_hours, rep2

source_name: Lps, 24_hours


title: Lps, 0.5_hours, rep2

source_name: Lps, 0.5_hours


title: HepG2 hypoxia (0.5%O2) treatment 4h, biological rep2


title: Cpg, 2_hours, rep1


title: HepG2 hypoxia (0.5%O2) treatment 0h, biological rep1


title: Lps, 24_hours, rep1


title: HepG2 hypoxia (0.5%O2) treatment 0h, biological rep3


title: Lps, 6_hours, rep2

source_name: Lps, 6_hours


title: Pic, 1_hours, rep1

source_name: Pic, 1_hours


title: U87-H3K4me3 ChIP-chip

description:
U87 H3K4me3 ChIP Normoxia Biological Rep 1-3 v.s. Inputs, Affymetrix Human Promoter 1.0R Array
test CEL file: U87_K4C1.CEL
test CEL file: U87_K4C2.CEL
test CEL file: U87_K4C3.CEL
control CEL file: U87-NI1.CEL
control CEL file: U87-NI2.CEL
control CEL file: U87-NI3.CEL

source_name: U87 H3K4me3 ChIP Normoxia

source_name: U87 H3K4me3 input Normoxia


title: Lps, 4_hours, rep2

source_name: Lps, 4_hours


title: Lps, 8_hours, rep1


title: Lps, 6_hours, rep1


title: Lps, 12_hours, rep1

source_name: Lps, 12_hours


title: Lps, 12_hours, rep2


title: Cpg, 1_hours, rep1

source_name: Cpg, 1_hours


title: Cpg, 0.5_hours, rep1

source_name: Cpg, 0.5_hours


title: Lps, 4_hours, rep1


title: Lps, 16_hours, rep1

source_name: Lps, 16_hours


title: U87-HIF1 ChIP-chip

description:
U87 HIF-1 ChIP Hypoxia Biological Rep 1-3 v.s. Normoxia Biological Rep 1-3, Affymetrix Human Promoter 1.0R Array
test CEL file: U87-Hy-HIFC1.CEL
test CEL file: U87-Hy-HIFC2.CEL
test CEL file: U87-Hy-HIFC3.CEL
control CEL file: U87-N-HIFC1.CEL
control CEL file: U87-N-HIFC2.CEL
control CEL file: U87-N-HIFC3.CEL

source_name: U87 HIF-1 ChIP Hypoxia

value: HIF-1α pAb (Novus Biologicals, NB 100-134)

source_name: U87 HIF-1 ChIP Normoxia


title: Lps, 1_hours, rep1

source_name: Lps, 1_hours


title: Lps, 2_hours, rep1

source_name: Lps, 2_hours


title: Lps, 2_hours, rep2