title: THP1, Untreated, biological rep 3

status: Public on Feb 28 2010

city: Newark

first: Richard

last: Pine

state: NJ

address: 225 Warren St

department: PHRI/Medicine

institute: UMDNJ-NJMS

description: Gene expression of untreated human THP-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip, Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner G3000.

data_processing: The data were analyzed using the affy package of Bioconductor with the following parameters selected: Background correction: MAS5, PM probe correction: MAS5; expression summary: medianpolish (RMA); normalization: scaled to average GAPDH probeset intensity and Loess normalized.

source_name: Human THP-1, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5/10? ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human THP-1 cells were grown and treated with phobol-12-myristate-13-acetate (PMA) for 1 day to induce differentiation to a macrophage-like state.

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

treatment_protocol: In multiple experiments, THP-1 cells were exposed to each of the following four conditions: not treated, IFN-g treated , M.tb. Infected and M.tb. Infected then IFN-g treated.

value: THP-1 macrophage


title: THP1, TB infected, IFN-g treated, biological rep 4

type: RNA

country: USA

description: Gene expression data from human THP-1 cells infected with M.tb. TN913 then stimulated with IFN-g

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human THP-1, TB infected, 72 hr., IFN-g treated, 2 hr.

tag: cell type


title: THP1, TB infected, biological rep 3

description: Gene expression data from human THP-1 cells infected with M.tb. TN913

source_name: Human THP-1, TB infected, 72 hr.


title: THP1, TB infected, IFN-g treated, biological rep 2


title: THP1, Untreated, biological rep 2


title: THP1, Untreated, biological rep 4


title: Stimulated (H2O2) vs Control 15 min_repl1

status: Public on Mar 01 2010

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

description: Technical replicate 1 of 3 at 15 min

hyb_protocol: Samples were hybridised to the microarrays at 42 ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in 0.1×SSC/0.1% SDS for 5 min at 42 ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.) Images were quantified using the GenePix v6.1 software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. J-Express Pro v2.7 (Dysvik and Jonassen 2001) software was used.

organism: Aliivibrio salmonicida LFI1238

source_name: Aliivibrio salmonicida LFI1238 stimulated (H2O2)

label_protocol: cDNA was generated and labelled with Cy3 and Cy5 by using 15 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).

extract_protocol: Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)

tag: sample type

value: Stimulated (H2O2) LFI1238 after 15 minutes

source_name: Aliivibrio salmonicida LFI1238 control

value: Control LFI1238 after 15 minutes


title: THP1, TB infected, biological rep 1


title: THP1, TB infected, biological rep 2


title: THP1, TB infected, IFN-g treated, biological rep 3


title: THP1, IFN-g treated, biological rep 1

description: Gene expression data from human THP-1 cells stimulated with IFN-g

source_name: Human THP-1, IFN-g treated, 2 hr.


title: THP1, Untreated, biological rep 1


title: THP1, TB infected, IFN-g treated, biological rep 1


title: THP1, TB infected, biological rep 4


title: THP1, IFN-g treated, biological rep 3


title: GO (control)

city: Houston

first: Filemon

last: Tan

state: TX

address: 6431 Fannin

department: Internal Medicine-Rheumatology

institute: UT Houston Medical School

description: Illumina humanRef-8

hyb_protocol: Illumina standard protocol

scan_protocol: Data accquired using Illumina Beadstation 500

data_processing: Background subtraction; rank invariant normalization

label: Biotin/Strepavidin Cy-3

source_name: Human umbilical vein endothelial cells

label_protocol: Illumina standard protocol

growth_protocol: Cells were cultured on collagen-coated 6-well plate in EBM medium supplemented with 10% fetal bovine serum, endothelial cell growth supplement mix at 37C under 5% CO2 in air

extract_protocol: RNA was extracted using Tri Reagent protocol and then was purified with the RNeasy Mini-kit (Qiagen)

value: HUVEC


title: THP1, IFN-g treated, biological rep 4


title: THP1, IFN-g treated, biological rep 2


title: day 2 male adult moth-1

status: Public on Feb 21 2010

city: Beibei

first: Qingyou

last: Xia

state: Chongqing

address: Tiansheng Road

department: College of Biotechnology

country: China

institute: Southwest University

hyb_protocol: The air-dried total RNAs were dissolved in 16 L hybridization liquid (15% formamide; 0.2% SDS; 3×SSC; 50×Denhardt's), hybridized under 42 ℃ over night. Subsequently, the array blocks were washed once under 42 ℃ for 4 min in liquid containing 0.2% SDS and 2 SSC, and once under room temperature for 4 min in 0.2×SSC. The slides were then spin-dried before scanning.

scan_protocol: The spin-dried slides were scanned using LuxScan 10K, the dual channel LASER-BASED SCANNERS（CapitalBio）.

data_processing: The spin-dried slides were scanned using LuxScan 10K, the dual channel LASER-BASED SCANNERS（CapitalBio), leading to rainbowlike scanograms (raw data file 1); The image signals were transformed into digital signals by using of the Image Analysis Software, GenePix Pro 4.0 (Axon Instruments), resulting in the GPR files (raw data file 2); 6 processed files were successively produced from the GPR files by runing a perl program, Nozip&Y3_gpr_parser_v2.2.pl. (1) Original_data catalog deposits original tables  (raw data file 3) containing the original information of GPR files, and are presented as 8 columns from left to right, Block, Column,Row，Name，ID，B532 SD， % > B532+2SD，Sum of Medians.(2) Filter_data catalog contains the *_filter tables (raw data file 4), which screen and define the original signals based on Original_data (raw data file 3). In details, a value 10 was assigned to Sum of Median≤0. Sum of Median＜300 was defined as ‘weak point'. Calculate the coefficien of variation (CV) of the triplicate signals for each miRNA (probe) on one block, leading to the additional CV column based on the original_data (raw data file 3). (3) The *_outlier_filtered tables (raw data file 5) are deposited under outlier_filtered_data catalog. These tables judge the CV value in the *_filter tables (raw data file 4) and define the discrete points when the CV is higher than 0.3, thus leading to one additional ‘outlier_filtered’column based on *_filter tables. (4) The calibrat_data catalog deposits *_calibrat tables (raw data file 6)，which have one more column, ‘Calibrat' (the calibrated value), on the base of the *_outlier_filtered tables. In principle, the global mean is common to the same microarray in one set of test. Calculate the global mean of valid signals on each slide and the average (AVG) of global mean of one set, then calculate the the scale of factor (SF) of each slide. Subsquently, calibrate all signals on each slide according to the scale factor. Please note that zip and Y3 are not included in calculating the valid signals. (5) Convert_data catalog deposits the *_convert tables (raw data file 7)，which extract the fourth column‘Name' and the eleventh column‘calibrat' of *_calibrat tables (raw data file 6). The extracted columns are then transpositioned from repeat-Y to repeat-X. After transpostion, calculate the average (AVG) of the calibrated repeat signals of each miRNA (probe) and count the repeats for each probe, resulting in the columns in order from left to right in these tables, including Name, repeat count, AVG and the signal value of each point (begining from column 4 of the tables in raw data file 6). (6) log2_data catalog deposits the *_log2 tables (raw data file 8), which comprise the log2-transformed data of *_convert tables (raw data file 7) except the first two columns. In all, 59 unique developmental timepoints were inspected in this study with 118 array slides. For the convenience of further analysis, the average (AVG) of the calibrated repeat signals of each probe is then extracted and merged into one common file by our perl program, ‘mergeTabs'. However, in the published paper, these merged files are separately presented in six groups only for the sake of better comparision and description. The internal and outernal controls in each merged file are deleted before cluster analysis as described in the paper.

organism: Bombyx mori

source_name: whole silkworm body

label_protocol: 15 µg total RNAs of samples were labeled with cy3 using the method based on T4 RNA ligase （Thomson,J.M., Parker,J., Perou,C.M., Hammond,S.M. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat.Methods 1, 47-53.）.The labeled miRNAs were then precipitated with ethanol and air-dried for microarray test.

growth_protocol: Female moths of the domesticated silkworm (B. mori), DaZao, were allowed to lay eggs for 4 h at 25°C. Developing eggs were incubated at 25°C from oviposition until hatching, the first day being the day of oviposition. When developing eggs were incubated at 25°C, head pigmentation occurred on day 7 (6×24 h after oviposition), body pigmentation appeared on day 9 (8×24 h after oviposition), and more than 95% of eggs hatched on the tenth day. To prevent entry into diapause, fertilized eggs were treated with a hydrochloric acid solution (4 N) at 46 ℃ for 6 minutes and then rinsed thoroughly with water. After hatching, silkworm larvae were reared on mulberry leaves at 25°C and 85% H.R. under a 12 h light/12 h dark photoperiod, and harvested at the desired developmental stages. To obtain populations of B. mori at various developmental stages, animals were synchronized after oviposition by means of cold storage and acid treatment, keeping the diapause eggs at 4°C for at least three months, followed by 5 min of treatment with hydrochloric acid solution at 46°C. Moreover, developmental landmarks, including hatching, larval molting, mounting, spinning, pupariation and eclosion, were employed for more precise staging.

extract_protocol: 1. Isolation of total RNAs  Total RNAs of all silkworm samples were extracted using Trizol-based one step method, and were subsequently condensed with isopropanol, quantified with spectrophotometer and finally analyzed by 1% denatured agrose gel containing formaldehyde.  2. Separation of miRNA  50-100.0 µg total RNA was used for separation of total RNAs using Ambion's miRNA Isolation Kit (Cat#.1560).

treatment_protocol: All biological materials were kept in the liquid nitrogen untill use.

tag: developmental stage

value: adult stage

tag: gender

value: male


title: day 2 male adult moth-2


title: 0-hour male adult moth-1


title: 0-hour male adult moth-2


title: day 8 male pupa-1

value: pupal stage


title: day 6 male pupa-1


title: day 8 male pupa-2


title: day 5 male pupa-2


title: day 4 male pupa-2


title: day 5 male pupa-1


title: day 4 male pupa-1


title: day 6 male pupa-2


title: day 7 male pupa-1


title: Control for chlorhexidine DMSO 6hrs 3

city: philadelphia

first: Ihab

last: Younis

state: PA

address: 415 Curie Blvd

department: Biochemistry and Biophysics

institute: University of Pennsylvania

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Hybridization cocktail including 5.5 ug of fragmented, end-labeled ssDNA was applied to GeneChip Human Exon 1.0 ST arrays. Hybridization was performed using F450-001 fluidics wash and stain script on the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software (GCOS)

data_processing: Probeset intensities from the CEL Files were calculated using the RMA algorithm with default settings in Partek Genomic Suite 6.4, using the core probe sets as defined by Affymetrix.

source_name: HeLa PV

label_protocol: Biotinylated sense strand DNA targets were prepared using Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay according to manufacturer's recommendations. Total RNA (1ug) was used as input for rRNA reduction with Invitrogen RiboMinus Transcriptome Isolation Kit. The total resulting volume was used for second round of amplification.

growth_protocol: HeLa cells were grown in DMEM + 10% FBS in humdified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from treated cells using RNeasy kit according to manufacturer's recommendation.

treatment_protocol: Cells were treated for 6 hours with compounds disolved in DMSO. Final DMSO concentration did not exceed 1%.

tag: cell line

value: HeLa

tag: treatment group

value: Control for chlorhexidine DMSO 6hrs


title: Treated Chlorhexidine 6hrs 3

value: Chlorhexidine 6hrs


title: Treated Chlorhexidine 6hrs 2


title: day 7 male pupa-2


title: Control for chlorhexidine DMSO 6hrs 2


title: day 3 male pupa-2


title: day 2 male pupa-2


title: day 3 male pupa-1


title: Treated Chlorhexidine 6hrs 1


title: Control for chlorhexidine DMSO 6hrs 1


title: day 2 male pupa-1


title: 24-hour male pupa-2


title: 0-hour male pupa-2


title: 12-hour male pupa-1


title: 12-hour male pupa-2


title: 24-hour male pupa-1


title: 0-hour male pupa-1


title: 0-hour male prepupa-2

value: prepupa


title: 0-hour spinning male larva-2

value: concoon spinning


title: day 2 egg-laid adult moth-2

value: female


title: day 2 egg-laid adult moth-1


title: 0-hour spinning male larva-1


title: Treated Flunarizine 6hrs 2

value: Flunarizine 6hrs


title: Treated Flunarizine 6hrs 3


title: Control DMSO 6hrs 1

value: Control DMSO 6hrs


title: Treated Flunarizine 6hrs 1


title: Control DMSO 6hrs 3


title: Control DMSO 6hrs 2


title: Treated Clotrimazole 6hrs 1

value: Clotrimazole 6hrs


title: 0-hour male prepupa-1


title: 0-hour egg-removed adult moth-1


title: Treated Clotrimazole 6hrs 2


title: day 8 female pupa-1


title: day 7 female pupa-1


title: 0-hour egg-bearing adult moth-2


title: day 7 female pupa-2


title: 0-hour egg-bearing adult moth-1


title: day 6 female pupa-1


title: Treated Clotrimazole 6hrs 3


title: day 8 female pupa-2


title: 0-hour egg-removed adult moth-2


title: day 5 female pupa-2


title: day 5 female pupa-1


title: day 4 female pupa-2


title: day 4 female pupa-1


title: day 3 female pupa-1


title: day 6 female pupa-2


title: day 3 female pupa-2


title: day 2 female pupa-2


title: 24-hour female pupa-2


title: 24-hour female pupa-1


title: 0-hour female pupa-2


title: 0-hour female pupa-1


title: 0-hour female prepupa-1


title: 0-hour female prepupa-2


title: 12-hour female pupa-2


title: female fifth-instar day 7 larva-2

value: Late larval stage


title: 0-hour spinning female larva-1


title: day 2 female pupa-1


title: female fifth-instar day 7 larva-1


title: male fifth-instar day 5 larva-2


title: male fifth-instar day 7 larva-2


title: female fifth-instar day 5 larva-1


title: male fifth-instar day 3 larva-2


title: female fifth-instar day 3 larva-2


title: male fifth-instar day 3 larva-1


title: female fifth-instar day 3 larva-1


title: female fifth-instar day 5 larva-2


title: male fifth-instar day 5 larva-1


title: 12-hour female pupa-1


title: 0-hour spinning female larva-2


title: fifth-instar day 2 larva-1

value: mixture


title: early 5th instar larva-2


title: late 4th molt larva-2


title: early 5th instar larva-1


title: male fifth-instar day 7 larva-1


title: late 4th molt larva-1


title: early 4th molt larva-1


title: early 4th molt larva-2


title: late 4th instar larva-1


title: fifth-instar day 2 larva-2


title: early 4th instar larva-2


title: early 4th instar larva-1


title: early 3rd instar larva-2

value: Early larval stage


title: late 3rd instar larva-2


title: late 3rd instar larva-1


title: late 3rd molt larva-2


title: early 3rd molt larva-1


title: early 3rd molt larva-2


title: late 3rd molt larva-1


title: late 2nd molt larva-1


title: early 2nd instar larva-2


title: late 2nd instar larva-1


title: late 2nd instar larva-2


title: late 2nd molt larva-2


title: late 4th instar larva-2


title: late 1st molt larva-2


title: late 1st instar larva-2


title: late 1st instar larva-1


title: early 2nd instar larva-1


title: early 1st instar larva-2

value: Embryo development


title: early 1st instar larva-1


title: day 9 embryo-2


title: day 3 embryo-2


title: early 3rd instar larva-1


title: day 9 embryo-1


title: day 6 embryo-1


title: day 6 embryo-2


title: late 1st molt larva-1


title: day 2 embryo-2


title: 24-hour embryo-2


title: day 2 embryo-1


title: day 3 embryo-1


title: 24-hour embryo-1


title: body wall of day 1 pupae_BW_1dPu-b, group 2

description: Group 2. Four tissues during metamorphosis

hyb_protocol: The air-dried small RNAs were dissolved in 16 L hybridization liquid (15% formamide; 0.2% SDS; 3×SSC; 50×Denhardt's), hybridized under 42 ℃ over night. Subsequently, the array blocks were washed once under 42 ℃ for 4 min in liquid containing 0.2% SDS and 2 SSC, and once under room temperature for 4 min in 0.2×SSC. The slides were then spin-dried before scanning.

data_processing: The spin-dried slides were scanned using LuxScan 10K, the dual channel LASER-BASED SCANNERS (CapitalBio), leading to rainbowlike scanograms (raw data file 1); The image signals were transformed into digital signals by using of the Image Analysis Software, GenePix Pro 4.0 (Axon Instruments), resulting in the GPR files (raw data file 2); 6 processed files were successively produced from the GPR files by runing a perl program, Nozip&Y3_gpr_parser_v2.2.pl. (1) Original_data catalog deposits original tables  (raw data file 3) containing the original information of GPR files, and are presented as 8 columns from left to right, Block, Column,Row，Name，ID，B532 SD， % > B532+2SD，Sum of Medians.(2) Filter_data catalog contains the *_filter tables (raw data file 4), which screen and define the original signals based on Original_data (raw data file 3). In details, a value 10 was assigned to Sum of Median≤0. Sum of Median＜300 was defined as ‘weak point'. Calculate the coefficien of variation (CV) of the triplicate signals for each miRNA (probe) on one block, leading to the additional CV column based on the original_data (raw data file 3). (3) The *_outlier_filtered tables (raw data file 5) are deposited under outlier_filtered_data catalog. These tables judge the CV value in the *_filter tables (raw data file 4) and define the discrete points when the CV is higher than 0.3, thus leading to one additional ‘outlier_filtered’column based on *_filter tables. (4) The calibrat_data catalog deposits *_calibrat tables (raw data file 6)，which have one more column, ‘Calibrat' (the calibrated value), on the base of the *_outlier_filtered tables. In principle, the global mean is common to the same microarray in one set of test. Calculate the global mean of valid signals on each slide and the average (AVG) of global mean of one set, then calculate the the scale of factor (SF) of each slide. Subsquently, calibrate all signals on each slide according to the scale factor. Please note that zip and Y3 are not included in calculating the valid signals. (5) Convert_data catalog deposits the *_convert tables (raw data file 7)，which extract the fourth column‘Name' and the eleventh column‘calibrat' of *_calibrat tables (raw data file 6). The extracted columns are then transpositioned from repeat-Y to repeat-X. After transpostion, calculate the average (AVG) of the calibrated repeat signals of each miRNA (probe) and count the repeats for each probe, resulting in the columns in order from left to right in these tables, including Name, repeat count, AVG and the signal value of each point (begining from column 4 of the tables in raw data file 6). (6) log2_data catalog deposits the *_log2 tables (raw data file 8), which comprise the log2-transformed data of *_convert tables (raw data file 7) except the first two columns. For further analysis, the average (AVG) of the calibrated repeat signals of each probe is then extracted and merged into one common file by our perl program, ‘mergeTabs'. The merged files of the six test groups are separately presented here as the Matrix tables. The internal and external controls in each merged file are deleted only for the convenience of cluster analysis as described in the paper.

source_name: day 1 pupae

label_protocol: 15 µg small RNAs of samples were labeled with cy3 using the method based on T4 RNA ligase （Thomson,J.M., Parker,J., Perou,C.M., Hammond,S.M. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat.Methods 1, 47-53.）.The labeled miRNAs were then precipitated with ethanol and air-dried for microarray test.

growth_protocol: A bivoltine strain (DaZao) of B.mori was used in this study. After hatching, larvae were reared on mulberry leaves at 25-27°C and 85% H.R. under a 12 h light/12 h dark photoperiod and harvested at the specific developmental stages.

extract_protocol: 1. Isolation of total RNAs  Total RNAs of all silkworm samples were extracted using Trizol-based one step method, and were subsequently condensed with isopropanol, quantified with spectrophotometer and finally analyzed by 1% denatured agrose gel containing formaldehyde.  2. Separation of miRNA  50-100.0 µg total RNA was used for separation of small RNAs using Ambion's miRNA Isolation Kit (Cat#.1560).

tag: tissue

value: body wall


title: 0 hour embryo-2


title: 12-hour embryo-1


title: 6-hour embryo-2


title: 0 hour embryo-1


title: 12-hour embryo-2


title: 6-hour embryo-1


title: fat body of day 2 pupa_FB_1dPu-b, group 2

value: fat body


title: fat body of day 2 pupa_FB_1dPu-a, group 2


title: body wall of day 1 pupae_BW_1dPu-a, group 2


title: fat body of 0-hour prepupae_FB_0hPPu-b, group 2

source_name: 0-hour prepupae


title: fat body of 0-hour prepupae_FB_0hPPu-a, group 2


title: silk gland of 0-hour prepupae_SG_0hPPu-b, group 2

value: silk gland


title: midgut of 0-hour prepupae_MG_0hPPu-a, group 2

value: midgut


title: midgut of 0-hour prepupae_MG_0hPPu-b, group 2


title: body wall of 0-hour prepupae_BW_0hPPu-b, group 2


title: body wall of 0-hour prepupae_BW_0hPPu-a, group 2


title: midgut of 0-hour spinning larvae_MG_0hSp-a, group 2

source_name: 0-hour spinning larvae


title: silk gland of 0-hour prepupae_SG_0hPPu-a, group 2


title: midgut of 0-hour spinning larvae_MG_0hSp-b, group 2


title: fat body of 0-hour spinning larvae_FB_0hSp-a, group 2


title: fat body of fifth instar day 7 larva_FB_7dIL5-a, group 2

source_name: fifth instar day 7 larvae


title: silk gland of 0-hour spinning larvae_SG_0hSp-a, group 2


title: body wall of 0-hour spinning larvae_BW_0hSp-b, group 2


title: silk gland of fifth instar day 7 larva_SG_7dIL5-b, group 2


title: fat body of fifth instar day 7 larva_FB_7dIL5-b, group 2


title: body wall of 0-hour spinning larvae_BW_0hSp-a, group 2


title: midgut of fifth instar day 7 larva_MG_7dIL5-a, group 2


title: silk gland of 0-hour spinning larvae_SG_0hSp-b, group 2


title: midgut of fifth instar day 7 larva_MG_7dIL5-b, group 2


title: fat body of 0-hour spinning larvae_FB_0hSp-b, group 2


title: malpighian tubule of male silkworm_MT(m)-b, group 1

description: Group 1. Tissues of fifth instar day 3 larvae

data_processing: The processed files were produced in order as described in Group 2 only except that all net signals in Group 1 were calibrated on the based of the internal positve controls, U6 and 5srRNA. The lowercases, a and b in the samples' and files' names represent block 1 and block 2, respectively.

source_name: fifth instar day 3 larvae

value: malpighian tubule

value: male


title: malpighian tubule of male silkworm_MT(m)-a, group 1


title: malpighian tubule of female silkworm_MT(f)-b, group 1


title: body wall of fifth instar day 7 larvae_BW_7dIL5-a, group 2


title: silk gland of fifth instar day 7 larva_SG_7dIL5-a, group 2


title: hemocyte of male silkworm_HC(m)-a, group 1

value: hemocyte


title: hemocyte of male silkworm_HC(m)-b, group 1


title: hemocyte of female silkworm_HC(f)-a, group 1


title: ovary (of female silkworm)_OV-b, group 1

value: gonad


title: hemocyte of female silkworm_HC(f)-b, group 1


title: ovary (of female silkworm)_OV-a, group 1


title: testis (of male silkworm)_TE-a, group 1


title: testis (of male silkworm)_TE-b, group 1


title: malpighian tubule of female silkworm_MT(f)-a, group 1


title: body wall of fifth instar day 7 larvae_BW_7dIL5-b, group 2


title: fat body of male silkworm_FB(m)-b, group 1


title: fat body of female silkworm_FB(f)-b, group 1


title: fat body of male silkworm_FB(m)-a, group 1


title: midgut of female silkworm_MG(f)-a, group 1


title: posterior silk gland of female silkworm_PSG(f)-b, group 1


title: posterior silk gland of male silkworm_PSG(m)-a, group 1


title: midgut of male silkworm_MG(m)-b, group 1


title: midgut of female silkworm_MG(f)-b, group 1


title: midgut of male silkworm_MG(m)-a, group 1


title: anterior silk gland of male silkworm_ASG(m)-a, group 1


title: anterior silk gland of male silkworm_ASG(m)-b, group 1


title: posterior silk gland of female silkworm_PSG(f)-a, group 1


title: posterior silk gland of male silkworm_PSG(m)-b, group 1


title: anterior silk gland of female silkworm_ASG(f)-b, group 1


title: anterior silk gland of female silkworm_ASG(f)-a, group 1


title: fat body of female silkworm_FB(f)-a, group 1


title: head of male silkworm_HD(m)-b, group 1

value: head


title: body wall of male silkworm_BW(m)-a, group 1


title: body wall of male silkworm_BW(m)-b, group 1


title: body wall of female silkworm_BW(f)-a, group 1

value: female


title: head of female silkworm_HD(f)-b, group 1


title: head of male silkworm_HD(m)-a, group 1


title: body wall of female silkworm_BW(f)-b, group 1


title: head of female silkworm_HD(f)-a, group 1


title: NY72-4-infected CNR grown at 37˚C, biological replicate 1

city: Hamilton

first: Bart

middle: Michal

last: Maslikowski

state: Ontario

address: 1280 Main St. West

department: Biology

country: Canada

institute: McMaster University

description: Gene expression data from NY72-4-infected CNR grown at 37˚C

hyb_protocol: cRNA was fragmented and hybridized onto Affymetrix Chicken GeneChip arrays for 16 hours at 45˚C. Washing, staining and scanning was done in accordance with the Affymetrix EukGE-WS2v4 protocol.

scan_protocol: Scanning was done using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were analysed using dChip software version 2007. Array data were normalized against the median intensity array for each experiment using the invariant set normalization method. Median array intensities for the experiments were scaled to the same value prior to normalization in order to provide comparable probe intensities for inter-experimental comparison. Expression levels were determined by the model-based expression index method using perfect-match probes only. CNR samples were normalized separately from the CEF samples to prevent skewing from tissue effects.

organism: Gallus gallus

source_name: NY72-4-infected CNR grown at 37˚C

label_protocol: 15 µg of total RNA was used to prepare biotin labeled complimentary RNA (cRNA). cDNA was generated by one-cycle target labeling protocol using SuperScript II (Invitrogen). Biotinylated cRNA was generated from purified cDNA using the Enzo IVT kit.

growth_protocol: CNR and CEF were cultured in high glucose Richter’s modified MEM medium (HyClone) supplemented 5% cosmic calf serum (HyClone), 5% tryptose phosphate broth, glutamine, penicillin and streptomycin.  All studies were performed with actively dividing cells cultured in medium replenished the day before sample preparation to avoid starvation and acidosis of the transformed cells.

extract_protocol: Total cell RNA was isolated using Trizol reagent (Invitrogen) according to manufacturer's instructions.

treatment_protocol: CEF were infected with the RSV strains wt SR-A, ts NY72-4 and td NY315 or with RCASBP-A, a derivative of avian sarcoma viruses lacking a viral Src gene. CNR cells do not proliferate in the absence of serum or a transforming v-Src kinase. Therefore CNR were infected with the temperature-sensitive mutant NY72-4 RSV at the permissive temperature of 37˚C and were expanded at the permissive temperature of 37˚C. Populations of ts NY72-4 RSV-infected CEF were cultured at the non-permissive temperature of 41.5˚C until transferred to the permissive temperature of 37˚C to induce transformation.

tag: chicken neuroretina cells derived from day 7 embryos (white leghorn strain)


title: NY72-4-infected CNR grown at 41.5˚C, biological replicate 2

description: Gene expression data from NY72-4-infected CNR grown at 41.5˚C

source_name: NY72-4-infected CNR grown at 41.5˚C


title: NY72-4-infected CNR grown at 37˚C, biological replicate 3


title: RCAS(BP)A-infected CEF grown at 37˚C, biological replicate 1

description: Gene expression data from RCAS(BP)A-infected CEF grown at 37˚C

source_name: RCAS(BP)A-infected CEF grown at 37˚C

tag: chicken embryonic fibroblast cells derived from day 10 embryos (white leghorn strain)


title: NY72-4-infected CNR grown at 41.5˚C, biological replicate 1


title: NY72-4-infected CEF grown at 37˚C, biological replicate 2

description: Gene expression data from NY72-4-infected CEF grown at 37˚C

source_name: NY72-4-infected CEF grown at 37˚C


title: NY72-4-infected CEF grown at 37˚C, biological replicate 1


title: NY72-4-infected CNR grown at 37˚C, biological replicate 2


title: RCAS(BP)A-infected CEF grown at 37˚C, biological replicate 3


title: RCAS(BP)A-infected CEF grown at 37˚C, biological replicate 2


title: NY72-4-infected CEF grown at 37˚C, biological replicate 3


title: SR-A-infected CEF, biological replicate 4

description: Gene expression data from SR-A-infected CEF

source_name: SR-A-infected CEF


title: SR-A-infected CEF, biological replicate 1


title: NY315-infected CEF, biological replicate 3

description: Gene expression data from NY315-infected CEF

source_name: NY315-infected CEF


title: SR-A-infected CEF, biological replicate 3


title: NY72-4-infected CEF grown at 41.5˚C, biological replicate 3

description: Gene expression data from NY72-4-infected CEF grown at 41.5˚C

source_name: NY72-4-infected CEF grown at 41.5˚C


title: NY72-4-infected CEF grown at 41.5˚C, biological replicate 2


title: SR-A-infected CEF, biological replicate 2


title: NY72-4-infected CNR grown at 41.5˚C, biological replicate 3


title: RCAS(BP)A-infected CEF, biological replicate 2

description: Gene expression data from RCAS(BP)A-infected CEF

source_name: RCAS(BP)A-infected CEF


title: NY315-infected CEF, biological replicate 1


title: RCAS(BP)A-infected CEF, biological replicate 1


title: NY315-infected CEF, biological replicate 2


title: NY72-4-infected CEF grown at 41.5˚C, biological replicate 1


title: nucleosomes_Fft3_2

status: Public on Feb 01 2010

type: genomic

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description:
Fft3 mutant S. pombe; replicate 2
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL

hyb_protocol: Arrays were hybridized at BEA Novum http://www.bea.ki.se/ 200 ul 1x hybridization mixture containing a final concentration of 7.5 ug of fragmented and labeled DNA target, 7% DMSO, 50 pM control oligo B2 (Affymetrix P/N 900301), BSA (0.5 mg/ml) and Herring sperm DNA (0.1 mg/ml) were prepared according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol. The final DNA target mixture was hybridized onto Affymetrix S. pombe Tiling 1.0FR arrays and incubated in a hybridization oven at 45 °C and 60 rpm for 16 h. See publication PMID: 19233281

scan_protocol: Arrays were scanned at BEA Novum http://www.bea.ki.se/ After hybridization of the arrays, the arrays were washed and stained with streptavidinâ€"phycoerythrin (SAPE, Invitrogen P/N S-866). The signals were amplified with biotinylated anti-streptavidin antibodies (Vector Laboratories, P/N BA-0500) in an Affymetrix Fluidics 450 wash station. Finally, the arrays were scanned in a 3000 7G scanner or similar, and the signal was quantified with the Affymetrix GeneChip Command Console Software (AGCC) to generate CEL files. See publication PMID: 19233281

data_processing: Raw data was processed using Affymetrix Tiling Array Software (TAS). We applied quantile normalization and a 50 bp averaging to obtain the log2 (nucleosomal fraction/input fraction) ratios for each sample.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Fft3 mutant S. pombe

label_protocol:
Samples were processed at BEA Novum http://www.bea.ki.se/
The isolated mononucleosomal DNA fragments and genomic control DNA were fragmented with DNaseI and labelled with terminal deoxynucleotidyl transferase according to Affymetrix GeneChip Mapping 10K Xba Assay Kit (P/N 900441). The purified fragments were diluted to 20 ug of DNA in a volume of 45 ul with 1× fragmentation buffer and freshly prepared fragmentation reagent (DNaseI) was added to a final concentration of 0.048 U/ul. The samples were incubated for 1 h in a preheated thermal cycler at 37 °C. The DNaseI was inactivated by incubating 15 min at 95°C. The samples were immediately placed on ice and the fragments were checked to have a size of about 50 bp with an Agilent bioanalyzer. Next, the fragmented samples were incubated at 37 °C in a thermal cycler with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ul) and 1× Terminal Deoxynucleotidyl Transferase Buffer as described in the Affymetrix GeneChip Mapping Assay Manual.
See publication PMID: 19233281

extract_protocol:
Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (MNase, Sigma-Aldrich) to yield about 90% mononucleosomes. DNA of mononucleosomal size was purified from agarose gels, fragmented to an average size of about 50 bp with DNaseI. DNAseI fragmented genomic DNA from S. pombe was used as hybridization control.
For full details, see publication PMID: 19233281

tag: strain

tag: genome/variation

value: Fft3 mutant

tag: fraction

value: nucleosomal DNA

source_name: wildtype and Mit1 mutant S. pombe

value: wildtype

value: Mit1 mutant

value: Genomic Input DNA (comprising the gDNA of wildtype and Mit1 mutant combined)


title: nucleosomes_Tup_1

description:
Nucleosomal DNA from Tup mutant S. pombe; replicate 1
Reference Raw data (CEL) files are the same as those in GSM401392.

hyb_protocol: Arrays were hybridized at BEA Novum http://www.bea.ki.se/

scan_protocol: Arrays were scanned at BEA Novum http://www.bea.ki.se/

data_processing: Raw data was processed using TAS. We applied quantile normalization and a 50 bp averaging to obtain the log ratios for each sample.

source_name: Nucleosomal DNA from Tup11/Tup12 mutant S. pombe

label_protocol: Samples were processed at BEA Novum http://www.bea.ki.se/

extract_protocol: Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (MNase, Sigma-Aldrich) to yield about 90% mononucleosomes. DNA of mononucleosomal size was purified from agarose gels, fragmented to an average size of about 50 bp with DNaseI. DNAseI fragmented genomic DNA from S. pombe was used as hybridization control.

value: Tup11/Tup12 mutant

value: Genomic Input DNA


title: nucleosomes_Mit1_2

description:
Mit1 mutant S. pombe; replicate 2
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL

source_name: Mit1 mutant S. pombe


title: nucleosomes_WT_3

description:
wildtype S. pombe; replicate 3
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL

source_name: wildtype S. pombe


title: nucleosomes_Mit1_1

description:
Mit1 mutant S. pombe; replicate 1
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL


title: nucleosomes_Fft3_1

description:
Fft3 mutant S. pombe; replicate 1
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL


title: nucleosomes_WT_4

description:
wildtype S. pombe; replicate 4
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL


title: nucleosomes_WT_1

description:
wildtype S. pombe; replicate 1
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL


title: MCF10AT

status: Public on Feb 15 2010

city: Rockville

first: Robert

middle: J

last: Clifford

state: MD

address: 2115 E Jefferson

department: CCR

institute: NCI

description: Hybridized to 250K_Sty

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Arrays were washed and stained in the Genechip Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions. Chips were scanned with the Affymetrix GeneChip Scanner 3000 using GeneChipOperating System 1.4

data_processing: *.CEL files were normalized using Affymetrix Power Tools version 1.85 gtype-probeset-genotype program. Copy number was determined using the Affymetrix Power Tools version 1.85 copynumber-pipeline program.

label: Biotin

source_name: cell line MCF10AT

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: DMEM/F12 medium supplemented with 5% horse serum, 10 μg/ml insulin, 20 ng/ml EGF, 0.5 μg/ml hydrocortisone, and 100 ng/ml cholera toxin

extract_protocol: DNA was isolated using the Qiagen Blood and Cell Culture midi Kit.

value: premalignant breast cell line MCF10AT generated by HRAS transformation of MCF10A


title: nucleosomes_Tup_2

description:
Nucleosomal DNA from Tup mutant S. pombe; replicate 2
Reference Raw data (CEL) files are the same as those in GSM401392.


title: miR-9 transfection replicate 2

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

description: miR-9 transfection in HeLa cells; replicated sample 2

hyb_protocol: Standard protocol recommended by Illumina using the Illumina “HYB” buffer

scan_protocol: Standard protocol recommended by Illumina using the Illumina BeadArray Reader

data_processing: Quantile normalization

source_name: HeLa cells with miR-9 transfection

label_protocol: T7 linear amplification with the MessageAmp TotalPrep kit (Ambion)

extract_protocol: Total RNA was extracted from the cell lysate using the mirVana kit (Ambion)

value: human cervical cancer cells


title: miR-200a transfection

description: miR-200a transfection in HeLa cells

source_name: HeLa cells with miR-200a transfection


title: miR-9 transfection replicate 1

description: miR-9 transfection in HeLa cells; replicated sample 1


title: nucleosomes_WT_2

description:
wildtype S. pombe; replicate 2
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL


title: Mock transfection (no RNA added)

description: Mock transfection sample

source_name: HeLa cells with mock transfection (no RNA added)


title: MCF10A

description: Hybridized to 250K_Sty

source_name: cell line MCF10A

value: non-tumorigenic breast cell line MCF10A


title: MCF10CA1a

description: Hybridized to 250K_Nsp

source_name: cell line MCF10CA1a

growth_protocol: DMEM/F12 medium plus 5% horse serum

value: poorly-differentiated malignant breast cell line MCF10CA1a derived from MCF10AT xenograft


title: MCF10A

description: Hybridized to 250K_Nsp


title: MCF10CA1a

description: Hybridized to 250K_Sty


title: MCF10CA1h

description: Hybridized to 250K_Nsp

source_name: cell line MCF10CA1h

value: well-differentiated malignant breast cell line MCF10CA1a derived from MCF10AT xenograft


title: MCF10AT

description: Hybridized to 250K_Nsp


title: Negative Control

description: Negative control sample

source_name: HeLa cells transfected with the negative control RNA


title: RCAS(BP)A-infected CEF, biological replicate 3


title: MCF10CA1h

description: Hybridized to 250K_Sty


title: A24_geno2_female_low_block6_Ch2

city: Toronto

first: Minyoung

last: Wyman

state: ON

address: 25 Willcocks Street

department: Ecology & Evolutionary Biology

institute: University of Toronto

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778984_A24.B6.G2.M.L._Ch1_.A24.B6.G2.F.L._Ch2_.txt

hyb_protocol: Hybridization: 80uL of hybridization buffer was added to each resuspended probe. The mixture incubated at at 65°C for 10min. The probe was placed on the array and placed in a sealed chamber in a 37°C waterbath for 16-18 hours. The array was washed 3 times for 15 min in pre-warmed 1xSSC, 0.1% SDS. The array was washed at room temperature with 1xSSC for <1min and then again with 0.1xSSC for <15sec. The array was scanned as soon as possible.

scan_protocol: Scan protocol: the Oligo14Kv1 microarrays were scanned with a Perking Elmer ScanArray scanner. The tiff files were processed using the QuantArray microarray quantification software.

data_processing: The data were not background corrected. We performed a series of normalizations on the log base 2 intensity measurements to adjust for local, global, and array-specific effects (Quackenbush 2002) using the limma package (Smyth and Speed 2003) for R v. 2.7.1 (R-Development-Core-Team 2008). We loess-normalized the intensities by print-tip-group (span=0.4) and within arrays (span=0.4) and across arrays with the quantile method. The normalized data were analyzed with PROC MIXED in SAS v. 9 with gene-specific ANOVAs.

organism: Drosophila melanogaster

source_name: genotype2, female, low condition

label_protocol: Reverse transcription: 40-60 ug of RNA was brought to a volume of 19uL for the reverse transcription reaction. 21uL of indirect RT master mix was added. The reaction mixture was incubated at 65°C for 5 min and then at 42°C for 5 min. 2uL of Superscript II RT was added and then incubated at 42°C for 3 hours. cDNA clean-up and precipitation: The cDNA from the reverse transcription was cleaned up by adding 8uL 1N NaOH, mixing the mixture, spinning it, and incubating at 65°C for 10 min. 4uL 1 M Tris (pH=7.5) was added, mixed, and spun. Then 38uL of water was added to bring the total volume to 100uL. The amino allyl-cDNA was purified with a Qiagen PCR clean up kit. Then 10uL 3M NaOAc, 1uL glycogen, and 120uL isopropanol was added. The solution was precipitated at -20°C for at least 75 min. The solution was spun at top speed for 30 min. The pellet was washed with 200uL of 75% EtOH and spun for 5 min. The EtOH was pipetted out of the tube and the pellet was left to air dry for <1 min. The pellet was resuspended in 5uL of water.Dye conjugation: 3uL 0.3M NaHCO3 was added to the resuspended amino allyl-cDNA. Then 2uL of dye (Alexa 647 or Alexa555) was added and allowed to incubate at room temperature in the dark for 1 hour. Then 90uL of ddH20 was added to the conjugated cDNA, purified with the purification kit, washed with 80% EtOH 3 times and eluted.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

value: hybrid offspring of We32(female) x We107(male) cross

tag: sex

tag: larval diet

value: low

tag: temporal block


title: A20_geno2_female_low_block5_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778979_A20.B5.G2.M.L._Ch1_.A20.B5.G2.F.L._Ch2_.txt


title: A23_geno2_male_high_block6_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778982_A23.B6.G2.F.H._Ch1_.A23.B6.G2.M.H._Ch2_.txt

source_name: genotype2, male, high condition

value: male

value: high


title: A15_geno2_male_high_block4_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778972_A15.B4.G2.F.H._Ch1_.A15.B4.G2.M.H._Ch2_.txt


title: A16_geno2_female_low_block4_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778974_A16.B4.G2.M.L._Ch1_.A16.B4.G2.F.L._Ch2_.txt

value: female


title: A17_geno2_female_high_block5_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778976_A17.B5.G2.F.L._Ch1_.A17.B5.G2.F.H._Ch2_.txt

source_name: genotype2, female, high condition


title: A19_geno2_male_high_block5_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778977_A19.B5.G2.F.H._Ch1_.A19.B5.G2.M.H._Ch2_.txt


title: A18_geno2_male_low_block5_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778978_A18.B5.G2.M.H._Ch1_.A18.B5.G2.M.L._Ch2_.txt

source_name: genotype2, male, low condition


title: A21_geno2_female_high_block6_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778980_A21.B6.G2.F.L._Ch1_.A21.B6.G2.F.H._Ch2_.txt


title: A13_geno2_female_high_block4_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778971_A13.B4.G2.F.L._Ch1_.A13.B4.G2.F.H._Ch2_.txt


title: A14_geno2_male_low_block4_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778973_A14.B4.G2.M.H._Ch1_.A14.B4.G2.M.L._Ch2_.txt


title: A12_geno1_female_low_block3_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755099_A12.B3.G1.M.L._Ch1_.A12.B3.G1.F.L._Ch2_.txt

source_name: genotype1, female, low condition

value: hybrid offspring of We61(female) x We29(male) cross


title: A11_geno1_male_high_block3_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755097_A11.B3.G1.F.H._Ch1_.A11.B3.G1.M.H._Ch2_.txt

source_name: genotype1, male, high condition


title: A22_geno2_male_low_block6_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778983_A22.B6.G2.M.H._Ch1_.A22.B6.G2.M.L._Ch2_.txt


title: A8_geno1_female_low_block2_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755081_A8.B2.G1.M.L._Ch1_.A8.B2.G1.F.L._Ch2_.txt


title: A4_geno1_female_low_block1_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13520755_A4.B1.G1.M.L._Ch1_.A4.B1.G1.F.L._Ch2_.txt


title: A9_geno1_female_high_block3_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755096_A9.B3.G1.F.L._Ch1_.A9.B3.G1.F.H._Ch2_.txt

source_name: genotype1, female, high condition


title: A6_geno1_male_low_block2_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755080_A6.B2.G1.M.H._Ch1_.A6.B2.G1.M.L._Ch2_.txt

source_name: genotype1, male, low condition


title: A7_geno1_male_high_block2_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755079_A7.B2.G1.F.H._Ch1_.A7.B2.G1.M.H._Ch2_.txt


title: A5_geno1_female_high_block2_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755078_A5.B2.G1.F.L._Ch1_.A5.B2.G1.F.H._Ch2_.txt


title: A3_geno1_male_high_block1_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13520753_A3.B1.G1.F.H._Ch1_.A3.B1.G1.M.H._Ch2_.txt


title: A23_geno2_female_high_block6_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778982_A23.B6.G2.F.H._Ch1_.A23.B6.G2.M.H._Ch2_.txt


title: A1_geno1_female_high_block1_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13520748_A1.B1.G1.F.L._Ch1_.A1.B1.G1.F.H._Ch2_.txt


title: A2_geno1_male_low_block1_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13520752_A2.B1.G1.M.H._Ch1_.A2.B1.G1.M.L._Ch2_.txt


title: A24_geno2_male_low_block6_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778984_A24.B6.G2.M.L._Ch1_.A24.B6.G2.F.L._Ch2_.txt


title: A21_geno2_female_low_block6_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778980_A21.B6.G2.F.L._Ch1_.A21.B6.G2.F.H._Ch2_.txt


title: A20_geno2_male_low_block5_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778979_A20.B5.G2.M.L._Ch1_.A20.B5.G2.F.L._Ch2_.txt


title: A18_geno2_male_high_block5_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778978_A18.B5.G2.M.H._Ch1_.A18.B5.G2.M.L._Ch2_.txt


title: A19_geno2_female_high_block5_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778977_A19.B5.G2.F.H._Ch1_.A19.B5.G2.M.H._Ch2_.txt


title: A7_geno1_female_high_block2_Ch1


title: A15_geno2_female_high_block4_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778972_A15.B4.G2.F.H._Ch1_.A15.B4.G2.M.H._Ch2_.txt


title: A17_geno2_female_low_block5_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778976_A17.B5.G2.F.L._Ch1_.A17.B5.G2.F.H._Ch2_.txt


title: A9_geno1_female_low_block3_Ch1


title: A8_geno1_male_low_block2_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755081_A8.B2.G1.M.L._Ch1_.A8.B2.G1.F.L._Ch2_.txt


title: A12_geno1_male_low_block3_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755099_A12.B3.G1.M.L._Ch1_.A12.B3.G1.F.L._Ch2_.txt


title: A11_geno1_female_high_block3_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755097_A11.B3.G1.F.H._Ch1_.A11.B3.G1.M.H._Ch2_.txt


title: A14_geno2_male_high_block4_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778973_A14.B4.G2.M.H._Ch1_.A14.B4.G2.M.L._Ch2_.txt


title: A3_geno1_female_high_block1_Ch1


title: A1_geno1_female_low_block1_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files is linked to a '_Ch1' and a '_Ch2' Sample.
raw data file: 13520748_A1.B1.G1.F.L._Ch1_.A1.B1.G1.F.H._Ch2_.txt


title: A10_geno1_male_low_block3_Ch2

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755098_A10.B3.G1.M.H._Ch1_.A10.B3.G1.M.L._Ch2_.txt


title: A10_geno1_male_high_block3_Ch1


title: A2_geno1_male_high_block1_Ch1


title: A5_geno1_female_low_block2_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755078_A5.B2.G1.F.L._Ch1_.A5.B2.G1.F.H._Ch2_.txt


title: A22_geno2_male_high_block6_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778983_A22.B6.G2.M.H._Ch1_.A22.B6.G2.M.L._Ch2_.txt


title: A13_geno2_female_low_block4_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778971_A13.B4.G2.F.L._Ch1_.A13.B4.G2.F.H._Ch2_.txt


title: A16_geno2_male_low_block4_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13778974_A16.B4.G2.M.L._Ch1_.A16.B4.G2.F.L._Ch2_.txt


title: A6_geno1_male_high_block2_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13755080_A6.B2.G1.M.H._Ch1_.A6.B2.G1.M.L._Ch2_.txt


title: H7_GSM378817

city: Stanford

first: Kitchener

middle: D.

last: Wilson

state: CA

address: S140 Grant Bldg

institute: Stanford University

hyb_protocol: Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with AGCC (Affymetrix Genechip Command Console).
Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.

source_name: Human Embryonic Stem Cells

label_protocol: Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen)

value: Human Embryonic Stem Cells

value: undifferentiated


title: H14_GSM378820


title: mit1-mutant-expression_replicate1

hyb_protocol: Hybridization was performed at BEA Novum http://www.bea.ki.se/

scan_protocol: Scanning was performed by at BEA Novum http://www.bea.ki.se/

data_processing: Raw data was processed using R/Bioconductor. Normalization and probeset expression values were calculated using GCRMA.

source_name: fission yeast

label_protocol: RNA labeling was performed at BEA Novum http://www.bea.ki.se/

extract_protocol: Total RNA preparations according to the hot phenol method (Xue,Y. et al.PMID 14745780).

value: mit1 mutant


title: wildtype-expression_replicate1

value: wild type


title: H9_GSM378818


title: wildtype-expression_replicate3


title: mit1-mutant-expression_replicate2


title: A4_geno1_male_low_block1_Ch1

description:
Although this was a co-hybridization experiment, each channel was analyzed and is represented separately, thus, each of the 24 raw data files are linked to two Samples (_Ch1 and _Ch2)
raw data file: 13520755_A4.B1.G1.M.L._Ch1_.A4.B1.G1.F.L._Ch2_.txt


title: H13_GSM378819


title: colony-T-t6.vs.t24

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description:
colony T
pooled mRNA from 5 queens, amplified

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: In brief, median signal and background levels for each probe were extracted from scanned microarray images using Axon Genepix software. Subsequently: We followed a standard microarray analysis procedure, guided by the documentation of the Bioconductor limma package (Smyth et al., 2005; Smyth, 2004; Gentleman et al., 2004). In brief, median signal and background levels for each probe were extracted from scanned microarray images using Axon Genepix software. The limma 2.16 package (Smyth, 2004) in R 2.8.1 (Team, 2007) was used for normexp background correction, print-tip loess normalization within arrays, and aquantile normalization between arrays (Smyth and Speed, 2003). The arrayQualityMetrics package (Kauffmann et al., 2009) and custom R scripts were used for quality control. The 18,444 Solenopsis invicta cDNA spots yielding a single PCR band (Wang et al., 2007) and passing visual and automated inspection were used for analysis. We constructed a design matrix incorporating effects for sampling times (t0, t6h and t24h), biological replicate (eight colonies) and the two dyes. The model that is fit to each gene may thus be represented as “expression=timepoint+replicate+dye”. The limma package was used for bayesian fitting of the model. Differential expression was determined for the contrasts “t24h vs. t0h”, “t24h vs. t6h, and “t6h vs. t0h” according to the nested F method in limma. Briefly, a moderated F test determined that 521 microarray clones were differentially expressed for at least one of the contrasts with a 10% False Discovery Rate (FDR;  Benjamini and Hochberg, 1995). Subsequently, significance of differential expression was assigned to one or several contrasts.

organism: Solenopsis invicta

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

growth_protocol: Eight monogyne S. invicta fire ant colonies, each containing at least 50 winged virgin queens and between 5,000 and 10,000 workers, were collected from a single population in Athens and Lexington, GA, USA in June 2006. There is genetic variability between colonies, however it is moderate because only few queens founded the North American S. invicta population when they were introduced from South America in the 1930s (Ross et al., 1993; Ross and Shoemaker, 2008). All colonies were returned to the laboratory and reared for one month under standard conditions (Jouvenaz et al., 1977). Queen- and male-destined brood were identified by their large size and removed weekly to ensure that only field-reared queens be used in for our experiment. Indeed, laboratory-reared queens do not normally grow to the same sizes as field-reared queens and rarely shed wings or initiate reproductive development after orphaning

extract_protocol: All collected queens were individually flash-frozen immediately after collection as described above. Samples were then stabilized until RNA isolation by the addition of 900 ul of cold Trizol reagent (Invitrogen) followed by homogenization with a FastPrep instrument (MP Biomedicals) and storage at -80°C. In summary, we had thus collected five queens at 0h , five queens at 6h and five queens at 24h from each of eight source colonies, constituting eight biological replicates for our experiment (See also Supporting Figure 1). We chose to pool five individuals from each replicate to reduce the impact of between-individual differences (Kendziorski et al., 2005), and conducted eight replicates to obtain sufficient statistical power with a feasible workload. In comparison, other studies that examined the effects of social context or mating used four replicates from a single Drosophila strain (McGraw et al., 2004), six replicates using different bees from a single colony (Kocher et al., 2008), six true biological replicates (Renn et al., 2008; Roberge et al., 2008), and examined pools of individuals from sixteen independent pairs of ant colonies (Wang et al., 2008).    Total RNA was isolated from all individuals using the Trizol protocol. RNA was pooled from 5 individuals per source colony for each time point and treated with DNA-free (Ambion). Subsequently, impurities were filtered away with MicroCon-30 spin columns (Millipore), and RNA quality was assessed on a 1% agarose gel prior to amplification using the MessageAmp II kit (Ambion). Amplified mRNA samples from the eight colonies at three timepoints (0h , 6h and 24h)) were labeled, hybridized to microarrays made from 22,560 independent fire ant cDNA spots (Microarray construction described in  Wang et al., 2007), and scanned as previously described (Wang et al., 2008). This was done according to a dye-balanced loop design (Supporting Figure 1). For all procedures, precautions including randomization of sample order were taken to avoid introducing unwanted biases.

treatment_protocol: We removed the mother queen and collected virgin queens just before orphaning as well as 6 and 24 hours after orphaning (subsequently referred to as time points t0h, t6h and t24h) to examine the onset of the molecular reaction to orphaning in virgin S. invicta queens. However, virgin queens emit pheromonal signals after orphaning that are similar to those of an functional queen and can thus influence each other (Vargo, 1999; Fletcher et al., 1983). We attempted to minimize such effects and simplify interpretation of results by taking advantage of the fact that S. invicta is a very opportunistic species that changes nests often in its native habitat which includes large flood plains (Tschinkel, 2006). We sampled queens according to the following setup: For t0h we haphazardly collected five virgin queens from the foraging area of each source colony and individually flash-froze them with liquid nitrogen in tubes containing 1g of 1.4mm Zirconium Silicate beads (QuackenBush). We placed ten additional virgin queens per source colony into individual small nests with 2g of mixed workers and brood. The density of workers and brood was comparable to that found in the source colonies. All virgin queens isolated in this manner are expected to shed their wings and initiate reproductive development (Fletcher and Blum, 1981; Burns et al., 2007). We thus simulated orphaning for a total of 80 virgin queens from a total of eight source colonies. We harvested half of the virgin queens thus treated after 6 hours and the remaining queens after 24 hours.

tag: time point


title: colony-R-t6.vs.t24

description:
colony R
pooled mRNA from 5 queens, amplified


title: colony-Q-t0.vs.t24

description:
colony Q
pooled mRNA from 5 queens, amplified


title: colony-N-t24.vs.t6

description:
colony N
pooled mRNA from 5 queens, amplified


title: colony-N-t0.vs.t24


title: colony-R-t0.vs.t6


title: colony-Q-t24.vs.t6


title: colony-T-t24.vs.t0


title: colony-T-t0.vs.t6


title: colony-R-t24.vs.t0


title: colony-K-t6.vs.t0

description:
colony K
pooled mRNA from 5 queens, amplified


title: wildtype-expression_replicate2


title: colony-Q-t6.vs.t0


title: colony-K-t24.vs.t6


title: colony-N-t6.vs.t0


title: colony-F-t6.vs.t24

description:
colony F
pooled mRNA from 5 queens, amplified


title: colony-K-t0.vs.t24


title: nucleosomes_Mit1_3

description:
Mit1 mutant S. pombe; replicate 3
Processed data file: bar
Raw data file(s)_nucleosomal fraction: mono*.CEL
Raw data file(s)_input fraction: genome*.CEL

source_name: Mit1 mutant S. pombe

value: Mit1 mutant

value: nucleosomal DNA

source_name: wildtype and Mit1 mutant S. pombe

value: wildtype

value: Genomic Input DNA (comprising the gDNA of wildtype and Mit1 mutant combined)


title: colony-F-t24.vs.t0


title: colony-A-t6.vs.t0

description:
colony A
pooled mRNA from 5 queens, amplified


title: colony-C-t24.vs.t0

description:
colony C
pooled mRNA from 5 queens, amplified


title: colony-C-t6.vs.t24


title: colony-C-t0.vs.t6


title: colony-F-t0.vs.t6


title: colony-A-t0.vs.t24


title: mouse myocyte - Sanguinarine, 25 ug/ml-8

first: David

middle: S

last: Loose

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Normalized data with quantile normalization in Genome Studio v1.0. Raw data are not background subtracted.

organism: Mus musculus

source_name: mouse myocyte - Sanguinarine, 25 ug/ml

label_protocol: Standard Illumina protocol, 200 ng total RNA

growth_protocol: Standard growth media

extract_protocol: Cells were washed with cold PBS and lysed with RNeasy (Quiagen, CA) and RNA was purified on a Quiagen Mini spin column.

treatment_protocol: Cells were grown to 85% confluency, treated for 60 minutes with vehicle (EtOH) or Sanguinarine at 1.5 ug/ml or 25 ug/ml. Total RNA extracted

value: primary mouse myocytes


title: Root Derived Callus Replicate 4

city: Pasadena

first: Yuling

last: Jiao

address: 1200 E California Blvd

institute: California Institute of Technology

description: Biological replicate 4 of 4. Control untreated tissue (d0).

hyb_protocol: Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix v5.0 analysis software.

data_processing: Data were processed using lowess normalization with the Resolver data analysis system (Rosetta Biosoftware, Seattle, WA).

organism: Arabidopsis thaliana

source_name: root d10

label_protocol: Dye-labeled antisense RNA was previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

growth_protocol: Root, cotyledon, or petal tissue from normal growth Arabidopsis Ler ecotype were excised.

extract_protocol: Total RNA extracted using Qiagen RNeasy following manufacturer's instructions

treatment_protocol: Callus was formed from explants on auxin-rich callus-inducing medium (CIM, Gautheret, R. J., 1966).

tag: ecotype

value: Ler

value: root

tag: treatment

value: CIM, 10 day

source_name: root d0

value: no CIM treatment


title: Cotyledon Derived Callus Replicate 2

description: Biological replicate 2 of 4. Control untreated tissue (d0).

source_name: coty d10

value: cotyledon

source_name: coty d0


title: colony-A-t24.vs.t6


title: Petal Derived Callus Replicate 3

description: Biological replicate 3 of 4. Control untreated tissue (d0).

source_name: petal d10

value: petal

source_name: petal d0


title: Petal Derived Callus Replicate 1

description: Biological replicate 1 of 4. Control untreated tissue (d0).


title: Cotyledon Derived Callus Replicate 4


title: mouse myocyte - Sanguinarine, 25 ug/ml-7

tag: cell type


title: Root Derived Callus Replicate 1


title: Petal Derived Callus Replicate 2


title: Petal Derived Callus Replicate 4


title: Cotyledon Derived Callus Replicate 1


title: Root Derived Callus Replicate 2


title: Root Derived Callus Replicate 3


title: mouse myocyte - Sanguinarine, 25 ug/ml-6


title: Cotyledon Derived Callus Replicate 3


title: mouse myocyte - Sanguinarine, 25 ug/ml-5


title: mouse myocyte - Sanguinarine, 25 ug/ml-3


title: mouse myocyte - Sanguinarine, 25 ug/ml-4


title: mouse myocyte - Sanguinarine, 25 ug/ml-2


title: mouse myocyte - Sanguinarine, 25 ug/ml-1


title: mouse myocyte - Sanguinarine, 1.5 ug/ml-4

source_name: mouse myocyte - Sanguinarine, 1.5 ug/ml


title: mouse myocyte - Sanguinarine, 1.5 ug/ml-2


title: mouse myocyte-control-7

source_name: mouse myocyte-control


title: mouse myocyte-control-6


title: mouse myocyte-control-4


title: mouse myocyte-control-2


title: mouse myocyte - Sanguinarine, 1.5 ug/ml-3


title: MSC_rep4

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description: US22502668_251485010289_S01_GE1-v5_91_0806_1_2.txt

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x GE hybridization buffer HI- RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (4x 44K) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) and air dried.

scan_protocol: Slides were scanned with an Agilent Technologies Scanner G2505B using a scan area of 61x21.6 mm, scan resolution of 5µm, dye channel set to green and green PMT set to 100%.

data_processing: Scans were quantified using Agilent Feature Extraction V10.1.1.1 Software using default parameters (protocols GE1-V5_91 and GE1-V5_95, as indicated by raw data file names). Control spots are removed, replicate oligos are averaged.

source_name: human mesenchymal stell cells replicate 4

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

growth_protocol: For all Wilms (primary Wilms tumor cultures from different patients) and MSC samples: cells were cultivated in MSCB-medium supplemented with Bullet Kit (Lonza). For CLS1 samples: cells were cultivated in Iscoves medium supplemented with 2mM L-Glutamine and 15% FCS. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the RNAeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendation with an included on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: bone marrow

value: human mesenchymal stell cells


title: MSC_rep5

description: US45103065_251485038459_S01_GE1-v5_95_Feb07_1_3.txt

source_name: human mesenchymal stell cells replicate 5


title: mouse myocyte-control-3


title: mouse myocyte-control-5


title: MSC_rep1

description: US22502668_251485010291_S01_GE1-v5_91_0806_1_1.txt

source_name: human mesenchymal stell cells replicate 1


title: mc-iPSC-1s

description: iPSC sublone 1

hyb_protocol: 825 ng of Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol. cRNA was hybridized to 4x44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer’s instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.

scan_protocol: The arrays were scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.

source_name: mc-iPSCs

label_protocol: Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent), cDNA was reverse transcribed from each RNA sample, as well as from a pooled reference control, and cRNA then transcribed and fluorescently labeled with Cy5/Cy3. cRNA was purified using an RNeasy kit (Qiagen).

growth_protocol: Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes  with mTESR-1 human ES Growth Medium (StemCell Technologies).

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen).

tag: differentiation state

value: iPS cells derived from human adipose stem cells using minicircle vector

source_name: Pooled RNA reference

value: pool of undifferentiated and differentiated hESCs, as well as fetal and neonatal tissues


title: mc-iPSC-2s

description: iPSC subclone 2

value: undifferentiated


title: mouse myocyte-control-1


title: MSC_rep2

description: US22502668_251485010288_S01_GE1-v5_91_0806_1_2.txt

source_name: human mesenchymal stell cells replicate 2


title: H7 hESC-2

description: H7 human embryonic stem cells replicate 2

source_name: H7 hESCs

value: embryonic stem cells


title: DHT stimulation, biological rep3

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: DHT stimulation, biological rep3

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100

source_name: LNCaP

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran

extract_protocol: QIAGEN RNeasy protocol and reagents for extraction of total RNA

treatment_protocol: LNCaP cells were maintained for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours

value: LNCaP

value: cancer cell culture


title: DHT stimulation, biological rep2

description: DHT stimulation, biological rep2


title: mouse myocyte - Sanguinarine, 1.5 ug/ml-1


title: H7 hESC-1

description: H7 human embryonic stem cells replicate 1


title: hASC-1_GSM374067

description: raw data file: GSM374067.txt

source_name: human adipose stem cell

extract_protocol: Total RNA samples were isolated in Trizol (Invitrogen) followed by purification over a Qiagen RNeasy column (Qiagen, Valencia, CA, USA).

value: differentiated

value: patient-derived adipose stem cell; primary cell line


title: DHT stimulation, biological rep1

description: DHT stimulation, biological rep1


title: control, biological rep2

description: control, biological rep2


title: control, biological rep3

description: control, biological rep3


title: hASC-2_GSM374068

description: raw data file: GSM374068.txt


title: MSC_rep3

description: US22502668_251485010290_S01_GE1-v5_91_0806_1_2.txt

source_name: human mesenchymal stell cells replicate 3


title: ERBB2 over-expression, biological rep1

description: ERBB2 over-expression, biological rep1

growth_protocol: MCF10A cells were maintained in DMEM/F12 base media supplemented with 5% horse serum, 20 ng/ml EGF, 0.5 microgram/ml hydrocortisone, 100 ng/ml cholera toxin, 10 microgram/ml insulin and penicillin/streptomycin.

treatment_protocol: The cells were transduced with retroviruses encoding vector control (pBabe) or pBabe-ErbB2. After infection cells were switched to assay medium supplemented with only 2% horse serum and no EGF. For EGF stimulation, cells transduced with empty vector were treated with EGF at 50 ng/ml for 2 hours before harvesting.

value: immortalized cell culture


title: ERBB2 over-expression, biological rep2

description: ERBB2 over-expression, biological rep2


title: EGF stimulation, biological rep1

description: EGF stimulation, biological rep1


title: EGF stimulation, biological rep3

description: EGF stimulation, biological rep3


title: EGF stimulation, biological rep2

description: EGF stimulation, biological rep2


title: control, biological rep1

description: control, biological rep1


title: heart_10days

status: Public on Jan 31 2010

city: Daejon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

hyb_protocol: Labeled cRNA (750 ng) were hybridized to a Mouse-8 Expression BeadChip for 16-18 h at 58 °C, according to the manufacturer's instructions (Illumina).

scan_protocol: Following attachment of Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences), arrays were scanned with an Illumina bead array reader.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: heart

label_protocol: Total RNA was amplified and purified to yield biotinylated cRNA using an Ambion Illumina RNA amplification kit (Ambion).

growth_protocol: Mice were maintained for two weeks prior to the experiment in a controlled environment of 22 ± 2 °C with a 12 h dark/light cycle.

extract_protocol: Total RNA from the brain, heart and liver tissues was isolated using TriPure Isolation Reagent according to the manufacturer's instructions (Roche Applied Science).

treatment_protocol: Aqueous extracts of Ephedra herba were administered orally at dosage of 50 mg/kg for 1 hr, 6 hrs, 12 hrs, 24 hrs, 3 days, 5 days and 10 days.

tag: age

value: Five-week-old

tag: gender

value: female

value: heart

tag: agent

value: Ephedra herba

tag: time


title: liver_3days

source_name: liver

tag: tissue

value: liver


title: liver_Untreated control

description: control

value: untreated

value: control


title: liver_1hr


title: liver_12hrs


title: liver_5days


title: liver_6hrs


title: vector control, biological rep3

description: vector control, biological rep3

tag: cell line


title: vector control, biological rep2

description: vector control, biological rep2


title: vector control, biological rep1

description: vector control, biological rep1


title: liver_10days

tag: strain


title: ERBB2 over-expression, biological rep3

description: ERBB2 over-expression, biological rep3


title: heart_3days


title: heart_24hrs


title: heart_5days


title: heart_12hrs


title: liver_24hrs


title: heart_6hrs


title: heart_Untreated control

description: control


title: heart_1hr


title: brain_10days

source_name: brain

value: brain


title: brain_5days


title: SAGE_sympathetic neuron axons

type: SAGE

anchor: NlaIII

city: London

first: Catia

last: Andreassi

address: Gower street, 1.03

department: MRC LMCB and Dept. of Neuroscience, Physiology and Pharmacology

country: United Kingdom

institute: University College London

description: Total axon mRNA was isolated from the axon compartments of 22 chambers.  Samples were purified as described above, concentrated by speed-vacuum centrifugation to 1 microL volume, and used for two rounds of linear amplification as previously described (Baugh et al, 2001).  The volume of the first-strand reaction was scaled down to 5 microL.  After the second round of amplification, contaminant cDNA was digested by treating the samples with RNAse-free DNAse (2.5U, USB).

data_processing: LongSAGE tags were extracted and counted using the perl script "LongSAGEbias.pl" from the Aalborg University SAGE software suite (Aalborg University SAGE software 2007 [http://www.bio.aau.dk/en/biotechnology/software_applications/]) (Lash et al, 2000). Duplicate ditags were included as recent evidence suggests that their removal may lead to significant error in LongSAGE analysis (Emmersen et al, 2007; Khattra et al, 2007).  An exact 17bp sequence match was considered significant.

organism: Rattus norvegicus

source_name: Axon mRNA from 12 DIV sympathetic neurons

growth_protocol: Five to six days after cell plating, NGF was lowered in the central compartment to 10 ng/ml and neurons were maintained with NGF (100 ng/ml) in the lateral compartment.  Cytosine arabinoside (ARA-C, 10 microM) was added 24 hours after plating to block the proliferation of non-neuronal cells.

extract_protocol: Total RNA was isolated from axon compartments using Micro-to-Midi Total RNA Purification System (Invitrogen), as indicated by the manufacturer with minor modifications.  Briefly, axons and cell body samples were collected from compartmentalized chambers by using lysis buffer (300 microL) containing 10% beta-mercaptoethanol.  Total mRNA was bound to the columns, washed and eluted twice in elution buffer (35 microL).

treatment_protocol: NGF

tag: Superior cervical ganglia were dissected from post-natal day 1 (P1) Wistar rats, enzymatically dissociated and plated in compartmentalized chambers, as previously described (Tsui-Pierchala et al, 1999).


title: brain_12hrs


title: brain_1hr


title: brain_3days


title: SAGE_sympathetic neuron cell bodies

description: Total cell bodies mRNA was isolated from the central compartments of 8 chambers.  Samples were purified as described above, concentrated by speed-vacuum centrifugation to 1 microL volume, and used for two rounds of linear amplification as previously described (Baugh et al, 2001).  The volume of the first-strand reaction was scaled down to 5 microL.  After the second round of amplification, contaminant cDNA was digested by treating the samples with RNAse-free DNAse (2.5U, USB).

source_name: Cell body mRNA from 12 DIV sympathetic neurons

extract_protocol: Total RNA was isolated from cell bodies compartments using Micro-to-Midi Total RNA Purification System (Invitrogen), as indicated by the manufacturer with minor modifications.  Briefly, axons and cell body samples were collected from compartmentalized chambers by using lysis buffer (300 microL) containing 10% beta-mercaptoethanol.  Total mRNA was bound to the columns, washed and eluted twice in elution buffer (35 microL).


title: brain_Untreated control

description: control


title: brain_24hrs


title: Lung_progressive_biological_rep4

city: Oxford

first: Ling-Pei

last: Ho

address: John Radcliffe Hospital

department: MRC Human Immunology Unit

institute: Weatherall Institute for Molecular Meicine, University of Oxford

hyb_protocol: Fragmented and labeled DNA (2500ng) was used in 100 µl hybridization cocktail containing control oligonucleotide B2 (50pM) and hybridization controls (Affymetrix #900454), of which 80 µl was hybridised to each chip for 17h in the hybridization oven at 45ºC and rotating at 60rpm. Arrays were processed using Genechip Fluidics Station 450 according to recommended protocols (FS450_007) of double-staining and post-hybridization washes using GeneChip hybridization, wash and stain kit (Affymetrix #900720).

scan_protocol: Fluorescent images were captured using gene Array scanner 3000 and GCOS 1.2 software (Affymetrix).

data_processing: Raw data were processed using Affymetrix Power Tools to generate RMA normalised intensities and subsequent analysis was carried out using R and BioConductor packages. Differential expression was assessed using the limma package and included an effect for cohort.

source_name: Lung biopsy sample from patient with progressive, fibrotic disease

label_protocol: Isolated total RNA was used with GeneChip WT cDNA synthesis and amplification kit (Affymetrix#900672) to produce fragmented single-stranded DNA, which was labeled using terminal labeling kit (Affymetrix#900670) to generate biotin-labeled sense targeted DNA probes.

extract_protocol: Total RNA from lung biopsies was extracted within 24 hours using the Qiagen RNeasy Mini kit, as per manufacturer's instructions

treatment_protocol: Samples were obtained by standard bronchial biopsy protocols (CT-targeted transbronchial biopsy) at the point of clinical presentation. Patients were followed up for 2 years and classified into 'nodular, self-limiting' and 'progressive, fibrotic' pulmonary disease groups, based on symptons, pulmonary function tests and CT scans

value: Lung biopsy

tag: disease type

value: Progressive, fibrotic (P-F)

tag: cohort

value: First

tag: date array hybridised

value: Male


title: Lung_progressive_biological_rep7

value: Second

value: Female


title: Lung_progressive_biological_rep3


title: Lung_self-limiting_biological_rep7

source_name: Lung biopsy sample from patient with nodular, self-limiting disease

value: Nodular, self-limiting (N-SL)


title: Lung_progressive_biological_rep1


title: Lung_progressive_biological_rep6


title: Lung_progressive_biological_rep2


title: Lung_self-limiting_biological_rep8


title: Lung_progressive_biological_rep5


title: Lung_self-limiting_biological_rep2


title: Lung_self-limiting_biological_rep6


title: Lung_self-limiting_biological_rep4


title: brain_6hrs


title: Lung_self-limiting_biological_rep3


title: Lung_self-limiting_biological_rep1


title: nonfasting sample, experiment 4

status: Public on Jan 30 2010

city: Iowa City

first: Christopher

last: Adams

state: IA

address: 540G EMRB, 200 Hawkins Drive

institute: University of Iowa

description: skeletal muscle RNA from fed mice

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Mouse Exon 1.0 ST arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.  Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
RMA normalization
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.d1.1.hg18.core.mps

source_name: skeletal muscle RNA from fed mice

label_protocol: 50 ng total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN.  Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Mice were allowed ad libitum access to food or fasted for 24 h before RNA was harvested from the tibilais anterior muscle.

value: 8 weeks

tag: sex

value: male

value: tibialis anterior


title: fasting sample, experiment 4

description: skeletal muscle RNA from fasted mice

source_name: skeletal muscle RNA from fasted mice


title: fasting sample, experiment 3

description: skeletal muscle RNA from fasted mice


title: fasting sample, experiment 1

description: skeletal muscle RNA from fasted mice


title: nonfasting sample, experiment 3

description: skeletal muscle RNA from fed mice


title: nonfasting sample, experiment 2

description: skeletal muscle RNA from fed mice


title: fasting sample, experiment 2

description: skeletal muscle RNA from fasted mice


title: ATF4 transfection, experiment 4

description: RNA from skeletal muscle transfected with plasmid encoding mouse ATF4

treatment_protocol: Skeletal muscles were transfected in vivo with plasmid DNA, and RNA was harvested from transfected muscles (under nonfasting conditions) 11 days later.


title: ATF4 transfection, experiment 3

source_name: RNA from skeletal muscle transfected with plasmid encoding mouse ATF4


title: pcDNA3 transfection, experiment 3

description: RNA from skeletal muscle transfected with empty plasmid vector


title: pcDNA3 transfection, experiment 4

source_name: RNA from skeletal muscle transfected with empty plasmid vector


title: ATF4 transfection, experiment 2


title: Lung_self-limiting_biological_rep5


title: ATF4 transfection, experiment 1


title: pcDNA3 transfection, experiment 2


title: nonfasting sample, experiment 1

description: skeletal muscle RNA from fed mice


title: FAIRE performed in human pancreatic islet cells, sample 2 (ENCODE regions)

city: San Diego

first: Kyle

middle: Jeffrie

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

description: Samples were amplified using ligation mediated (LM) PCR.

hyb_protocol: Hybridizations were performed in a MAUI hybridization station for 16 h at 42°C

scan_protocol: Arrays were scanned with an Axon Scanner 4000B

data_processing: log2 ratios of Cy5/Cy3 normalized so that the mean ratio is 0

source_name: FAIRE processed DNA from pancreatic islets

label_protocol: Sample labeled by incorporation of cyanine dyes by polymerization with Klenow fragment primed by random nonomers

extract_protocol: DNA extracted using phenol-chloroform

tag: sample type

value: Human pancreatic islet chromatin crosslinked with 1% formaldehyde solution for 10 min and then sheared by sonication.

value: pancreatic islet

source_name: Input DNA from pancreatic islets

value: Human pancreatic islet DNA sheared by sonication.


title: diploid strain_7% ethanol_rep1

city: Tianjin

first: Bing-Zhi

last: Li

address: Weijin Road 92#

institute: Tianjin University

description: gene expression at exponential phase

hyb_protocol: The biotin-labeled cRNA was hybridized to the GeneChip® Yeast Genome 2.0 Array from Affymetrix (California, US) after dilution and fragmentation according to Affymetrix’s protocol

scan_protocol: Microarrays were scanned with the Genechip Scanner 3000

data_processing: The data were analyzed with GeneChip Operation System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Saccharomyces cerevisiae

source_name: diploid strain, 7% ethanol, exponential stage

label_protocol: Total RNA labeling was conducted according to the Affymetrix GeneChip Expression analysis technical manual (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: strains were incubated in 5-L fermentors with a 3-L working volume. YPD medium (10 g/L yeast extract, 20 g/L peptone, 100 g/L glucose) with different ethanol concentration were used. The initial cell density was OD600 of 0.5.

extract_protocol: Total RNA was isolated according to the hot phenol method

treatment_protocol: Cultures for microarray analysis were collected at mid-exponential phase

value: ethanol tolerant strain, diploid