title: FRTL-5, TSHR-L629F, no_iodine, replicate 2

status: Public on Dec 01 2010

type: RNA

city: Leipzig

first: Knut

last: Krohn

address: Philipp-Rosenthal-Straße 55

department: Medizinische Fakultät

country: Germany

institute: University Leipzig

description: SB5 sub-clone of FRTL-5

hyb_protocol: Following fragmentation, 25 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2.0. An Affymetrix Fluidics Station 400 was used for washing and staining.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChipScanner 3000 with the 7G upgrade.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Thyroid cell line

label_protocol:
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
staining protocol: 3 rounds total composed of staining with streptavidin phycoerythrin (SAPE) in two rounds which are intermitted by a round of anti-SAPE antibody staining.

growth_protocol: FRTL-5 cells were cultured under standard conditions with 5 mU/ml bovine TSH.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by a column purification with Qiagen RNeasy kit.

treatment_protocol: The cells were treated with 1mM sodium iodide or 1mM sodium chloride as an isotonic control.

tag: iodine treatment

tag: chloride treatment

tag: stable human tsh receptor expression


title: FRTL-5, TSHR-WT, no_iodine, replicate 2

description: SB5 sub-clone of FRTL-5

value: WT


title: QNR/v-src 41°C vs QNR/v-src/RBP-Jk-VP16 41°C

city: orsay

first: georges

last: calothy

address: Bat.110-Centre Universitaire

country: France

institute: institut curie

data_processing:
LOWESS-normalized by:
FHRC Genomics Resource
DNA array laboratory
1100 fairview ave N, DE-740
Seattle, WA 98109
http://www.fhcrc.org/science/shared_resources/genomics/index.html

organism: Gallus gallus

source_name: QNR/v-src 41°C culture2

label_protocol:
The array has been processed by:
        FHRC Genomics Resource
        DNA array laboratory
        1100 fairview ave N, DE-740
        Seattle, WA 98109
       http://www.fhcrc.org/science/shared_resources/genomics/index.html

growth_protocol: Quail neuroretina cells were dissected on 7-day old embryos and infected, one day after seeded, with a Rous sarcoma virus mutant expressing a thermolabile v-Src oncoprotein. At the restrictive temperature (41°C), QNR/v-src cells ceased to divide and presented a non-transformed phenotype.

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

tag: cell line

value: quail neuroretina (QNR) cells, expressing v-Src oncoprotein

tag: temperature

source_name: QNR/v-src/RBP-Jk-VP16 41°C

growth_protocol: Stable expression of a constitutively activated human CBF form (RBP-Jk-VP16), transcription factor partner of ICN, in QNR/v-src cells reproduced QNR/v-src/ICN phenotype and  suppressed v-Src-mediated transformation. At the restrictive temperature (41°C), QNR/v-src/RBP-Jk-VP16 cells proliferated and presented a normal phenotype.

tag: stably expressing


title: FRTL-5, TSHR-L629F, no_iodine, replicate 1

description: SB5 sub-clone of FRTL-5


title: Proliferative-hypertrophic transition zone, Biol rep 1

city: Stockholm

first: Ola

last: Nilsson

address: Karolinska University Hospital, Q2:08

department: Dept. Woman and Child Health

country: Sweden

institute: Karolinska Institute

description: Proliferative-hypertrophic transition zone microdissected from proximal tibiae of animal 1

hyb_protocol: 15 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000

data_processing: Raw data was preprocessed to produce signal values using the MAS5 statistical algorithm.

label: Biotin

label_protocol: 50-100ng of total RNA was amplified and labeled using the Two-Cycle Target Labeling and Control Reagents (Affymetrix, P/N 900494) according to Expression Analysis Technical Manual, version 701021 Rev.5 (Affymetrix)

growth_protocol: Rats, no treatment, standard chow

extract_protocol: Total RNA was extracted from microdissected cartilage by guanidinium thiocyanate, proteinas K digestion, phenol-chloroform extraction, isopropanol precipitation, LiCl-precipitation as previously described except that one tenth of every volume was used (Heinrichs C et al. Endocrinology 1994;135:1113-8).

treatment_protocol: Proximal tibiae were excised, trimmed of cortical bone, embedded in OCT, and stored at -80C. 60um frozen sections were fixed, stained and dehydrated before being manually microdissected into individual growth plate zones under a xylene droplet using scalpel blades and hypodermic needles (Nilsson et al J Endocrinol 2007;193:75-84).

tag: age

value: 1 week

tag: castrated

value: No

tag: growth plate zone


title: QNR/v-src/RBP-Jk-VP16 41°C vs QNR/v-src 41°C

description: dye swap

hyb_protocol: processed by:         FHRC Genomics Resource         DNA array laboratory         1100 fairview ave N, DE-740         Seattle, WA 98109         http://www.fhcrc.org/science/shared_resources/genomics/index.html


title: Proliferative-hypertrophic transition zone, Biol rep 4

description: Proliferative-hypertrophic transition zone microdissected from proximal tibiae of animal 4


title: Proliferative-hypertrophic transition zone, Biol rep 5

description: Proliferative-hypertrophic transition zone microdissected from proximal tibiae of animal 5


title: FRTL-5, TSHR-L629F, iodine, replicate 2

description: SB5 sub-clone of FRTL-5


title: FRTL-5, TSHR-WT, iodine, replicate 1

description: SB5 sub-clone of FRTL-5


title: Proliferative-hypertrophic transition zone, Biol rep 3

description: Proliferative-hypertrophic transition zone microdissected from proximal tibiae of animal 3


title: Epiphyseal cartilage, Biol rep 5

description: Epiphyseal cartilage microdissected from proximal tibiae of animal 5

source_name: Epiphyseal cartilage

value: Epiphyseal cartilage


title: Epiphyseal cartilage, Biol rep 2

description: Epiphyseal cartilage microdissected from proximal tibiae of animal 2


title: QNR/v-src 37°C vs QNR/v-src/ICN 37°C

scan_protocol: processed by:         FHRC Genomics Resource         DNA array laboratory         1100 fairview ave N, DE-740         Seattle, WA 98109         http://www.fhcrc.org/science/shared_resources/genomics/index.html

source_name: QNR/v-src 37°C culture1

growth_protocol: Quail neuroretina cells were dissected on 7-day old embryos and infected, one day after seeded, with a Rous sarcoma virus mutant expressing a thermolabile v-Src oncoprotein. At the permissive temperature (37°C), QNR/v-src cells divided and were transformed.

source_name: QNR/v-src/ICN 37°C

growth_protocol: Stable expression of Notch intra cellular domain (ICN) in QNR/v-src cells suppressed v-Src-mediated transformation without altering oncoprotein expression and activity.

value: ICN


title: Epiphyseal cartilage, Biol rep 4

description: Epiphyseal cartilage microdissected from proximal tibiae of animal 4


title: QNR/v-src 41°C vs QNR/v-src/ICN 41°C

source_name: QNR/v-src 41°C culture1

source_name: QNR/v-src/ICN 41°C

growth_protocol: Stable expression of Notch intra cellular domain (ICN) in QNR/v-src cells suppressed v-Src-mediated transformation without altering oncoprotein expression and activity. At the restrictive temperature (41°C), ICN expression allowed proliferation of QNR/v-src/ICN cells.


title: Proliferative-hypertrophic transition zone, Biol rep 2

description: Proliferative-hypertrophic transition zone microdissected from proximal tibiae of animal 2


title: QNR/v-src 37°C vs QNR/v-src/RBP-Jk-VP16 37°C

source_name: QNR/v-src 37°C culture2

source_name: QNR/v-src/RBP-Jk-VP16 37°C

growth_protocol: Stable expression of a constitutively activated human CBF form (RBP-Jk-VP16), transcription factor partner of ICN, in QNR/v-src cells reproduced QNR/v-src/ICN phenotype and  suppressed v-Src-mediated transformation.


title: Epiphyseal cartilage, Biol rep 1

description: Epiphyseal cartilage microdissected from proximal tibiae of animal 1


title: QNR/v-src/ICN 41°C vs QNR/v-src 41°C

description: dye swap


title: FRTL-5, TSHR-WT, no_iodine, replicate 1

description: SB5 sub-clone of FRTL-5


title: FRTL-5, TSHR-WT, iodine, replicate 2

description: SB5 sub-clone of FRTL-5


title: FRTL-5, TSHR-L629F, iodine, replicate 1

description: SB5 sub-clone of FRTL-5


title: S. oneidensis with L.lactis_MFC anode_rep2

city: Ithaca

first: Miriam

last: Rosenbaum

state: NY

address: 325 Riley-Robb Hall

department: Biological and Environmental Engineering

country: USA

institute: Cornell University

description: Gene expression data from wild-type S. oneidensis MR-1, grown in a co-culture with L.lactis. The anode biofilm, was mainly composed of S. oneidensis.

hyb_protocol: 10 µg of RNA sample was used for cDNA synthesis, followed by reverse transcription, cDNA purification, and cDNA-fragmentation. This was followed by labeling of cDNA and 16 hours of hybridization at 45°C on S. oneidensis arrays. The labeled arrays were subjected to several cycles of washing and staining using Affymetrix Wash buffers A and B, Goat IgG, Streptavidin, Anti-streptavidin and SAPE according to the Affymetrix protocol for prokaryotic arrays in the Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Shewanella oneidensis MR-1

source_name: S. oneidensis anaerobic MFC anode biofilm in co-culture experiment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown anaerobically at 30°C in a contiuous bioelectrochemical system (BES) with defined medium (modified M4) and 10 mM glucose. The BES anode was the only electron acceptor. S. oneidensis grew as anode biofilm, while planktonic L.lactis converted glucose to lactate.

extract_protocol: The biofilm was scraped off the frozen carbon electrode with a sterile razor blade. Biofilm-carbon sludge was combined with 7 mL ice-cold phosphate buffer saline (PBS), vortexed, sonicated at 7 W for 30 s on ice (3 repetitions), and centrifuged. The pellets were resuspended in NAES buffer (50 mM sodium acetate buffer, 10 mM EDTA and 1 % SDS at pH 5). RNA was isolated with a phenol:chloroform extraction protocol. The isolated RNA was purified with Ambion DNase I treatment following the manufacturer’s instructions.

treatment_protocol: BES carbon paper electrodes from continuous BES operation were dipped in Qiagen RNA-protect and frozen at -80°C until total RNA extraction.

tag: genotype

value: wild type

tag: culture type

value: contiuous BES anode culture in modified M4 medium with glucose as carbon source and homolactic fermenter Lactococcus lactis LM 0230


title: FR13A_control_rep2

city: Wuhan

first: Huaiyang

last: Xiong

address: Eighty one road

country: China

institute: Wuhan University

description: Gene expression levels in non-submerged FR13A

hyb_protocol: Labeled cRNA of 1 µg was used for hybridization in a rice 4×44K oligo microarray (Agilent Technologies). The hybridization was performed at 65℃for 17 h in a rotating Agilent hybridization oven (G2545A).

scan_protocol: microarray slides were scanned using a DNA microarray scanner (G2505C, Agilent) with one color scan setting (Scan resolution 5 um, PMT is set to 100% and 10%).

data_processing: Signal intensities were extracted by Feature Extraction software (version 10.5.1.1, Agilent Technologies) at the default settings. Data were quantile normalized across all samples with the GeneSpring GX 10.0.

organism: Oryza sativa

source_name: FR13A, control, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 μg total RNA using the Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Approximately 60 pre-germinated seeds were sown in 0.50 L plastic pots filled with paddy fields soil. The plants were grown without fertilizer in a glasshouse with an air temperature range of 24-28℃under natural daylight, and thinned to 20 plants per pot.

extract_protocol: Leaves of approximately 20 plants for each genotype and treatment were harvested from various pots and pooled to make one sample for RNA extraction. Total RNAs were extracted using Trizol (Invitrogen Life Technologies), and further purified with Qiagen Rneasy mini kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: Fourteen-day-old seedlings were submerged in a 300 L plastic tank with water 70 cm deep for 3 d. The distance from the tip of the shoot to the water surface was 52.7 ±2.3 and 45.9 ± 2.9 cm per seedling at the start of complete submergence for FR13A and Goda Heenati, respectively. Controls were set out in a plastic tank without water.Daily air temperature ranged between 24℃ and 28℃ and the water temperature range was 22–25℃ during the experimental period.

tag: developmental stage

value: 14 d-old-seedlings

tag: tissue

value: leaf

tag: cultivar


title: FR13A_control_rep1

source_name: FR13A, control, replicate1


title: Goda Heenati_submergence_3 d_rep2

description: Gene expression levels in Goda Heenati submerged for 3 d

source_name: Goda Heenati, submerged for 3 d, replicate2

value: Goda Heenati


title: Goda Heenati_submergence_3 d_rep1

source_name: Goda Heenati, submerged for 3 d, replicate1


title: FR13A_submergence_3 d_rep1

description: Gene expression levels in FR13A submerged for 3 d

source_name: FR13A,submerged for 3 d,replicate1


title: Liver_HE_animal#16

status: Public on Nov 30 2010

city: Lexington

first: Shengfa

middle: F

last: Liao

state: KY

address: 214 WP Garrigus Bldg

department: Dept of Animal & Food Sciences

institute: University of Kentucky

description: Liver tissue was collected immediately after the animal was killed.

hyb_protocol: Following fragmentation, 10 μg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the GeneChip Hybridization Oven 640 (Affymetrix Technical Analysis Manual). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.   GeneChips were stained with R-Phycoerythrin Streptavidin, followed by an antibody solution and a second R-Phycoerythrin Streptavidin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.

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

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the “.cel” files from the raw methylation measurements) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO).  The algorithm of Robust Multichip Averaging adjusted with GC oligo content was implemented for background correction.  The background-corrected data were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

source_name: Liver tissue from HE-treatment steers (grazing High-Endophyte pasture)

label_protocol: Biotinylated cRNA was prepared from 4 μg of total RNA as per the standard labeling protocol described in the Affymetrix GeneChip Technical Analysis Manual (2005; Affymetrix, Santa Clara, CA).  Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers.  Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA) incorporating biotinylated UTP.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen Corporation, Carlsbad, CA).

treatment_protocol: The treatment protocol (i.e., LE and HE pastures) has been described in the “overall design” section above.

value: Biopsied liver (right lobe) tissue

tag: treatment

value: high toxic endophyte infected tall fescue


title: Goda Heenati_control_rep3

description: Gene expression levels in non-submerged Goda Heenati

source_name: Goda Heenati, control, replicate3


title: Goda Heenati_submergence_3 d_rep3

source_name: Goda Heenati, submerged for 3 d, replicate3


title: FR13A_control_rep3

source_name: FR13A, control, replicate3


title: Liver_HE_animal#11


title: S. oneidensis_MFC anode_rep2

description: Gene expression data from wild-type S. oneidensis MR-1

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: S. oneidensis anaerobic MFC anode biofilm

growth_protocol: Cells were grown anaerobically at 30°C in a contiuous bioelectrochemical system (BES) with defined medium (modified M4) and 20 mM lactate. The BES anode was the only electron acceptor.

value: contiuous BES anode culture in modified M4 medium


title: Liver_HE_animal#6


title: Liver_HE_animal#15


title: Liver_HE_animal#17


title: Liver_HE_animal#10


title: Liver_LE_animal#5

source_name: Liver tissue from LE-treatment steers (grazing Low-Endophyte pasture)

value: low toxic endophyte infected tall fescue


title: Liver_HE_animal#3


title: Goda Heenati_control_rep1

source_name: Goda Heenati, control, replicate1


title: Liver_HE_animal#1


title: S. oneidensis_MFC anode_rep1

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000

treatment_protocol: BES carbon paper electrodes from continuous BES operation were dipped in Qiagen RNA-protect and frozen at -80°C until total RNA extraction


title: S. oneidensis with L.lactis_MFC anode_rep1


title: LD_Sire_7_progeny_98

city: Brisbane

first: Ross

middle: L

last: Tellam

state: QLD

address: 306 Carmody Road St.Lucia

department: Level 6 Queensland Biosciences Precinct

country: Australia

institute: CSIRO Animal, Food and Health Sciences

description: Gene expression data from LD muscle of a Poll Dorset sheep, progeny of sire 7, classified as High Estimated Breeding Value (EBV) for Eye Muscle Depth (EMD)

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genomer Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, GCOSvs1.4

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

organism: Ovis aries

source_name: longissimus dorsi

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

growth_protocol: Progeny (40) from six Poll Dorset sires were raised and grown according to Australian industry standards.

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

treatment_protocol: LD muscle was dissected from each animal at a pre-determined site within 15 minutes of euthanasia, snap frozen under liquid nitrogen and stored at -80oC.

tag: ebv

value: HIGH


title: Liver_LE_animal#19


title: Liver_LE_animal#14


title: Liver_LE_animal#18


title: FR13A_submergence_3 d_rep2

source_name: FR13A,submerged for 3 d,replicate2


title: LD_Sire_7_progeny_18


title: Liver_LE_animal#13


title: LD_Sire_5_progeny_63

description: Gene expression data from LD muscle of a Poll Dorset sheep, progeny of sire 5, classified as Low Estimated Breeding Value (EBV) for Eye Muscle Depth (EMD)

value: LOW


title: LD_Sire_7_progeny_58


title: Liver_HE_animal#9


title: LD_Sire_5_progeny_80


title: LD_Sire_5_progeny_94


title: Liver_LE_animal#4


title: LD_Sire_5_progeny_30


title: Liver_LE_animal#7


title: LD_Sire_2_progeny_66

description: Gene expression data from LD muscle of a Poll Dorset sheep, progeny of sire 2, classified as High Estimated Breeding Value (EBV) for Eye Muscle Depth (EMD)


title: Liver_LE_animal#12


title: Liver_HE_animal#2


title: LD_Sire_7_progeny_69


title: FR13A_submergence_3 d_rep3

source_name: FR13A,submerged for 3 d,replicate3


title: LD_Sire_2_progeny_57


title: LD_Sire_5_progeny_34


title: Liver_LE_animal#8


title: LD_Sire_5_progeny_41


title: Goda Heenati_control_rep2

source_name: Goda Heenati, control, replicate2


title: LD_Sire_5_progeny_11


title: LD_Sire_5_progeny_32


title: LD_Sire_2_progeny_5


title: LD_Sire_2_progeny_3


title: LD_Sire_2_progeny_62


title: LD_Sire_2_progeny_46


title: LD_Sire_17_progeny_88

description: Gene expression data from LD muscle of a Poll Dorset sheep, progeny of sire 17, classified as Low Estimated Breeding Value (EBV) for Eye Muscle Depth (EMD)


title: LD_Sire_17_progeny_39


title: LD_Sire_17_progeny_85


title: LD_Sire_11_progeny_35

description: Gene expression data from LD muscle of a Poll Dorset sheep, progeny of sire 11, classified as High Estimated Breeding Value (EBV) for Eye Muscle Depth (EMD)


title: LD_Sire_17_progeny_79


title: LD_Sire_11_progeny_42


title: LD_Sire_16_progeny_61

description: Gene expression data from LD muscle of a Poll Dorset sheep, progeny of sire 16, classified as Low Estimated Breeding Value (EBV) for Eye Muscle Depth (EMD)


title: LD_Sire_11_progeny_51


title: LD_Sire_16_progeny_2


title: LD_Sire_16_progeny_65


title: LD_Sire_11_progeny_27


title: LD_Sire_11_progeny_101


title: LD_Sire_11_progeny_60


title: LD_Sire_11_progeny_100


title: LD_Sire_16_progeny_31


title: LD_Sire_11_progeny_91


title: LD_Sire_16_progeny_45


title: LD_Sire_16_progeny_43


title: LD_Sire_16_progeny_99


title: spleen UMC cy3, animal 6

status: Public on Nov 01 2010

city: St. Paul

first: John

last: Garbe

state: MN

address: 1988 Fitch Ave

department: Animal Science

institute: University of Minnesota

hyb_protocol: The microarrays were prehybridized for 1 hr with 0.2% I-Block (Tropix, Bedford, MA) in 1X PBS solution at 42 °C, then were washed with distilled water at room temperature for 10 min and finally were again washed with isopropanol at room temperature for 5 min using a rotary shaker. The arrays were dried by centrifugation for 5 min at 1000g. The cDNA and fluorescence dye hybridization steps were accomplished by a modification to the 3DNA array 350 kit protocol (Genisphere Inc., Hatfield, PA). A total of 20 µl of Cy3 (10 µl) and Cy5 (10 µl) labeled cDNA samples was hybridized to each array at 55 °C in a water bath for 16 hr in a dark humidified chamber. The arrays were then washed for 15 min with 2X SSC/0.2% SDS at 55 °C, for 15 min in 2X SSC at room temperature, and finally washed again for 15 min in 0.2X SSC at room temperature. The arrays were again dried by centrifugation for 5 min at 1000g. Both Cy3 and Cy5 capture reagents were combined with the hybridization buffer and were hybridized to an array for 4 hr at 55 °C in a water bath. The arrays were rewashed and dried as previously described (Galbraith et al. 2004).

scan_protocol: At UMC the arrays were immediately scanned on an Axon Genepix 4000B laser scanner (Axon Instruments, Foster City, CA), while at UMN, the arrays were scanned on a GSI Lumonics ScanArray 5000 laser scanner (GSI Lumonics, Watertown, MA). The image data were extracted using BlueFuse for microarrays (BlueGnome, Cambridge, UK)

data_processing: Spots with a quality score of 0 or with a confidence score of less than 0.1 were removed from the data. The filtered data for each array were log2 transformed and with-in slide normalized by performing a confidence-weighted LOESS regression for each print-tip to correct for an physical effects introduced by the printer head as well as to compensate for other spatial variation across the slides {{40 Smyth,G.K. 2003}}. Scale differences between slides due to variations in scanner settings and sample preparation were corrected for by standardizing intensity values to have a zero mean and unit variance using JMP Genomics (SAS Institute, Cary, NC).

source_name: bovine spleen UMC

label_protocol: Five micrograms of total RNA was used to synthesize cDNA for each dye using 8 thermal cycles at 52 °C for 10 sec and 44 °C for 15 min. The reaction was stopped with 3.5 µl of 0.5 M NaOH/50 mM EDTA and then heated at 65 °C for 15 min. The solution was neutralized with 5 µl of 1 M Tris-HCl (pH 7.5). Finally, 10 µl of cDNA was purified using a MinElute PCR purification kit (Qiagen, Valencia, CA).  The fluorescence dye hybridization steps were accomplished by a modification to the 3DNA array 350 kit protocol (Genisphere Inc., Hatfield, PA).

extract_protocol: Total RNA was extracted using 3 ml of TRI reagent (Ambion, Austin, TX) per 250-300 mg of tissue from each sample. The extract was treated with 0.02 Units of DNase1 (Ambion) and cleaned up using phenol:chloroform:isoamyl alcohol (25:24:1), a Phase Lock Gel Heavy tube (Eppendorf, Hamburg, Germany) and a YM30 microcon tube (Millipore, Billerica, MA).

tag: array

tag: animal

value: spleen

tag: site

value: UMC


title: thymus UMC cy3, animal 2

source_name: bovine thymus UMC

value: thymus


title: liver UMC cy3, animal 2

source_name: bovine liver UMC

value: liver


title: thymus UMC cy5, animal 5


title: small intestine UMC cy3, animal 4

source_name: bovine small intestine UMC

value: small intestine


title: spleen UMC cy5, animal 2


title: small intestine UMC cy5, animal 1


title: liver UMC cy5, animal 4


title: spleen UMC cy5, animal 3


title: adrenal UMC cy3, animal 2

source_name: bovine adrenal UMC

value: adrenal


title: spleen UMC cy5, animal 1


title: adrenal gland UMC cy5, animal 5

source_name: bovine adrenal gland UMC

value: adrenal gland


title: spleen UMC cy3, animal 3


title: spleen UMC cy3, animal 5


title: adrenal gland UMC cy5, animal 2


title: anterior pituitary UMC cy5, animal 6

source_name: bovine anterior pituitary UMC

value: anterior pituitary


title: thymus UMC cy3, animal 3


title: liver UMC cy5, animal 1


title: anterior pituitary gland UMC cy3, animal 5

source_name: bovine anterior pituitary gland UMC

value: anterior pituitary gland


title: anterior pituitary UMC cy5, animal 3


title: anterior pituitary gland UMC cy3, animal 1


title: liver UMC cy3, animal 3


title: LD_Sire_2_progeny_47


title: anterior pituitary UMC cy5, animal 4


title: thymus UMC cy5, animal 6


title: small intestine UMC cy5, animal 3


title: adrenal UMC cy3, animal 6


title: anterior pituitary gland UMC cy3, animal 4


title: adrenal gland UMC cy5, animal 4


title: adrenal UMC cy3, animal 5


title: adrenal gland UMC cy5, animal 3


title: anterior pituitary UMC cy5, animal 5


title: anterior pituitary gland UMC cy3, animal 2


title: thymus UMC cy5, animal 3


title: small intestine UMC cy5, animal 2


title: thymus UMC cy3, animal 6


title: thymus UMC cy3, animal 5


title: thymus UMC cy5, animal 1


title: anterior pituitary gland UMC cy3, animal 6


title: anterior pituitary gland UMC cy3, animal 3


title: small intestine UMC cy3, animal 6


title: thymus UMC cy5, animal 4


title: small intestine UMC cy3, animal 1


title: thymus UMC cy3, animal 1


title: adrenal UMC cy3, animal 1


title: LD_Sire_17_progeny_71


title: liver UMC cy5, animal 2


title: spleen UMC cy3, animal 1


title: spleen UMC cy5, animal 5


title: anterior pituitary UMC cy5, animal 2


title: adrenal UMC cy3, animal 4


title: thymus UMC cy3, animal 4


title: liver UMC cy3, animal 5


title: spleen UMC cy5, animal 4


title: anterior pituitary UMC cy5, animal 1


title: adrenal UMC cy3, animal 3


title: spleen UMC cy3, animal 2


title: LD_Sire_16_progeny_21


title: liver UMC cy3, animal 1


title: adrenal gland UMC cy5, animal 6


title: liver UMC cy5, animal 5


title: spleen UMC cy5, animal 6


title: spleen UMC cy3, animal 4


title: adrenal gland UMC cy5, animal 1


title: small intestine UMC cy3, animal 3


title: small intestine UMC cy5, animal 6


title: liver UMC cy5, animal 3


title: small intestine UMC cy5, animal 4


title: small intestine UMC cy3, animal 5


title: small intestine UMC cy5, animal 5


title: liver UMC cy3, animal 6


title: liver UMC cy3, animal 4


title: small intestine UMC cy3, animal 2


title: spleen UMN cy3, animal 6

source_name: bovine spleen UMN

value: UMN


title: spleen UMN cy5, animal 2


title: thymus UMN cy5, animal 5

source_name: bovine thymus UMN


title: liver UMC cy5, animal 6


title: liver UMN cy5, animal 4

source_name: bovine liver UMN


title: thymus UMN cy3, animal 2


title: anterior pituitary gland UMN cy3, animal 4

source_name: bovine anterior pituitary gland UMN


title: liver UMN cy3, animal 2


title: small intestine UMN cy3, animal 4

source_name: bovine small intestine UMN


title: small intestine UMN cy5, animal 1


title: adrenal gland UMN cy5, animal 2

source_name: bovine adrenal gland UMN


title: spleen UMN cy3, animal 3


title: adrenal UMN cy3, animal 2

source_name: bovine adrenal UMN


title: spleen UMN cy3, animal 5


title: thymus UMN cy5, animal 6


title: liver UMN cy5, animal 1


title: liver UMN cy3, animal 3


title: small intestine UMN cy3, animal 1


title: adrenal gland UMN cy5, animal 4


title: adrenal UMN cy3, animal 6


title: thymus UMN cy3, animal 3


title: anterior pituitary UMN cy5, animal 6

source_name: bovine anterior pituitary UMN


title: anterior pituitary UMN cy5, animal 4


title: anterior pituitary UMN cy5, animal 3


title: anterior pituitary gland UMN cy3, animal 1


title: spleen UMN cy5, animal 3


title: adrenal gland UMN cy5, animal 5


title: spleen UMN cy5, animal 1


title: small intestine UMN cy5, animal 3


title: adrenal UMN cy3, animal 5


title: anterior pituitary gland UMN cy3, animal 2


title: adrenal gland UMN cy5, animal 3


title: anterior pituitary UMN cy5, animal 5


title: adrenal UMN cy3, animal 1


title: thymus UMC cy5, animal 2


title: thymus UMN cy5, animal 3


title: thymus UMN cy3, animal 6


title: small intestine UMN cy5, animal 2


title: small intestine UMN cy3, animal 6


title: thymus UMN cy5, animal 2


title: thymus UMN cy3, animal 1


title: anterior pituitary UMN cy5, animal 2


title: LVS8 Spleen Rep 1

city: Fort Collins

first: Luke

last: Kingry

state: CO

address: 2025 IDRC at Foothills Campus Delivery

institute: Colorado State University

description: Array contains 250 negative control spots  spaced randomly throughout the array.  100 housekeeping genes printed in triplicate randomly throughout the array for positive controls and normalization

hyb_protocol: Dye coupled cDNA, was combined with yeast tRNA (10mg/mL), and hybridization buffer (formamide, 20XSSC and 10%SDS) and heated.  Single channel (Cy3) hybridization was carried out in triplicate for each sample.

scan_protocol: Data were generated by Genepix Pro 4000b scanner and Genepix Pro software

data_processing: Background correction and normalized to the global mean of the entire data set for each organ

molecule: polyA RNA

organism: Mus musculus

source_name: LVS Inf, 120h Spleen

label_protocol: Messenger RNA was converted to cDNA using poly(T) primers and amplified in the presence of modified dUTPs using the AminoAllyl Message Amplification Kit (Ambion, Foster City, CA).  Indirect labeling of cDNA for hybridization was conducted by conjugating Cy3 dye with modified dUTPs in a subsequent reaction.

extract_protocol: RNA was stabilized and recovered from mouse organs by the addition of TRIzol reagent and organic partitioning.  Total RNA was extracted from the TRIzol by the addition of chloroform (1:1) to achieve a bi-phase separation, then precipitated by the addition of isopropanol and subjected to Dnase treatment, and purified using a Qiagen RNeasy kit (Valencia, CA).

tag: gender

value: Female

tag: strain


title: LVS7 Spleen Rep 2


title: anterior pituitary gland UMN cy3, animal 3


title: spleen UMN cy5, animal 6


title: LVS7 Spleen Rep 1


title: LVS6 Spleen Rep 3

source_name: LVS Inf, 48h Spleen


title: LVS8 Spleen Rep 2


title: LVS6 Spleen Rep 1


title: thymus UMN cy3, animal 5


title: LVS6 Spleen Rep 2


title: thymus UMN cy5, animal 4


title: LVS8 Spleen Rep 3


title: anterior pituitary UMN cy5, animal 1


title: spleen UMN cy5, animal 5


title: thymus UMN cy5, animal 1


title: thymus UMN cy3, animal 4


title: anterior pituitary gland UMN cy3, animal 6


title: LVS7 Spleen Rep 3


title: LVS5 Spleen Rep 1


title: LVS5 Spleen Rep 3


title: LVS5 Spleen Rep 2


title: spleen UMN cy3, animal 4


title: LVS3 Spleen Rep 3

source_name: LVS Inf, 24h Spleen


title: liver UMN cy5, animal 2


title: LVS4 Spleen Rep 3


title: LVS4 Spleen Rep 2


title: LVS1 Spleen Rep 3

source_name: LVS Inf, 12h Spleen


title: liver UMN cy3, animal 1


title: LVS2 Spleen Rep 3


title: spleen UMN cy3, animal 2


title: LVS3 Spleen Rep 2


title: LVS3 Spleen Rep 1


title: Schu7 Spleen Rep 3

source_name: Schu4 Inf, 120h Spleen


title: Schu8 Spleen Rep 3


title: Schu7 Spleen Rep 1


title: LVS2 Spleen Rep 1


title: LVS4 Spleen Rep 1


title: liver UMN cy5, animal 5


title: Schu6 Spleen Rep 3

source_name: Schu4 Inf, 48h Spleen


title: liver UMN cy3, animal 5


title: adrenal gland UMN cy5, animal 6


title: LVS1 Spleen Rep 1


title: spleen UMN cy5, animal 4


title: LVS1 Spleen Rep 2


title: spleen UMN cy3, animal 1


title: adrenal UMN cy3, animal 3


title: LVS2 Spleen Rep 2


title: anterior pituitary gland UMN cy3, animal 5


title: adrenal gland UMN cy5, animal 1


title: Schu8 Spleen Rep 1


title: Schu8 Spleen Rep 2


title: Schu7 Spleen Rep 2


title: Schu6 Spleen Rep 2


title: Schu5 Spleen Rep 3


title: adrenal UMN cy3, animal 4


title: small intestine UMN cy5, animal 6


title: Schu4 Spleen Rep 2

source_name: Schu4 Inf, 24h Spleen


title: small intestine UMN cy3, animal 5


title: small intestine UMN cy5, animal 4


title: small intestine UMN cy3, animal 3


title: Schu1 Spleen Rep 3

source_name: Schu4 Inf, 12h Spleen


title: liver UMN cy3, animal 6


title: Schu3 Spleen Rep 3


title: Schu2 Spleen Rep 3


title: Control 2 Spleen Rep 3

source_name: Uninfected Control Mouse Spleen


title: Schu5 Spleen Rep 2


title: Schu3 Spleen Rep 1


title: Schu4 Spleen Rep 1


title: Schu1 Spleen Rep 2


title: Schu2 Spleen Rep 2


title: liver UMN cy3, animal 4


title: liver UMN cy5, animal 6


title: Schu5 Spleen Rep 1


title: Control 2 Spleen Rep 1


title: Schu2 Spleen Rep 1


title: liver UMN cy5, animal 3


title: Schu1 Spleen Rep 1


title: Schu3 Spleen Rep 2


title: Control 1 Spleen Rep 2


title: small intestine UMN cy5, animal 5


title: Control 2 Spleen Rep 2


title: LVS7 Lung Rep 3

source_name: LVS Inf, 120h Lung


title: LVS8 Lung Rep 2


title: small intestine UMN cy3, animal 2


title: LVS8 Lung Rep 1


title: Control 1 Spleen Rep 1


title: LVS4 Lung Rep 3

source_name: LVS Inf, 24h Lung


title: LVS4 Lung Rep 2


title: LVS5 Lung Rep 2

source_name: LVS Inf, 48h Lung


title: LVS7 Lung Rep 1


title: LVS2 Lung Rep 1

source_name: LVS Inf, 12h Lung


title: LVS6 Lung Rep 3


title: LVS3 Lung Rep 1


title: LVS2 Lung Rep 3


title: LVS6 Lung Rep 2


title: Control 1 Spleen Rep 3


title: LVS7 Lung Rep 2


title: LVS5 Lung Rep 3


title: LVS2 Lung Rep 2


title: LVS4 Lung Rep 1


title: LVS6 Lung Rep 1


title: LVS3 Lung Rep 2


title: LVS5 Lung Rep 1


title: LVS1 Lung Rep 3


title: LVS3 Lung Rep 3


title: LVS1 Lung Rep 1


title: LVS1 Lung Rep 2


title: Schu8 Lung Rep 3

source_name: Schu4 Inf, 120h Lung


title: Schu7 Lung Rep 2


title: Schu7 Lung Rep 3


title: Schu8 Lung Rep 2


title: Schu7 Lung Rep 1


title: Schu5 Lung Rep 3

source_name: Schu4 Inf, 48h Lung


title: Schu6 Lung Rep 2


title: Schu2 Lung Rep 2

source_name: Schu4 Inf, 12h Lung


title: Schu8 Lung Rep 1


title: Schu2 Lung Rep 3


title: Schu5 Lung Rep 1


title: Schu2 Lung Rep 1


title: Schu5 Lung Rep 2


title: Schu6 Lung Rep 1


title: Schu4 Lung Rep 3

source_name: Schu4 Inf, 24h Lung


title: Control 2 Lung Rep 2

source_name: Uninfected Control Mouse Lung


title: Schu6 Lung Rep 3


title: Schu3 Lung Rep 2


title: Schu1 Lung Rep 2


title: Schu1 Lung Rep 1


title: Schu3 Lung Rep 1


title: Schu4 Lung Rep 1


title: Schu1 Lung Rep 3


title: Control 2 Lung Rep 3


title: Schu3 Lung Rep 3


title: Control 2 Lung Rep 1


title: Control 1 Lung Rep 3


title: Schu4 Lung Rep 2


title: Schu6 Spleen Rep 1


title: GASpos_sample9

city: San Antonio

first: Jeffrey

last: Livezey

state: TX

address: 3400 Rawley E Chambers Ave

department: Clinical Investigation

institute: Brooke Army Medical Center

hyb_protocol: Microarrays were pre-hybridized for 10 minutes with nuclease-free water at 65°C and then for 30 minutes at 45°C wit hpre-hybridization solution (Combimatrix). Five 5µg of biotin labelled RNA was then fragmented with10X Fragmentation Buffer (Combimatrix) for 20 minutes at 70°C. The fragmented RNA was then hybridized to the microarray using Hybridization solution (Combimatrix) at 45°C for 16 hours.The microarray was then washed 3 times with 6X SSPET (Combimatrix) and then 3 times with 3X SSPET (Combimatrix). The array was then washed 1 time with PBST (Combimatrix). The microarray was then blocked using Blocking Buffer (Combimatrix) for 5 minutes at room temperature and then the Biotin Labeling Solution was added (Combimatrix) and incubated with the microarray for 30 minutes at room temperature. The microarray was then washed 2 times with PBST then TMB Rinse Solution (Combimatrix) beofre being placed into the ElectraSense reader (Combimatrix).

scan_protocol: Microarrays were inserted into the ElectraSense Microarray Reader and scanned using the ElectraSense application software (Combimatrix). Raw data was stored as an .ECD file.

data_processing: Factory built in negative controls were used for background subtraction.   The mean of the lowest 10% of the negative controls was subtracted from all values.  To avoid negative numbers, 2 standard deviations of the mean was used to replace all negative numbers.  All samples were normalized using a median quantile method performed with ProbeWeaver software (Combimatrix Corporation). The Feature # 0 in the raw file corresponds with ID #1 for the GPL10562 full array layout.

organism: Homo sapiens

source_name: human pharyngeal/tonsilar swab

label_protocol: One hundred ng of total RNA was amplified using the MessageAmp II-Bacteria Kit (Applied Biosystems). The RNA was labeled with biotin-11-UTP (Perkin Elmer) according to the kit's protocol during the in vitro transcription of aRNA

growth_protocol: Throat swabs containing GAS were maintained at -80°C until nucleic acid extraction was performed.

extract_protocol: Throat swabs were incubated in 2ml of lysis buffer (Biomerieux) at 60°C for 30 minutes and then nucleic acids were extracted using the EasyMag automated nucleic acid extraction system (Biomerieux). Genomic DNA was removed using Dnase (Ambion) and verified using PCR.

value: <18 years old

tag: culture results

value: GAS positive


title: GASpos_sample11


title: GASneg_sample1

value: GAS negative


title: GASneg_sample2


title: GASpos_sample10


title: Schu4 Spleen Rep 3


title: GASneg_sample3


title: GASpos_sample2


title: Control 1 Lung Rep 2


title: GASpos_sample3


title: GASpos_sample7


title: GASpos_sample8


title: GASpos_sample4


title: GASpos_sample6


title: Control 1 Lung Rep 1


title: GASpos_sample5


title: GASpos_sample1


title: atrium_SlnKO_rep3

city: Newark

first: Gopal

middle: J

last: Babu

state: NJ

address: 185 South Orange Ave

department: CELL BIOLOGY AND MOLECULAR MED

institute: University of Medicine & Dentistry of New Jersey-NJMS

description: Gene expression data from Sln knockout

hyb_protocol: RNA samples were hybridizaed with Affymetrix expression arrays offering whole-transcript coverage. After hybridization, non-specific binding was washed off according to the manufacturer's protocol.

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner.

data_processing: In the Expression Console software, hybridization intensity data were normalized using the Robust Multichip Average (RMA) method.

source_name: mouse SlnKO atrium

label_protocol: Biotinylated cRNA were prepared from total RNA as described by Affymetrix.

growth_protocol: No growth protocol. Atrial tissues were taken from 4-5 months old SLN knockout and C57/BL6 control mice

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

treatment_protocol: No treatment prior to experiment was applied.

value: sln-/-

value: heart atrium

value: male

value: 4-5 months


title: atrium_SlnKO_rep2

description: Gene expression data from Sln knockout


title: radiation treated  [chip A]

city: Delhi

first: Vibha

last: Tandon

state: Delhi

address: University of Delhi

department: Department of Chemistry

country: India

institute: University of Delhi

hyb_protocol: 20µg of the labeled aRNA in 200µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins and 100µl was used for hybridization with the Human 40KA and Human 40KB separately printed at Ocimum Biosolutions,Hyderabad.Hybridization was performed at 50°C for two hours on Tecan HS4800 automated Hyb station.

scan_protocol: Hybridized chips were scanned using Affymetrix 428 Array scanner at three different PMT gains.

data_processing: Initial dataset that consisted of 40,320 probes was filtered to exclude QC probes and empty spots.The data was transformed using log-transformation (log2) and median absolute deviation was performed. An exploratory approach consisting of two-stages to detect outliers from bivariate population and determining differentially expressed candidates from these outliers.The approach provides the fold-change value considering the scatter of observations and thereby provides up and down regulated genes across samples. Thus, for functional classification, differentially expressed genes were identified by Multivariate Outlier Detection Method.

source_name: Human Embryonic Kidney

label_protocol: Five microgram of total RNA was used for amplification using ExpressArt mRNA amplification kit by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA is reverse transcribed followed by second strand synthesis priming with a oligo(dT) primer bearing T7 promoter in a thermal cycler. The resulting cDNA was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA is then labelled with Cy3 post-labelling reactive dye pack at room temperature and unincorporated Cy3 molecules were removed by purification process.

extract_protocol: HEK, human embryonic kidney cells, were subjected to DNA minor groove binding ligand and ionizing radiation treatment. RNA was extracted using TriReagent and further purified using Qiagen Rneasy minikit according to manufacturer's protocol.RNA quality was checked by agarose gel electrophoresis and spectrophotometry.

treatment_protocol: HEK cell line was plated 24 hrs prior to the experiment. The treatment conditions followed were- control (untreated), ligand(50uM treated), radiation (2 Gy treated), Ligand+radiation(50uM+2Gy treated).Cells were then incubated further for 4 hrs following these treatment conditions and RNA samples were prepared.

tag: cell line

value: Human Embryonic Kidney

value: 2Gy radiation


title: ligand and radiation treated  [chip A]

value: 50µM ligand + 2Gy radiation


title: LVS8 Lung Rep 3


title: atrium_control_rep3

description: Gene expression data from Control C57

source_name: mouse wildtype atrium

value: wild type

tag: age


title: atrium_SlnKO_rep1

description: Gene expression data from Sln knockout


title: hybrid deleted for RPD3 repeat #2 Cy3

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

description:
RPD3_hybrid2
raw data file (block, dye) = RPD3.srr (block #2, Cy3)

hyb_protocol: Agilent Gene Expression Hybridization Kit p/n 5188-5242

scan_protocol: Arrays were scanned using Agilent Microarray Scanner (p/n G2565BA) with a 5 micron resolution and photomultiplier tube (PMT) set to 100 and then rescanned with PMT=10. The images analyzed were from the PMT=100 unless data has reached saturation. The raw images  were analyzed and quantified using Spotreader software (Niles scientific).

data_processing: Raw hybridization intensities were background subtracted and log2-transformed. Results of different samples from the same condition were converted into the same distribution using percentile normalization. Probes were then sorted into 10 bins of similar %GC and the log-intensities of each bin were renormalized to the mean and Std of all probes. Finally, the normalized expression was averaged over the technical repeats of each probe (each probe was placed at 3-4 different positions on the array).

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: S. cerevisiae BY4741 X  S. paradoxus CBS432 (ho::kanMX4/ho::nat1 MATa/MATα)

label_protocol: Agilent Low RNA Input Amplificarion Kit (LRIAK) plus, two color p/n 5188-5340

growth_protocol: All samples were collected at log-phase growth. Starters were grown over night, dluted to OD(600)=0.1 in 10ml medium and harvested ~5 hours after dilution when OD(600)=~0.5

extract_protocol: Total RNA was extracted using MasterPure™ Yeast RNA purification Kit (EPICENTRE).

tag: organism(s)

value: hybrid

tag: genotype/variation

value: RPD3 deletion mutant

tag: growth protocol

value: YPD rich medium at 30°C


title: S.cerevisiae and S.paradoxus each deleted for TUP1 repeat #2 Cy5

description:
TUP1_species2
raw data file (block, dye) = TUP1.srr (block #2, Cy5)

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

source_name: S. cerevisiae (BY4741 ho::kanMX4  MATa), S. paradoxus (CBS432 ho::nat1 MATα)

value: pooled sample of both species

value: TUP1 deletion mutant


title: atrium_control_rep2

description: Gene expression data from Control C57

tag: genotype


title: hybrid deleted for RPD3 repeat #1 Cy5

description:
RPD3_hybrid1
raw data file (block, dye) = RPD3.srr (block #1, Cy5)


title: atrium_control_rep1

description: Gene expression data from Control C57


title: 50uM+8.5Gy

description: ligand and radiation treated

hyb_protocol: 20µg of the labeled aRNA in 200µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins and 100µl was used for hybridization with the Human 40KA and Human 40KB separately printed at Ocimum Biosolutions,Hyderabad. Hybridization was performed at 50°C for two hours on Tecan HS4800 automated Hyb station.

extract_protocol: U87, human glioma cells, were subjected to DNA minor groove binding ligand and ionizing radiation treatment.RNA was extracted using TriReagent and further purified using Qiagen Rneasy minikit according to manufacturer's protocol.RNA quality was checked by agarose gel electrophoresis and spectrophotometry.

treatment_protocol: U87 cell line was plated 24 hrs prior to the experiment. The treatment conditions followed were- control (untreated), ligand(50uM treated), radiation (8.5 Gy treated), Ligand+radiation(50uM+8.5Gy treated).Cells were then incubated further for 4 hrs following these treatment conditions and RNA samples were prepared.

tag: cell type

value: glioma


title: radiation treated  [chip B]


title: untreated [chip B]


title: Control

description: untreated

source_name: Control


title: S.cerevisiae and S.paradoxus each deleted for TUP1 repeat #1 Cy3

description:
TUP1_species1
raw data file (block, dye) = TUP1.srr (block #1, Cy3)


title: 50uM

description: ligand treated


title: ligand and radiation treated  [chip B]


title: 8.5 Gy

description: radiation treated


title: ligand treated  [chip A]

value: 50µM ligand


title: untreated [chip A]


title: S.cerevisiae and S.paradoxus each deleted for RPD3 repeat #2 Cy5

description:
RPD3_species2
raw data file (block, dye) = RPD3.srr (block #2, Cy5)


title: S.cerevisiae and S.paradoxus each deleted for RPD3 repeat #1 Cy3

description:
RPD3_species1
raw data file (block, dye) = RPD3.srr (block #1, Cy3)


title: hybrid deleted for HAP4 repeat #2 Cy3

description:
HAP4_hybrid2
raw data file (block, dye) = HAP4.srr (block #2, Cy3)

value: HAP4 deletion mutant


title: S.cerevisiae and S.paradoxus each deleted for HAP4 repeat #1 Cy3

description:
HAP4_species1
raw data file (block, dye) = HAP4.srr (block #1, Cy3)


title: S.cerevisiae and S.paradoxus each deleted for HAP4 repeat #2 Cy5

description:
HAP4_species2
raw data file (block, dye) = HAP4.srr (block #2, Cy5)


title: hybrid deleted for BRE1 repeat #1 Cy5

description:
BRE1_hybrid1
raw data file (block, dye) = BRE1.srr (block #1, Cy5)

value: BRE1 deletion mutant


title: S.cerevisiae and S.paradoxus each deleted for RAD6 repeat #2 Cy5

description:
RAD6_species2
raw data file (block, dye) = RAD6.srr (block #2, Cy5)

value: RAD6 deletion mutant


title: hybrid deleted for RAD6 repeat #2 Cy3

description:
RAD6_hybrid2
raw data file (block, dye) = RAD6.srr (block #2, Cy3)


title: hybrid deleted for GCN5 repeat #2 Cy3

description:
GCN5_hybrid2
raw data file (block, dye) = GCN5.srr (block #2, Cy3)

value: GCN5 deletion mutant


title: hybrid deleted for HAP4 repeat #1 Cy5

description:
HAP4_hybrid1
raw data file (block, dye) = HAP4.srr (block #1, Cy5)


title: hybrid deleted for BRE1 repeat #2 Cy3

description:
BRE1_hybrid2
raw data file (block, dye) = BRE1.srr (block #2, Cy3)


title: hybrid deleted for GCN5 repeat #1 Cy5

description:
GCN5_hybrid1
raw data file (block, dye) = GCN5.srr (block #1, Cy5)


title: S.cerevisiae and S.paradoxus each deleted for BRE1 repeat #2 Cy5

description:
BRE1_species2
raw data file (block, dye) = BRE1.srr (block #2, Cy5)


title: hybrid deleted for RAD6 repeat #1 Cy5

description:
RAD6_hybrid1
raw data file (block, dye) = RAD6.srr (block #1, Cy5)


title: S.cerevisiae and S.paradoxus each deleted for GCN5 repeat #2 Cy5

description:
GCN5_species2
raw data file (block, dye) = GCN5.srr (block #2, Cy5)


title: ligand treated  [chip B]


title: hybrid deleted for ISW1 repeat #1 Cy5

description:
ISW1_hybrid1
raw data file (block, dye) = ISW1.srr (block #1, Cy5)

value: ISW1 deletion mutant


title: S.cerevisiae and S.paradoxus each deleted for GCN5 repeat #1 Cy3

description:
GCN5_species1
raw data file (block, dye) = GCN5.srr (block #1, Cy3)


title: S.cerevisiae and S.paradoxus each deleted for RAD6 repeat #1 Cy3

description:
RAD6_species1
raw data file (block, dye) = RAD6.srr (block #1, Cy3)


title: PGC-1alpha L2L3M_rep6

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: Manufacturer suggested

scan_protocol: GeneChip HT Scanner (Affymetrix P/N 00-0172)

data_processing: For the gene selection reported in the associated manuscript, the data were processed in dChip software; expresion data were log2-trasformed and normalized invariant set normalization with running median smoothing; expression was modelled by MBEI based on PM-MM differences. Single, array and probe outliers were considered.

source_name: hMEC, L2L3

label_protocol: Affymetrix 1-cycle IVT

growth_protocol: Primary human mammary epithelial cells were cultured in MEBM (Cambrex, East Rutherford, NJ) with MEGM bullet kit and supplemented with 5mg/ml transferrin and 10-5M isoproterenol.

extract_protocol: RNeasy mini kit (Qiagen, Valencia, CA)

treatment_protocol: hMECs were serum starved for 36h followed by infection with MOI=150 of adenoviruses expressing two variants of PGC1alpha, a protein ligand for ERRalpha: PGC-1alpha2x9 or PGC-1alpha L2L3M.

value: mammary epitheliel


title: hybrid deleted for ISW1repeat #2 Cy3

description:
ISW1_hybrid2
raw data file (block, dye) = ISW1.srr (block #2, Cy3)


title: S.cerevisiae and S.paradoxus each deleted for ISW1 repeat #2 Cy5

description:
ISW1_species2
raw data file (block, dye) = ISW1.srr (block #2, Cy5)


title: PGC-1alpha L2L3M_rep5


title: PGC-1alpha L2L3M_rep3


title: PGC-1alpha L2L3M_rep7


title: PGC-1alpha L2L3M_rep4


title: S.cerevisiae and S.paradoxus each deleted for ISW1 repeat #1 Cy3

description:
ISW1_species1
raw data file (block, dye) = ISW1.srr (block #1, Cy3)


title: PGC-1alpha L2L3M_rep10


title: PGC-1alpha L2L3M_rep8


title: PGC-1alpha L2L3M_rep9


title: PGC-1alpha L2L3M_rep2


title: PGC-1alpha L2L3M_rep1


title: hybrid deleted for HTZ1 repeat #2 Cy3

description:
HTZ1_hybrid2
raw data file (block, dye) = HTZ1.srr (block #2, Cy3)

value: HTZ1 deletion mutant


title: S.cerevisiae and S.paradoxus each deleted for HTZ1 repeat #2 Cy5

description:
HTZ1_species2
raw data file (block, dye) = HTZ1.srr (block #2, Cy5)


title: PGC-1alpha2x9_rep10

source_name: hMEC, 2x10


title: hybrid deleted for HTZ1 repeat #1 Cy5

description:
HTZ1_hybrid1
raw data file (block, dye) = HTZ1.srr (block #1, Cy5)


title: hybrid deleted for SET1 repeat #1 Cy5

description:
SET1_hybrid1
raw data file (block, dye) = SET1.srr (block #1, Cy5)

value: SET1 deletion mutant


title: S.cerevisiae and S.paradoxus each deleted for HTZ1 repeat #1 Cy3

description:
HTZ1_species1
raw data file (block, dye) = HTZ1.srr (block #1, Cy3)


title: PGC-1alpha2x9_rep5

source_name: hMEC, 2x9


title: PGC-1alpha2x9_rep7


title: PGC-1alpha2x9_rep3


title: PGC-1alpha2x9_rep8


title: PGC-1alpha2x9_rep9


title: S.cerevisiae and S.paradoxus each deleted for SET1 repeat #2 Cy5

description:
SET1_species2
raw data file (block, dye) = SET1.srr (block #2, Cy5)


title: hybrid deleted for TUP1 repeat #1 Cy5

description:
TUP1_hybrid1
raw data file (block, dye) = TUP1.srr (block #1, Cy5)


title: PGC-1alpha2x9_rep6


title: PGC-1alpha2x9_rep1


title: PGC-1alpha2x9_rep4


title: hybrid deleted for TUP1 repeat #2 Cy3

description:
TUP1_hybrid2
raw data file (block, dye) = TUP1.srr (block #2, Cy3)


title: PGC-1alpha2x9_rep2


title: hybrid deleted for SET1 repeat #2 Cy3

description:
SET1_hybrid2
raw data file (block, dye) = SET1.srr (block #2, Cy3)


title: S.cerevisiae and S.paradoxus each deleted for SET1 repeat #1 Cy3

description:
SET1_species1
raw data file (block, dye) = SET1.srr (block #1, Cy3)


title: L1 larvae treated with gfp(RNAi), replicate 3

status: Public on Oct 31 2010

city: Fribourg

first: Claude-Olivier

last: Marti

address: Chemin du Musée 10

department: Biology

country: Switzerland

institute: University of Fribourg, Zoology

description:
Gene expression from L1 larvae treated with gfp(RNAi) = reference, replicate 3.
gfp_RNAi_L1_batch3

hyb_protocol: Done by the FGCZ, Zurich: Biotin-labeled cRNA samples (15 ug) were fragmented randomly to 35-200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371) and were mixed in 300 μl of Hybridization Mix (Affymetrix Inc., P/N 900720) containing Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip® C. elegans Genome Arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 FS450_0004 protocol. An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Done by the FGCZ, Zurich: Raw data processing was performed using the Affymetrix AGCC software (version 2.0.1). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al. 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). Genes with a p-value < 0.01 and fold change (fc) >2 fold (upregulated) or <-2 fold (downregulated) were defined as deregulated genes.

organism: Caenorhabditis elegans

source_name: L1 larvae treated with gfp(RNAi)

label_protocol: Done by the Functional Genomics Center Zurich (FGCZ), Zurich: The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies,Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260nm/280nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (2 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc.,P/N900371). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371), and its quality and quantity were determined using NanoDrop ND 1000 and Bioanalyzer 2100.

growth_protocol: Synchronized wild type L4 larvae (N2, Bristol strain)  were transferred to plates seeded with HT115 bacteria expressing the different dsRNA constructs at 25°C. Gravid adults were bleached and embryos were synchronized on NGM plates without food at 25°C. The L1 larvae were collected just after hatching and fed for 3 hours at 25°C with HT115 bacteria carrying the different dsRNA constructs to recover from starvation. RNAi constructs used: 1) gfp(RNAi) as reference: pPE128.110 in HT115 bacteria; 2) let-418(RNAi): pFG97 in HT115, 440bp of let-418 cDNA into pPD129.36; and 3) mep-1(RNAi): pMP167 in HT115, 900bp of mep-1 in pPD129.36 in HT115 bacteria.

extract_protocol: To each worm pellet (40-50μl of packed worms), 450μl QIAzol (Qiagen, cat. 79306) were added, and vortexed vigorously for 15sec. The mixture was flash frozen in liquid N2, thawed at RT, and then vortexed. The freeze/thaw cycle was repeated 3x, and the mixture stored at -80°C until all samples were collected. To maximize RNA isolation, 7.5µg linear polyacrylamide (GenElute-LPA, Sigma, cat. 56575-1ML) was added to the thaw samples. Samples were vortexed and transferred to pre-spun MaXtract High Density 2ml tubes (Qiagen, cat. 129056). 90μl chloroform were added and the tubes were shaken vigorously for 15sec by hand AND NOT vortexed! The tubes were centrifuged at 12,000g for 10 minutes at 4°C. The top aqueous layer was removed to a fresh ED tube. 0.7-0.8 volume of isopropanol were added, and the tubes mixed well, and then transferred at -20°C overnight.  Next day, the tubes were centrifuged at top speed for 25min at 4°C. The RNA pellets were then washed in 500μl 75% EtOH (in DEPC-ddwater), spun at top speed, for 5 minutes at 4°C. Supernatant was remove and the pellets were briefly air-dried (1min), and then dissolved in 100μl RNAse free ddH2O. The samples were incubated at 55°C for 5min to facilitate dissolution.Purification of total RNA was performed using RNeasy Mini kit (Qiagen, cat no 74104), according to manufacturer protocol (4th editon, April 2006). On-column DNase digestion was performed (Rnase-Free DNase Set, Qiagen, cat. no. 79254) to eliminate DNA.  RNA was eluted with 30μl of RNAse-free water. Samples were stored at -80°C.

treatment_protocol: The L1 larvae were washed off of NGM plates using M9 and washed twice with M9 to obtain a worm pellet (40-50μl of packed worms).

value: N2 Bristol

tag: background genotype

tag: developmental stage

value: L1 larvae

tag: rnai

value: gfp

tag: sample type

value: reference

tag: batch


description:
Gene expression from L1 larvae treated with let-418(RNAi), replicate 2.
let418_RNAi_L1_batch2

scan_protocol: Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.) was used to measure the fluorescent intensity emitted by the labeled target.

source_name: L1 larvae treated with let-418(RNAi)

value: wild type


description:
Gene expression from L1 larvae treated with mep-1(RNAi), replicate 2.
mep1_RNAi_L1_batch2

source_name: L1 larvae treated with mep-1(RNAi)


title: L1 larvae treated with gfp(RNAi), replicate 2

description:
Gene expression from L1 larvae treated with gfp(RNAi) = reference, replicate 2.
gfp_RNAi_L1_batch2


title: L1 larvae treated with gfp(RNAi), replicate 1

description:
Gene expression from L1 larvae treated with gfp(RNAi) = reference, replicate 1.
gfp_RNAi_L1_batch1


description:
Gene expression from L1 larvae treated with let-418(RNAi), replicate 1.
let418_RNAi_L1_batch1


description:
Gene expression from L1 larvae treated with let-418(RNAi), replicate 3.
let418_RNAi_L1_batch3


description:
Gene expression from L1 larvae treated with mep-1(RNAi), replicate 1.
mep1_RNAi_L1_batch1


description:
Gene expression from L1 larvae treated with mep-1(RNAi), replicate 3.
mep1_RNAi_L1_batch3


title: CAX1/CAX3 mutant replicate 1

status: Public on Oct 20 2010

city: Glen Osmond

first: Ute

last: Baumann

state: SA

address: Hartley Grove

department: Australian Centre for Plant Functional Genomics

institute: University of Adelaide

description: whole plant

hyb_protocol: The array was hybridized overnight at 45°C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain. Signal amplification was done using biotinylated antistreptavidin. Microarrays experiments were performed at Baylor College of Medicine Microarray Core Facility .

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1.2. Data were processed using the Bioconductor packages implemented in R. RMA background correction was applied to probe intensities, gene level expression were summarized from the corrected intensities and quantile normalized.

organism: Arabidopsis thaliana

label_protocol: Samples were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five µg of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was quantified using the NanoDrop® ND-1000 spectrophotometer. 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration. A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip® array.

growth_protocol: Wild type (Col-0 ecotype) and cax1cax3 double mutant lines were grown on 0.5X MS media supplemented with 0.5% Sucrose for 10 days (16hr day/8hr night) at an irradiance of 150 µmol photons m-2 s-1, and at 22°C. The 10-day-old seedlings were then transferred into soil (Sunshine Mix) and grown for 3 weeks until the cax1cax3 plants started to display necrotic lesions.

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer instructions.

tag: ecotype

value: Cax1/Cax3 double mutant

tag: tissue

value: whole plant

value: 40 days old


title: Columbia-0 replicate 3

description: whole plant

source_name: Col-0 wt


title: Columbia-0 replicate 2

description: whole plant


title: Liver MWTP - 2

status: Public on Oct 30 2010

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)

scan_protocol: The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA)

data_processing:
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.
The intensity of each spot was summarized by the median pixel intensity. A log2 transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.

organism: Pimephales promelas

source_name: Liver from male fathead minnow exposed to a wastewater treatment plant

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)

growth_protocol: Adult (ca. 6 month old) male FHM were cultured at the University of Minnesota.  Effluent was transported to the laboratory.  Briefly, each day approximately 700 L (maximum trucking capacity) of effluent was pumped from the effluent channel into polypropylene containers (Nalgene) using a submersible pump.  After being trucked to the lab, it was pumped using submersible pumps into a large fiberglass tank where it was heated to 25˚C (± 1˚C) using submersible heaters (Process Technologies, 1800 watts) before being pumped again into a head tank for delivery to exposure tanks. 	Exposures were performed as static renewal with effluent delivered at full strength (400 ml/min, for 4 hours) twice daily into exposure aquaria containing 3 females and 9 males (N=2 runs).  Control tanks had the same number of fish but only received well water during the same 4 hour dosing periods. Fish exposure lasted 3 weeks. At the conclusion of the exposure, blood samples were collected for analysis of Vtg plasma concentrations. Liver and gonad samples were removed and stored in RNA later (Applied Biosystems/Ambion, Austin, TX). All procedures involving live fish were reviewed and approved by the University of Minnesota Institutional Animal Care and Use Committee (IACUC).

extract_protocol: Total RNA was isolated with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Fathead minnow liver exposed in vivo for 3 weeks to Metropolitan Wastewater Treatment Plant

tag: gender

value: male

tag: agent

value: exposed in vivo to Metropolitan Wastewater Treatment Plant

tag: tissue type

value: liver

source_name: Reference

tag: reference

value: The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).


title: Gonad Control - 4

description: Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

source_name: Gonad from control male fathead minnow

treatment_protocol: Fathead minnow gonad exposed in vivo for 3 weeks to clean water

value: control

value: gonad


title: Gonad MWTP - 4

source_name: Gonad from male fathead minnow exposed to a wastewater treatment plant

treatment_protocol: Fathead minnow gonad exposed in vivo for 3 weeks to Metropolitan Wastewater Treatment Plant


title: Liver Control - 4

source_name: Liver from control male fathead minnow

treatment_protocol: Fathead minnow liver exposed in vivo for 3 weeks to clean water


title: Gonad Control - 3


title: IL12 Pmel-1

status: Public on Oct 19 2010

city: Los Angeles

first: Robert

middle: M

last: Prins

address: 1506 Gonda

department: Neurosurgery

institute: UCLA

description: IL12 primed CD8+ Pmel-1 T-cells

hyb_protocol: All labeling and hybridization was done by the UCLA Microarray Core Facility.

data_processing: This data was analyzed using the R/Bioconductor package OneChannelGUI.  RMA was used as the normalization method.

source_name: IL12 primed CD8+ Pmel-1 T-cells

growth_protocol: Collected after 6 days of growth at 37C according to cytokine priming used.

extract_protocol: RNA was collected according to manufacturer's instructions (Invitrogen Rneasy kit).

treatment_protocol: Naïve cells were collected fresh from Pmel-1 spleens and sorted for CD8+ Thy1.1+ cells.  IL-2 and IL-12 primed cells were primed in the presence of cognate antigen (gp100) for 4 days and stimulated with either IL-2 or IL-12 for six days.

tag: strain

value: Pmel-1 TCR transgenic

value: female

value: spleen

value: CD8+ T-cells

tag: treatment protocol

value: primed with cognate antigen gp100, stimulated with cytokine IL12


title: Liver MWTP - 1


title: Liver Control - 2


title: IL2 Pmel-1

description: IL2 primed CD8+ Pmel-1 T-cells

scan_protocol: All labeling and hybridization was done by the UCLA Microarray Core Facility.

source_name: IL2 primed CD8+ Pmel-1 T-cells

tag: genotype/variation

value: primed with cognate antigen gp100, stimulated with cytokine IL2


title: Liver MWTP - 3


title: CAX1/CAX3 mutant replicate 3

description: whole plant

tag: age


title: CAX1/CAX3 mutant replicate 2

description: whole plant


title: Gonad Control - 2


title: Gonad MWTP - 1


title: Liver MWTP - 4


title: Gonad MWTP - 2


title: Gonad MWTP - 3


title: Liver Control - 3


title: Liver Control - 1


title: IL12 Pmel-2

description: IL12 primed CD8+ Pmel-1 T-cells

label_protocol: All labeling and hybridization was done by the UCLA Microarray Core Facility.


title: IL2 Pmel-2

description: IL2 primed CD8+ Pmel-1 T-cells


title: Gonad Control -1


title: Naive Pmel-2

description: Naïve Pmel CD8+ T-cells

source_name: Naïve Pmel CD8+ T-cells

value: naïve control


title: Columbia-0 replicate 1

description: whole plant

value: wild type


title: Naive Pmel-1

description: Naïve Pmel CD8+ T-cells


title: S.cerevisiae and S.paradoxus each deleted for BRE1 repeat #1 Cy3

description:
BRE1_species1
raw data file (block, dye) = BRE1.srr (block #1, Cy3)

source_name: S. cerevisiae (BY4741 ho::kanMX4  MATa), S. paradoxus (CBS432 ho::nat1 MATα)

tag: organism(s)

value: pooled sample of both species

value: BRE1 deletion mutant

tag: growth protocol

value: YPD rich medium at 30°C


title: Control patient_CTL013

status: Public on Oct 15 2010

city: Aurora

first: Tzu Lip

last: Phang

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Affymetrix Power Tools, using RMA normalization.
probe group file: HuEx-1.0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: Control

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

growth_protocol: not applicable

extract_protocol: Platelets were isolated from whole blood with differential centrifugation followed by passing over a MACS separation column employing microbeads conjugated to anti-CD45 antibody for leukocyte removal.  Platelet purity was checked with flow cytometry of anti-platelet and anti-WBC antibody labeled aliquots followed by RNA isolation employing an RNeasy mini kit (Qiagen, Valencia, CA).  RNA was amplified to generate cDNA with the WT-Ovation Pico RNA Amplification System (NuGEN Technologies, San Carlos, CA)

treatment_protocol: not applicable

tag: disease state


title: Control 4h-A

status: Public on Oct 01 2010

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

description: Caco-2 cells (human, Caucasian, colon, adenocarcinoma) were treated with Bifidobacterium bifidum PRL2010 for 2h or 4h, and their gene expression profile was compared to non-stimulated cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

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

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method.

source_name: Caco2 cells, 4h, Control

label_protocol: Fragmented and biotin-labelled cRNA was synthesized from 8 ug purified RNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: 2x105 Caco-2 cells in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum, penicillin, streptomycin, amphotericin B and L-glutamine were seeded into the upper compartments of a six-well transwell plate. The lower compartments contained 3.0 ml of the same medium. The cells were incubated at 37 °C in a 5% CO2 atmosphere until they reached three days post-confluence. The cells were then washed with Hank’s solution, and DMEM medium supplemented with L-glutamine, sodium selenite and transferrin was added and incubation continued for a further 24 h.

extract_protocol: Total RNA was extracted with an RNeasy kit (Qiagen) and included a DNAse I step (Qiagen).

treatment_protocol: Caco-2 cells (4 days post-confluence on transwells) were incubated with Bifidobacterium bifidum PRL2010 (exponentially growing in 8 ml of ‘MRS’ medium (~108 CFU/ml)). 100 µl of bacterial suspension was added to experimental wells while the control wells received the same amount of medium without bacterial cells. Caco-2 cells were harvested for analyses after 2h and 4h of incubation.

tag: time point

tag: cell line


title: Control 4h-B


title: Control patient_CTL012


title: THP-1 Cells: Uninfected + CAM vs. C. burnetii NMII infected + CAM - bio rep1, tech rep1

city: STILLWATER

first: SAUGATA

last: MAHAPATRA

state: OK

address: 307 LSE, OSU

department: MICROBIOLOGY AND MOLECULAR GENETICS

institute: OKLAHOMA STATE UNIVERSITY

description: Biological replicate 1 of 3 - Technical replicate 1.

hyb_protocol: Labeled AA-aRNA (2μg) with a dye incorporation efficiency range of 18 -34 picomol/microgram, were mixed pair-wise and hybridized overnight to Human OneArray™ microarrays (Phalanx Biotech Group, Palo Alto, CA). Human OneArrays contain 32,050 oligonucleotides; 30968 human genome probes and 1082 experimental control probes formed as 60-mer sense-strand DNA elements. Arrays were hybridized, washed and dried rapidly according to the manufacturer’s instructions.

scan_protocol: Signal intensity of the hybridized arrays were measured by ScanArray Express (PerkinElmer, Boston, MA, USA) and the images were processed using GenePix Pro version 4.0 (Axon, Union City, CA, USA)

data_processing: The processed GenePix Pro 4.0 output was further analyzed using Loess-Global intensity dependent normalization through the GenePix Auto Processor (http://darwin.biochem.okstate.edu/gpap3/)

label: Alexa Fluor® 555-GREEN

source_name: Total RNA was harvested from Uninfected THP-1 human monocytic leukemia cells treated with Chloramphenicol

label_protocol: Approximately 6-10μg of aminoallyl-aRNA (AA-aRNA) was used for labeling. Alexa Fluor® 555-GREEN (Invitrogen, Carslbad, CA) was used to label the uninfected AA-aRNA and CAM treated uninfected AA-aRNA, while Alexa Fluor® 647-RED (Invitrogen) was used to label the AAaRNA from the C. burnetii infected cells and also for the CAM treated AAaRNA from the C. burnetii infected cells.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Total RNA (500 ng) from each sample was then amplified using an Epicentre® Biotechnologies (Madison, WI) TargetAmp™ 1-Round AminoallylaRNA Amplification Kit, yielding approximately 6-10μg of aminoallyl-aRNA (AA-aRNA).

treatment_protocol: 10μg/ml of Chloramphenicol was added 48hpi and total RNA was harvested at 72hpi

tag: treatment

value: Chloramphenicol

tag: infection

value: uninfected

tag: passage

tag: cell type

value: Monocytic leukemia cells derived from peripheral blood

label: Alexa Fluor® 647-RED

source_name: Total RNA was harvested from C.burnetii infected THP-1 human monocytic leukemia cells treated with Chloramphenicol at 48hpi for 24 hours

growth_protocol: Non-adherent THP-1 human monocytic leukemia cells (TIB-202; ATCC) were propagated in RPMI 1640 medium (Gibco, Carlsbad, CA) supplemented with 1mM sodium pyruvate, and 10% fetal bovine serum (FBS) at 37°C in 5% CO2.Purified C. burnetii NMII SCVs at a genome equivalent MOI of 15 were used to establish a synchronous infection

value: C. burnetii infected


title: Lung cancer patient_LCA016

source_name: Lung Cancer

value: Lung cancer


title: THP-1 Cells: Uninfected vs. C. burnetii NMII infected - bio rep1, tech rep2

description: Biological replicate 1 of 3 - Technical replicate 2.

source_name: Total RNA was harvested from Uninfected THP-1 human monocytic leukemia cells

growth_protocol: Non-adherent THP-1 human monocytic leukemia cells (TIB-202; ATCC) were propagated in RPMI 1640 medium (Gibco, Carlsbad, CA) supplemented with 1mM sodium pyruvate, and 10% fetal bovine serum (FBS) at 37°C in 5% CO2

treatment_protocol: No treatment

source_name: Total RNA was harvested from C.burnetii infected THP-1 human monocytic leukemia cells


title: THP-1 Cells: Uninfected vs. C. burnetii NMII infected - bio rep3, tech rep2

description: Biological replicate 3 of 3 - Technical replicate 2.


title: THP-1 Cells: Uninfected + CAM vs. C. burnetii NMII infected + CAM - bio rep3, tech rep2


title: UOK257-2, siFLCN/TFE3

status: Public on Oct 11 2010

city: Bethesda

first: Seung-Beom

last: Hong

state: MD

address: 10 Center Dr.

department: National Cancer Institute

institute: National Institutes of Health

description: S2 Si-5_(HG-U133_Plus_2)

hyb_protocol: Chips were hybridized with probes at 45 degrees C for 16 hours in the Affymetrix hybridization oven. The Affymetrix  GeneChip Fluidics Station 450  was used to wash and stain the arrays.

scan_protocol: The Affymetrix 7G GeneChip scanner was used for scanning.

data_processing:
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console

source_name: UOK257-2 cells, transfected

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

growth_protocol: DMEM, 10% FBS, Penicillin/Streptomycin

extract_protocol: Trizol reagent and Rneasy mini kit

treatment_protocol: siRNA transfection

value: UOK257-2 renal cancer cell line

tag: protocol

value: siFLCN/TFE3 transfection


title: THP-1 Cells: Uninfected + CAM vs. C. burnetii NMII infected + CAM - bio rep2, tech rep2

description: Biological replicate 2 of 3 - Technical replicate 2.


title: UOK257-2, siTFE3

description: S2 Si-4_(HG-U133_Plus_2)

value: siTFE3 transfection


title: Lung cancer patient_LCA020


title: THP-1 Cells: Uninfected vs. C. burnetii NMII infected - bio rep1, tech rep1


title: THP-1 Cells: Uninfected vs. C. burnetii NMII infected - bio rep2, tech rep1

description: Biological replicate 2 of 3 - Technical replicate 1.


title: THP-1 Cells: Uninfected vs. C. burnetii NMII infected - bio rep2, tech rep2


title: THP-1 Cells: Uninfected + CAM vs. C. burnetii NMII infected + CAM - bio rep2, tech rep1


title: THP-1 Cells: Uninfected vs. C. burnetii NMII infected - bio rep3, tech rep1

description: Biological replicate 3 of 3 - Technical replicate 1.


title: THP-1 Cells: Uninfected + CAM vs. C. burnetii NMII infected + CAM - bio rep3, tech rep1


title: Control patient_CTL011


title: Control patient_CTL009


title: UOK257-2, siFLCN

description: S2 Si-2_(HG-U133_Plus_2)

value: siFLCN transfection


title: UOK257-2, scrambled

description: S2 Si-1_(HG-U133_Plus_2)

value: scrambled transfection


title: THP-1 Cells: Uninfected + CAM vs. C. burnetii NMII infected + CAM - bio rep1, tech rep2


title: Lung cancer patient_LCA019


title: Lung cancer patient_LCA017


title: Lung cancer patient_LCA018


title: Control patient_CTL008


title: Control patient_CTL004


title: Control 2h-A

source_name: Caco2 cells, 2h, Control

tag: agent


title: B. bifidum 2h-A

source_name: Caco2 cells, 2h, Bifidobacterium bifidum PRL2010

value: Bifidobacterium bifidum PRL2010


title: Human_osteoblast_sample_#001rep2_PGE2_treated_24h

city: Montreal

first: Elin

last: Grundberg

address: 740 Dr Penfield Avenue

country: Canada

institute: McGill University

hyb_protocol: Equivalent amount of cRNA (750ng) was hybridized on each array according to the standard Illumina hybridization protocol.

scan_protocol: The BeadArrays were scanned according to the standard Illumina scanning protocol using the Illumina®BeadArray Reader (version 1.7.0.44) and the BeadScan software (version 3.5.31.17122).

data_processing: The images were analyzed in Illumina®BeadStudio 3 application and raw data were outputted in txt files. The raw data was then imported to BioConductor in  R 2.5.0 using the lumi package for variance-stabilizing transformation and robust spline normalization.

source_name: Primary human osteoblasts, PGE2, 24h

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

growth_protocol: The cells were grown in medium containing α-MEM supplemented with 2 mmol/l L-Glutamine, 100U/mL penicillin, 100mg/mL streptomycin, and 10% fetal bovine serum at 37°C with 5% CO2. The culture medium was changed twice weekly.

extract_protocol: RNA was extracted from cell lysates resuspended in 600µl RLT lysis buffer using the RNeasy® Mini Kit. High RNA quality was confirmed for all samples using the Agilent 2100 BioAnalyzer and the concentrations were determined using Nanodrop ND-1000. The PTH-treated samples failed in the RNA isolation experiment and thus were not included in the subsequent expression profiling experiment.

treatment_protocol: At 70-80% confluence, the cells were passaged and sub-cultured in 6-well plates (100,000 cells/well) for 12 days. The culture medium was changed twice weekly. Prior to treatment, the cells were starved for 20h by adding complete cell medium containing 0.5% fetal bovine serum. The cells were then incubated for 2h and 24h with 0.1 µg/ml of rhBMP-2 (bone morphogenetic protein 2), 100 nM of DEX (dexamethasone), 100 nM of IGF-1 (insulin-like growth factor 1), 1µM of PGE2 (prostaglandin E2), 100 nM of PTH (parathyroid hormone) (1-34), 0.1 nM of TNF-α (tumor necrosis factor alpha) 100 nM of 1.25 VitD3 (vitamin D3) and with the same concentration of vehicle, respectively. At the two time points, the cell medium was removed and the cells were harvested by adding 600µL of RLT buffer (Qiagen, GmbH, Germany). The cell lysates were homogenized by using QIAshredder (Qiagen, GmbH, Germany) homogenizers and stored in -70°C until RNA extraction.

tag: tissue

value: trabecular bone

value: osteoblasts

tag: condition

value: prostaglandin E2 (PGE2)

tag: timepoint

tag: gender

value: male


title: Human_osteoblast_sample_#001rep3_Ctrl1_treated_24h

source_name: Primary human osteoblasts, control vehicle 1, 24h

value: control vehicle


title: B. bifidum 4h-A

source_name: Caco2 cells, 4h, Bifidobacterium bifidum PRL2010


title: Human_osteoblast_sample_#001rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#001rep2_TNFa_treated_24h

source_name: Primary human osteoblasts, tumor necrosis factor alpha (TNFalpha), 24h

value: tumor necrosis factor alpha (TNFalpha)


title: Human_osteoblast_sample_#001rep3_VitD_treated_24h

source_name: Primary human osteoblasts, 1.25VitD3, 24h


title: Human_osteoblast_sample_#001rep1_TNFa_treated_24h


title: Human_osteoblast_sample_#001rep2_Ctrl1_treated_24h


title: Human_osteoblast_sample_#001rep1_Ctrl1_treated_24h


title: Control patient_CTL005


title: Human_osteoblast_sample_#001rep2_IGF1_treated_24h

source_name: Primary human osteoblasts, IGF1, 24h

value: insulin-growth factor 1 (IGF1)


title: Control 2h-B


title: Human_osteoblast_sample_#001rep3_DEX_treated_24h

source_name: Primary human osteoblasts, DEX, 24h

value: dexamethasone


title: Human_osteoblast_sample_#001rep2_VitD_treated_24h


title: B. bifidum 2h-B


title: Human_osteoblast_sample_#001rep1_Ctrl2_treated_24h

source_name: Primary human osteoblasts, control vehicle 2, 24h


title: Human_osteoblast_sample_#001rep1_IGF1_treated_24h


title: Human_osteoblast_sample_#001rep3_Ctrl2_treated_24h


title: Human_osteoblast_sample_#001rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#001rep3_TNFa_treated_24h


title: Human_osteoblast_sample_#001rep2_Ctrl2_treated_24h


title: Human_osteoblast_sample_#001rep3_IGF1_treated_24h


title: Human_osteoblast_sample_#001rep2_DEX_treated_24h


title: Human_osteoblast_sample_#001rep1_BMP2_treated_24h

source_name: Primary human osteoblasts, BMP2, 24h

value: bone morphogenetic protein 2 (BMP2)


title: Human_osteoblast_sample_#001rep1_DEX_treated_24h


title: Human_osteoblast_sample_#001rep3_BMP2_treated_24h


title: Human_osteoblast_sample_#001rep1_VitD_treated_24h


title: Human_osteoblast_sample_#001rep2_BMP2_treated_24h


title: Human_osteoblast_sample_#001rep3_Ctrl2_treated_2h

source_name: Primary human osteoblasts, control vehicle 2, 2h


title: Human_osteoblast_sample_#001rep2_Ctrl1_treated_2h

source_name: Primary human osteoblasts, control vehicle 1, 2h


title: Human_osteoblast_sample_#001rep3_Ctrl1_treated_2h


title: Human_osteoblast_sample_#001rep1_TNFa_treated_2h

source_name: Primary human osteoblasts, tumor necrosis factor alpha (TNFalpha), 2h


title: Human_osteoblast_sample_#001rep2_VitD_treated_2h

source_name: Primary human osteoblasts, 1.25VitD3, 2h


title: Human_osteoblast_sample_#001rep3_DEX_treated_2h

source_name: Primary human osteoblasts, DEX, 2h


title: Human_osteoblast_sample_#001rep1_VitD_treated_2h


title: Human_osteoblast_sample_#001rep3_PGE2_treated_2h

source_name: Primary human osteoblasts, PGE2, 2h


title: Human_osteoblast_sample_#001rep3_IGF1_treated_2h

source_name: Primary human osteoblasts, IGF1, 2h


title: Human_osteoblast_sample_#001rep2_TNFa_treated_2h


title: Human_osteoblast_sample_#001rep3_BMP2_treated_2h

source_name: Primary human osteoblasts, BMP2, 2h


title: Human_osteoblast_sample_#001rep1_Ctrl1_treated_2h


title: Human_osteoblast_sample_#648rep1_PGE2_treated_24h

source_name: Primary human osteoblasts, PGE2, 24h


title: Human_osteoblast_sample_#001rep2_DEX_treated_2h


title: Human_osteoblast_sample_#001rep3_VitD_treated_2h


title: Human_osteoblast_sample_#001rep1_Ctrl2_treated_2h


title: Human_osteoblast_sample_#001rep1_IGF1_treated_2h


title: Human_osteoblast_sample_#001rep1_BMP2_treated_2h


title: Human_osteoblast_sample_#001rep2_Ctrl2_treated_2h


title: Human_osteoblast_sample_#001rep2_PGE2_treated_2h


title: Human_osteoblast_sample_#646rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#001rep3_TNFa_treated_2h


title: Human_osteoblast_sample_#001rep1_PGE2_treated_2h


title: Human_osteoblast_sample_#001rep2_IGF1_treated_2h


title: Human_osteoblast_sample_#001rep2_BMP2_treated_2h


title: Human_osteoblast_sample_#645rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#001rep1_DEX_treated_2h


title: Human_osteoblast_sample_#646rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#644rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#645rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#648rep2_PGE2_treated_24h


title: B. bifidum 4h-B


title: Human_osteoblast_sample_#644rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#643rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#642rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#642rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#643rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#634rep2_PGE2_treated_24h

value: female


title: Human_osteoblast_sample_#634rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#633rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#633rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#631rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#628rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#628rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#627rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#630rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#629rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#630rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#632rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#632rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#627rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#626rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#629rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#626rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#623rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#631rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#625rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#625rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#620rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#624rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#620rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#622rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#621rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#623rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#622rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#619rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#624rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#621rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#618rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#619rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#616rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#615rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#617rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#614rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#614rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#617rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#616rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#618rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#615rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#613rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#613rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#609rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#612rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#607rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#612rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#611rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#607rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#608rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#611rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#608rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#606rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#602rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#603rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#602rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#605rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#605rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#600rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#603rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#604rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#597rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#598rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#601rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#597rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#598rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#609rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#595rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#595rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#606rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#601rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#594rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#593rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#593rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#594rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#596rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#591rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#591rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#590rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#589rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#587rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#588rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#583rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#586rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#592rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#587rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#582rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#585rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#592rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#590rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#585rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#582rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#583rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#579rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#578rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#581rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#580rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#576rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#581rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#577rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#579rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#580rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#578rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#577rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#575rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#576rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#573rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#600rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#573rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#570rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#566rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#557rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#572rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#554rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#557rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#566rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#575rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#555rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#567rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#550rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#567rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#586rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#565rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#554rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#551rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#553rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#550rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#548rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#565rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#548rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#555rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#544rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#546rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#543rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#541rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#537rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#536rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#540rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#546rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#544rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#543rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#531rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#531rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#540rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#526rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#528rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#526rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#525rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#528rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#534rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#523rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#529rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#572rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#570rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#525rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#524rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#529rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#589rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#524rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#523rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#521rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#518rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#521rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#519rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#516rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#517rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#519rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#515rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#516rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#518rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#551rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#517rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#522rep1_PGE2_treated_24h


title: Human_osteoblast_sample_#513rep3_PGE2_treated_24h


title: Human_osteoblast_sample_#514rep2_PGE2_treated_24h


title: Human_osteoblast_sample_#511rep1_PGE2_treated_24h