title: B6_E18.5_1

status: Public on Jul 31 2012

type: RNA

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: based on Affymetrix protocols

scan_protocol: based on Affymetrix protocols

data_processing: Data was processed/normalized by RMA algorithm using Affymetrix Expression Console version 1.1.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: B6 mice lung RNAs in E18.5

label_protocol: based on Affymetrix protocols

extract_protocol: Lungs from 3 litters (3 males/litter as one pool) of A/J and B6 mouse strain were used at each gestational and postnatal time point (E15.5, E16.5, E17.5, E18.5 and PN0 for B6; E15.5, E16.5, E17.5, E18.5, E19.5, E20.5 and PN0 for A/J).  RNA was isolated from whole right lung homogenates using an RNAeasy Protect mini kit (Qiagen, Valencia, CA).

tag: tissue

value: Lung

tag: time

tag: strain


title: B6_E17.5_3

source_name: B6 mice lung RNAs in E17.5


title: B6_PN0_1

source_name: B6 mice lung RNAs in PN0


title: B6_E17.5_2


title: B6_E15.5_2

source_name: B6 mice lung RNAs in E15.5


title: B6_E16.5_1

source_name: B6 mice lung RNAs in E16.5


title: B6_E15.5_1


title: B6_E18.5_3


title: B6_E16.5_2


title: B6_E15.5_3


title: B6_E17.5_1


title: B6_PN0_3


title: B6_PN0_2


title: B6_E18.5_2


title: AJ_E20.5_2

source_name: A/J mice lung RNAs in E20.5

value: A/J


title: B6_E16.5_3


title: AJ_E20.5_1


title: AJ_E20.5_3


title: AJ_PN0_3

source_name: A/J mice lung RNAs in PN0


title: AJ_PN0_2


title: AJ_PN0_1


title: AJ_E18.5_1

source_name: A/J mice lung RNAs in E18.5


title: AJ_E18.5_2


title: AJ_E18.5_3


title: B6_E18.5_2b


title: AJ_E19.5_2

source_name: A/J mice lung RNAs in E19.5


title: AJ_E17.5_3

source_name: A/J mice lung RNAs in E17.5


title: AJ_E16.5_2

source_name: A/J mice lung RNAs in E16.5


title: AJ_E19.5_1


title: AJ_E16.5_3


title: AJ_E17.5_2


title: AJ_E17.5_1


title: AJ_E15.5_3

source_name: A/J mice lung RNAs in E15.5


title: AJ_E15.5_2


title: AJ_E15.5_1


title: Str/ort, 40 weeks old, rep4

city: London

first: Andrew

last: Pitsilides

address: Royal College Street

department: Comparative Biomedical Sciences

country: United Kingdom

institute: The Royal Veterinary College

hyb_protocol: Hybridisation was performed according to the manufacturer's instructions (Affymetrix, Inc)

scan_protocol: Scanning of arrays was performed according to the manufacturer's instructions (Affymetrix, Inc)

data_processing: The data were analyzed with R/Bioconductor, RMA normalized values were obtained with the affy() package

source_name: articular cartilage

label_protocol: In vitro transcription was made using the Bioarray high yield RNA transcript labeling kit (P/N 900182, Affymetrix, Inc). Unincorporated nucleotides were removed using the RNeasy column

growth_protocol: Male CBA (Charles River, Kent, UK) and Str/ort mice were kept in prolypropylene cages, subjected to 12 hour light and dark cycles, at 21±2˚C and fed a standard RM1 maintenance diet ad libitum (Rat and Mouse No.1; Special Diet Services, Witham UK). All procedures complied with the Animals (Scientific Procedures) Act 1986 and local ethics committee.

extract_protocol: Articular cartilage samples from n=3/4 Str/ort and CBA at each ages were removed from RNAlater and immersed in QIAzol (Qiagen, Mississauga, Ontario, Canada). After homogenisation using plastic pestle, total RNA was isolated using the Mini Kit, according to the instructions of the manufacturer (Qiagen).

treatment_protocol: Three ages were used in this study for both CBA and Str/ort male mice: 8-10wks, 18-20wks and 40-42wks.

value: articular cartilage

tag: age

value: 40 weeks

value: Str/ort


title: CBA, 40 weeks old, rep4

value: CBA


title: CBA, 40 weeks old, rep3


title: AJ_E19.5_3


title: Str/ort 18 weeks old, rep3

value: 18 weeks


title: Str/ort, 40 weeks old, rep1


title: AJ_E16.5_1


title: Str/ort 18 weeks old, rep4


title: Str/ort 18 weeks old, rep1


title: Str/ort, 40 weeks old, rep2


title: Str/ort 18 weeks old, rep2


title: CBA, 40 weeks old, rep2


title: CBA, 18 weeks old, rep1


title: Str/ort 8 weeks old, rep2

value: 8 weeks


title: Str/ort 8 weeks old, rep1


title: CBA 18 weeks old, rep4


title: CBA, 18 weeks old, rep2


title: CBA, 40 weeks old, rep1


title: Gastric Cancer Cell8

city: Seoul

first: Han Sang

last: Kim

address: Shin chon dong

department: Internal medicine

country: South Korea

institute: Yonsei Cancer Center

hyb_protocol: Hybridization and washing procedures were carried out following a modified CMRC protocol using total RNA as described previously. Briefly, 2 μg of amplified mRNA was labeled with Cy3- or Cy5-dUTP during reverse transcription. The final probe was concentrated to 40 μl, using a Microcon YM-30 column (Millipore, Bedford, MA) and denatured at 100°C for 2 min. Before hybridization, slides were preblocked in solution containing 10 mg/ml bovine serum albumin, 3.5× SSC and 0.1% SDS to prevent nonspecific hybridization. Probes were hybridized onto the preblocked microarray in 25% formamide, 5× SSC and 0.1% SDS at 42°C for 16 hr.

scan_protocol: After washing and drying the hybridized microarray, fluorescence signals were acquired using a GenePix 4000B scanner (Axon Instruments, Foster City, CA). Scanned images were processed using GenePix Pro 4.1 software (Axon Instruments, Foster City, CA).

data_processing: The raw Cy5/Cy3 data were log 2 -transformed. Systemic errors were corrected by normalization using intensity dependent, within-print, tip normalization based on the Lowess function.

organism: Homo sapiens

source_name: Gastric Cancer cell

label_protocol: The test samples were labeled with Cy5 and individually cohybridized with Cy3-labeled Yonsei reference RNA.

extract_protocol: Total RNA was extracted from each cell line using TRIzol reagent (Invitrogen,  Carlsbad,  CA,  USA)  according  to  the  manufacturer's instructions. The Yonsei reference RNA (Cancer Metastasis Research Center, Seoul, Korea) was prepared by pooling equivalent amounts of total RNA  from the  following 11  human cancer cell lines:  YCC-B1 (breast cancer), HCT-116 (colon cancer), SK-HEP-1 (liver cancer), A549 (lung cancer), HL-60 (acute promyelocyte leukemia), MOLT-4 (acute lymphoblastic  leukemia),  HeLa  (cervical  cancer),  Caki-2  (kidney cancer),  T98G  (glioblastoma),  HT1080  ( ﬁ brosarcoma)  and  YCC-3 (gastric cancer).

tag: cell line

source_name: Yonsei reference RNA


title: Gastric Cancer Cell11

value: YCC-B1 (breast cancer), HCT-116 (colon cancer), SK-HEP-1 (liver cancer), A549 (lung cancer), HL-60 (acute promyelocyte leukemia), MOLT-4 (acute lymphoblastic  leukemia),  HeLa  (cervical  cancer),  Caki-2  (kidney cancer),  T98G  (glioblastoma),  HT1080  ( ﬁ brosarcoma)  and  YCC-3 (gastric cancer)


title: SaurCOL-[40min]-[pool]-C

city: Greifswald

first: Jan

last: Pané-Farré

address: F.-L.-Jahn-Str. 15

department: Department of Microbial Physiology

country: Germany

hyb_protocol: Hybridizations were done in a total sample volume of 40 µl for 17 hours at 65°C at 10 rpm in a dedicated hybridization chamber (Agilent) and hybridisation oven (Robbins Scientific, Sunnyvale, CA, USA). After hybridization the slides were washed for one minute at room temperature in wash buffer 1 followed by a one minute washing step at 37°C with wash buffer 2. The slides were dried under nitrogen flow. Blocking reagents, hybridization buffer (Gene Expression Hybridization Kit) and washing solutions (Gene Expression Wash Buffer Kit) were purchased from Agilent.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.v.10.2.1.3). Agilent Technologies Scanner G2505C US45103079

data_processing: Agilent Feature Extraction Software (v.  10.2.1.3) was used for background subtraction and LOWESS normalization. Only probes that mapped to the genome of S. aureus strain COL, the strain used for the amicoumacin A experiments, were analyzed. Therefore the data table includes only 4023 out of a possible 6608 rows.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus pool

label_protocol: Synthesis of Cy5-dCTP or Cy3-dCTP (Perkin-Elmer, Waltham, USA) labeled cDNA was done with 10 µg of total RNA as template by direct reverse-transcription using Superscript II (Invitrogen, Darmstadt, Germany) and random hexamers (Promega, Madison, USA) according to the manufacturer’s instructions. To degrade the RNA after cDNA synthesis the reaction mix was incubated for 30 min at room temperature with E. coli RNase H (Invitrogen, Darmstadt, Germany).Labeled cDNA was then purified with the QIAquick PCR Purification Kit (Qiagen, Mannheim Germany). The Cy-dye incorporation was analysed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, USA). A sample volume corresponding to 30 pmol incorporated dye of the labeled cDNA was used for two-colour competitive hybridization experiments.

growth_protocol: S. aureus COL was grown in BHI

extract_protocol: Total RNA was isolated from S. aureus COL as described in Igo, M. M., and R. Losick. 1986. Regulation of a promoter that is utilized by minor forms of RNA polymerase holoenzyme in Bacillus subtilis. J. Mol. Biol. 191:615-624.DNA was removed using RNase-free RQ1 DNase (Promega, Madison, WI).  The quality of RNA was checked by gel electrophoresis and an Agilent bioanalyzer.

treatment_protocol: amicoumacin A treatment at OD600=0.5 for 10 and 40 min reducing growth by 12% and 20%, respectively

value: COL

source_name: Staphylococcus aureus 10 min treatment (C)


title: Gastric Cancer Cell12


title: CBA 18 weeks old, rep3


title: Str/ort 8 weeks old, rep3


title: SaurCOL-[control]-[pool]-C

source_name: Staphylococcus aureus control (C)


title: SaurCOL-[40min]-[pool]-B

source_name: Staphylococcus aureus 40 min treatment (B)


title: Gastric Cancer Cell10


title: CBA, 8 weeks old, rep4


title: Gastric Cancer Cell9


title: SaurCOL-[10min]-[pool]-C


title: CBA, 8 weeks old, rep2


title: CBA, 8 weeks old, rep3


title: SaurCOL-[40min]-[pool]-A

source_name: Staphylococcus aureus 40 min treatment (A)


title: Gastric Cancer Cell5

value: AGS


title: CBA, 8 weeks old, rep1


title: Str/ort, 40 weeks old, rep3


title: Gastric Cancer Cell4


title: SaurCOL-[control]-[pool]-B

source_name: Staphylococcus aureus control (B)


title: Gastric Cancer Cell6


title: Gastric Cancer Cell7


title: SaurCOL-[10min]-[pool]-B

source_name: Staphylococcus aureus 10 min treatment (B)


title: SaurCOL-[10min]-[pool]-A

source_name: Staphylococcus aureus 10 min treatment (A)


title: SaurCOL-[control]-[pool]-A

source_name: Staphylococcus aureus control (A)


title: Gastric Cancer Cell3


title: Oviduct_Underfed_CW10_D8

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

country: France

institute: INRA

description: Syntax of the sample names: Tissue_Diet_Individual_DayOfCycle. Where the tissue is either the oviduct, the endometrium or the corpus luteum. Where the diet is control or underfed. Where the day of cycle is either D4, D8, D12, D15. Experimental variables: Diet = control (100% INRA requirements during 140 days), underfed (40% of control diet during the dry period (60 days), 80% of control diet during the first 80 days of postpartum). Additional data: - High producing dairy cows (n=8). Holstein breed. Induced ovulation in post-partum - Surgical tissue sampling at 4 days (a day per diet, n=8) - Corpus Luteum: biopsies at one day per diet (n=8) - Oviduct:  ipsi- and contra-lateral biopsies per day, and diet (n=16) - Endometrium:  ipsi- and contra-lateral biopsies per day, and diet (n=16)

hyb_protocol: Prehybridisation in ExpressHybTM Hybridization Solution (Clontech) at 68°C during 1h (14ml). Hybridisation using new ExpressHybTM Hybridization Solution (Clontech) at 68°C overnight (10ml). Arrays were washed four times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68°C for 30 min each. They were then exposed to phosphor-screens (Amersham) for 5 days as described in Degrelle et al., 2008.

scan_protocol: Scanner: STORM 760 from Molecular Dynamics. Raw data set: Feature extraction with Imagene 5.5 software from BioDiscovery (Proteigene)

data_processing: Intensity = Signal Mean. Normalization = Signal mean were log2 transformed and median centred. To normalize our data, we used  R version 2.13.0. As the data were only log2 transformed and median centered (=basic R functions), we didn't used any microarray packages.

organism: Bos taurus

label_protocol: 30µg of total RNA were retro-transcribed and directly labelled with 33P dATP as described  (Degrelle et al., 2008). Total RNA were mixed with 500ng of random hexamers in a volume of 25µl. The mixture was incubated at 70°C for 10 min and chilled on ice. cDNA was synthesised by the addition of 5µl 10X PCR buffer, 5µl 25mM MgCl2, 5 µl 0,1 mM DTT, 2,5µl 10mM mix dGTP, dCTP and dTTP, 2,5µl water, 50 µCi 33P dATP and 200U Superscript II (Invitrogen) at 42°C for 50min. The RNA template was removed by the addition of 1µl RNAse H- and incubation at 37°C for 20 min. Labelled targets were then purified on Sephadex columns (G-50).

extract_protocol: RNA samples: Corpus luteum (n=8, a day per diet) - Oviduct (n=8, a day per diet. Pooled RNA from ipsi-contra biopsies) - Endometrium (n=8, a day per diet. Pooled RNA from ipsi-contra biopsies). Total RNA from endometrium, corpus luteum and oviduct were extracted with Chomczynski & N. Sacchi protocol and purified using Rneasy Mini kit (Quiagen). RNA quality was first verified by A260/280 absorbance ratios.

treatment_protocol: Tissues were collected and immediately snap-frozen.

value: Oviduct

tag: diet

value: Underfed

tag: day of cycle


title: Oviduct_Underfed_CW18_D15


title: Gastric Cancer Cell1


title: Oviduct_Control_CW14_D15

value: Control


title: KLF9 over-expression 4 days

city: Hamburg

first: Florian

last: Spoerl

address: Unnastr. 48

department: Aged Skin

institute: Beiersdorf AG

description: Gene expression after 4d KLF9 over-expression

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.2-1.65 ug Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: Raw data of the hybridized microarrays were normalized using the R-Project-Bioconductor package Linear models for microarray data (limma). Background-correction was performed using the normexp function and the between-array-normalization quantile. An offset of 20 was added to stabilize the background correction and subsequently signals were log2 transformed. Genes were considered to be expressed if the background subtracted signal was above 2.6 times the standard deviation of the background signal in at least 75% of the microarrays.

source_name: KLF9 over-expression 4 days

label_protocol: For the linear T7-based amplification step, 100 ng of all samples were used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies)

growth_protocol: Normal human epidermal neonatal foreskin keratinocytes of three donors (NHEK-pool) were purchased from Lonza (Rockland, ME), seeded in 75 cm2 plastic flasks and cultured in complete Keratinocyte Growth Medium 2 (KGM-2) with growth factor supplements (Lonza, Rockland, ME) and 1 mM CaCl2. Cells were cultivated at 37 °C, 7% CO2 and 95% relative humidity.

extract_protocol: Cells were harvested and total RNA was isolated using the High Pure RNA Isolation Kit (Roche Diagnostics, Mannheim, Germany) according to manufacturer’s instructions.

treatment_protocol: NHEK cells were cultivated in 6-well dishes to 30%-50% confluence and infected using 1/50 final volume of 100x concentrated lentivirus containing pLenti6/V5Dest expression vectors for GFP and KLF9, respectively and 8 µg/ml protamine sulfate (Sigma-Aldrich, Hamburg, Germany). Cells were selected for 24 hours after transduction using 10 µg/ml puromycin for 24h.

tag: cell type

value: Primary human neonatal foreskin keratinocytes

tag: transgene

value: 4 d


title: HEK293_Brd4_KD_Replicate_2

first: Iouri

last: Chepelev

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description:
BRD4_KD_rep2
Biological replicate 2 of 2. Brd4 shRNA knockdown HEK293 cells.

hyb_protocol: Equal quantities of the Cy5- and Cy3-labeled cRNAs were mixed and competitively hybridized to Agilent 4x44K cDNA microarrays for 18 hrs using an Agilent hybridization kit.

scan_protocol: Slides were washed according to manufacturer protocols and scanned using an Agilent G2565BA.

data_processing: Raw image data were extracted, and subjected to standard background subtraction and linear and lowess normalization using Agilent Feature Extraction Software v9.5.

source_name: Brd4 knockdown HEK293 cells

label_protocol: For each sample, 400ng RNA was linearly amplified and labeled with Cy5-CTP using Low RNA Linear Amplification reagents (Agilent technologies). For the reference, RNA from WT HEK293 cells was purified, amplified and labeled with Cy3 in the same manner.

extract_protocol: RNA was extracted and purified with an RNeasy kit (Qiagen) from Brd4, HP1β and control shRNA knockdown HEK293 cells.

treatment_protocol: HEK293 cells were infected with lentiviral MISSION® (Sigma-Aldrich) shRNA vectors (pLKO.1-puro) harboring shRNAs to Brd4 (clone # TRCN0000062223), HP1β (clone # TRCN0000021427) or control (empty pLKO.1-puro vector). After 72 hours, the infected cells were selected with puromycin by manufacturer protocols (Sigma Aldrich).

tag: genotype

value: Brd4 knockdown

source_name: WT HEK293 cells

value: WT


title: Oviduct_Underfed_CW17_D12


title: Oviduct_Control_CW12_D12


title: Oviduct_Control_CW15_D4


title: Oviduct_Underfed_CW16_D4


title: Oviduct_Control_CW11_D8


title: HEK293_Brd4_KD_Replicate_1

description:
BRD4_KD_rep1
Biological replicate 1 of 2. Brd4 shRNA knockdown HEK293 cells.


title: Endometrium_Underfed_CW10_D8

value: Endometrium


title: HEK293_Control_shRNA_KD_Replicate_1

description:
Control_KD_rep1
Biological replicate 1 of 2. shRNA control knockdown HEK293 cells.

source_name: shRNA control knockdown HEK293 cells

value: shRNA control knockdown


title: HEK293_Control_shRNA_KD_Replicate_2

description:
Control_KD_rep2
Biological replicate 2 of 2. shRNA control knockdown HEK293 cells.


title: KLF9 over-expression 7 days

description: Gene expression after 7d KLF9 over-expression

source_name: KLF9 over-expression 7 days

value: 7 d


title: Endometrium_Underfed_CW16_D4


title: KLF9 over-expression 2 days

description: Gene expression after 2d KLF9 over-expression

source_name: KLF9 over-expression 2 days

value: 2 d


title: Time point 2 (7.30 pm) subject 18

description: Gene expression at 7.30 pm

source_name: Suction blister epidermis

extract_protocol: RNA extraction was performed using the Trizol method according to standard protol.

treatment_protocol: No treatment was performed. Epidermal suction blister samples were harvested at the indicated time points and instantly snap frozen in liquid nitrogen.

value: Epidermis

tag: time point

value: Time point 2 (7.30 pm)


title: HEK293_HP1b_KD

description:
HP1b_KD
HP1b shRNA knockdown HEK293 cells.

source_name: HP1b knockdown HEK293 cells

value: HP1b knockdown


title: Endometrium_Underfed_CW17_D12


title: Endometrium_Control_CW14_D15


title: Endometrium_Underfed_CW18_D15


title: Endometrium_Control_CW15_D4


title: Endometrium_Control_CW12_D12


title: GFP over-expression 4 days

description: Gene expression after 4d GFP over-expression

source_name: GFP over-expression 4 days

value: GFP


title: Endometrium_Control_CW11_D8


title: Time point 2 (7.30 pm) subject 17

description: Gene expression at 7.30 pm


title: Time point 2 (7.30 pm) subject 16

description: Gene expression at 7.30 pm


title: GFP over-expression 7 days

description: Gene expression after 7d GFP over-expression

source_name: GFP over-expression 7 days


title: GFP over-expression 2 days

description: Gene expression after 2d GFP over-expression

source_name: GFP over-expression 2 days


title: Time point 2 (7.30 pm) subject 20

description: Gene expression at 7.30 pm


title: CorpusLuteum_Underfed_CW18_D15

value: Corpus luteum


title: CorpusLuteum_Underfed_CW17_D12


title: CorpusLuteum_Control_CW11_D8


title: Time point 2 (7.30 pm) subject 15

description: Gene expression at 7.30 pm


title: CorpusLuteum_Underfed_CW16_D4


title: Time point 2 (7.30 pm) subject 11

description: Gene expression at 7.30 pm


title: Time point 2 (7.30 pm) subject 14

description: Gene expression at 7.30 pm


title: CorpusLuteum_Control_CW15_D4


title: Time point 2 (7.30 pm) subject 10

description: Gene expression at 7.30 pm


title: CorpusLuteum_Control_CW12_D12


title: CorpusLuteum_Underfed_CW10_D8


title: Time point 2 (7.30 pm) subject 8

description: Gene expression at 7.30 pm


title: Time point 2 (7.30 pm) subject 12

description: Gene expression at 7.30 pm


title: Time point 2 (7.30 pm) subject 13

description: Gene expression at 7.30 pm


title: Time point 2 (7.30 pm) subject 5

description: Gene expression at 7.30 pm


title: CorpusLuteum_Control_CW14_D15


title: Time point 2 (7.30 pm) subject 7

description: Gene expression at 7.30 pm


title: Time point 2 (7.30 pm) subject 9

description: Gene expression at 7.30 pm


title: EHMT1 siRNA + TNF

city: pasadena

first: chee-kwee

last: ea

state: CA

address: 1200 E california blvd

department: biology

institute: california institute of technology

description: gene expression data from EHMT1 siRNA transfected HeLa cells treated with TNFa for 2 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: See standard Affymetrix protocols

data_processing: Data Acquisition was done by GeneChip Operating System using default setting. Data were then analyzed with the Rosetta Resolver gene expression data analysis system (Rossetta Inpharmatics). Expression differences (compare to Control siRNA sample) equal to or greater than 2-fold with a P value less than 0.01 were considered significant.

source_name: HeLa cells transfected with EHMT1 siRNA plus TNF

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: DMEM+10% FBS+ penn/Strep

extract_protocol: Qiagen Rneasy kit

treatment_protocol: 10nM siRNAs transfected with calcium phosphate precipitation

value: HeLa


title: Time point 2 (7.30 pm) subject 6

description: Gene expression at 7.30 pm


title: Gastric Cancer Cell2

source_name: Gastric Cancer cell

source_name: Yonsei reference RNA

value: YCC-B1 (breast cancer), HCT-116 (colon cancer), SK-HEP-1 (liver cancer), A549 (lung cancer), HL-60 (acute promyelocyte leukemia), MOLT-4 (acute lymphoblastic  leukemia),  HeLa  (cervical  cancer),  Caki-2  (kidney cancer),  T98G  (glioblastoma),  HT1080  ( ﬁ brosarcoma)  and  YCC-3 (gastric cancer)


title: Control siRNA + TNF

description: gene expression data from control siRNA transfected HeLa cells treated with TNFa for 2 hours

source_name: HeLa cells transfected with control siRNA plus TNF


title: Control siRNA

description: gene expression data from control siRNA transfected HeLa cells

source_name: HeLa cells transfected with control siRNA


title: EHMT1 siRNA

description: gene expression data from EHMT1 siRNA transfected HeLa cells

source_name: HeLa cells transfected with EHMT1 siRNA


title: U2OS_etoh-vs-dex_rep3

city: San Francisco

first: Samantha

middle: B.

last: Cooper

department: Cellular and Molecular Pharmacology

institute: UC San Francisco

description: Grown in DMEM with 5% FBS

hyb_protocol: Hyb in Maui chamber at 65C in 3X SSC, 25 mM Hepes 7.4, 0.25% SDS, 0.25 mg/ml yeast tRNA

scan_protocol: Scan on GenePix 4000B with GenePix Pro 5.0.0.51

data_processing: Gridding with SpotReader (Niles Scientific)

source_name: U2OS-GR_vehicle control_3 hrs

label_protocol: Label aa-dUTP with Cy3 or Cy5 NHS ester (resuspended in DMSO just before labeling). Labeling reaction with 50 mM sodium bicarbonate, pH 9.0

growth_protocol: Cells were maintained in a humid incubator with 5% carbon dioxide.

extract_protocol: RNA was isolated with Triazol.

treatment_protocol: Cells were treated at confluence with 1 micromolar dexamethasone in ethanol or vehicel control

tag: cell line origin

value: bone osteosarcoma

tag: treated with

value: vehicle (ethanol) for 3hr

source_name: U2OS-GR_dexamethasone treated_3 hrs

value: 1µM dexamethasone in ethanol for 3hr


title: Time point 2 (7.30 pm) subject 4

description: Gene expression at 7.30 pm


title: Mets MM 81

city: Saint Louis

first: Michael

middle: D

last: Onken

state: MO

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

description: Metastatic liver tumor from same patient as primary enucleated uveal melanoma 81

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline normalization and background subtraction with GenomeStudio Gene Expression Module

source_name: Metastatic melanoma tumor

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

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

tag: collection

value: Aspiration Biopsy of liver tumor immediately prior to chemoembolization

value: liver tumor


title: U2OS_dex-vs-etoh_rep1

description: Grown in DMEM with 5% FBS


title: T47D ERα17p

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

hyb_protocol: RNA was hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), on HGU133A plus 2 chips.

scan_protocol: Signals were detected by an Affymetrix microarray chip reader.

data_processing:
Normalization and analysis was performed with the raw data using Genespring GX V11.0 (Agilent, Foster City, CA)
Summarization Algorithm: RMA
Technology: Affymetrix.GeneChip.HG-U133_Plus_2
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: T47D cells, treated for 3 hours with 10-6M ERα17p

label_protocol: RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual)

growth_protocol: The human breast cancer cell line T47D was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

treatment_protocol: T47D cells were incubated with Estradiol or ERα17p for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS

tag: protocol

value: ERα17p treated cells 3h


title: MB 100 B

description: Uveal melanoma from enucleation 100 mock biopsy B

source_name: Primary uveal melanoma tumor

value: Fine Needle Aspiration Biopsy of tumor post enucleation

value: eye tumor


title: Time point 2 (7.30 pm) subject 3

description: Gene expression at 7.30 pm


title: NB 23

description: Uveal melanoma from pre-plaque fine needle biopsy 23

value: Fine Needle Aspiration Biopsy of tumor immediately prior to plaque brachytherapy


title: T47D Estradiol

source_name: T47D cells, treated for 3 hours with 10-6M estradiol

value: estradiol treated cells 3h


title: MM 100

description: Uveal melanoma from enucleation 100

value: Fresh frozen sample from enucleated eye


title: NB 24

description: Uveal melanoma from pre-plaque fine needle biopsy 24


title: U2OS_dex-vs-etoh_rep2

description: Grown in DMEM with 5% FBS


title: Nalm6_etoh-vs-dex_rep2

description: Grown in RPMI with 10% FBS

source_name: Nalm6_vehicle control_3 hrs

value: acute lymphoblastic leukemia

source_name: Nalm6_dexamethasone_3 hrs


title: Nalm6_dex-vs-etoh_rep3

description: Grown in RPMI with 10% FBS


title: Time point 2 (7.30 pm) subject 2

description: Gene expression at 7.30 pm

source_name: Suction blister epidermis

value: Epidermis

value: Time point 2 (7.30 pm)


title: Time point 2 (7.30 pm) subject 1

description: Gene expression at 7.30 pm


title: T47D control ETOH (vehicle)

source_name: T47D cells, treated for 3 hours with 0.1% Ethanol

value: ethanol treated cells (vehicle) 3h


title: SKBR3 Estradiol

source_name: SKBR3 cells, treated for 3 hours with 10-6M estradiol

growth_protocol: The human breast cancer cell line SKBR3 were obtained from ATCC-LGC Standards (Wesel, Germany) and cultured in McCoy’s medium, supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2

treatment_protocol: SKBR3 cells were incubated with Estradiol or ERα17p for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS


title: SKBR3 ERα17p

source_name: SKBR3 cells, treated for 3 hours with 10-6M ERα17p


title: SKBR3 control ETOH (vehicle)

source_name: SKBR3 cells, treated for 3 hours with 0.1% Ethanol


title: Time point 1 (2.30 pm) subject 20

description: Gene expression at 2.30 pm

value: Time point 1 (2.30 pm)


title: Time point 1 (2.30 pm) subject 19

description: Gene expression at 2.30 pm


title: NB 18

description: Uveal melanoma from pre-plaque fine needle biopsy 18


title: Mets MM 77

description: Metastatic liver tumor from same patient as primary enucleated uveal melanoma 77


title: MB 101 C

description: Uveal melanoma from enucleation 101 mock biopsy C


title: A549_dex-vs-etoh_rep2

description: Grown in DMEM with 5% FBS

source_name: A549_dexamethasone treated_3 hrs

value: Lung carcinoma

source_name: A549_vehicle control_3 hrs


title: Nalm6_etoh-vs-dex_rep1

description: Grown in RPMI with 10% FBS


title: Time point 1 (2.30 pm) subject 17

description: Gene expression at 2.30 pm


title: A549_etoh-vs-dex_rep3

description: Grown in DMEM with 5% FBS


title: MM 99

description: Uveal melanoma from enucleation 99


title: MM 101

description: Uveal melanoma from enucleation 101


title: MB 101 A

description: Uveal melanoma from enucleation 101 mock biopsy A


title: MB 101 B

description: Uveal melanoma from enucleation 101 mock biopsy B


title: Time point 1 (2.30 pm) subject 15

description: Gene expression at 2.30 pm


title: Time point 1 (2.30 pm) subject 16

description: Gene expression at 2.30 pm


title: MB 100 A

description: Uveal melanoma from enucleation 100 mock biopsy A


title: MDA-MB-231 control ETOH (vehicle)

source_name: MDA-MB-231 cells, treated for 3 hours with 0.1% Ethanol

growth_protocol: The human breast cancer cell line MDA-MB-231 was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

treatment_protocol: MDA-MB-231 cells were incubated with Estradiol or ERα17p for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS


title: MDA-MB-231 ERα17p

source_name: MDA-MB-231 cells, treated for 3 hours with 10-6M ERα17p


title: MDA-MB-231 Estradiol

source_name: MDA-MB-231 cells, treated for 3 hours with 10-6M estradiol


title: A549_dex-vs-etoh_rep1

description: Grown in DMEM with 5% FBS


title: Time point 1 (2.30 pm) subject 18

description: Gene expression at 2.30 pm


title: HeLa_treated_with_siRNA_against_HCFC1_rep2

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description: HeLa, cycling

hyb_protocol: RNA samples were hybridized to GeneChip Human Genome U133 Plus 2.0 Array.

scan_protocol: The chips were scanned as described in the Affymetrix protocol and the .CEL files were generated.

data_processing: 3 biological replicates were used for each condition. The intensities of each probeset were normalized and summarized using the Robust Multi-array Analysis algorithm (RMA, {Irizarry, 2003 #114}) and differential expression was assessed using the LIMMA package {Smyth, 2004 #115}.

source_name: adherent HeLa cells

label_protocol: RNA samples were then labeled using the MessageAmp II-Biotin Enhanced kit  (Ambion 1791)

growth_protocol: Adherent HeLa were grown in Dulbecco’s modified Eagles’s medium (DMEM) with 10% of fetal bovine serum.

extract_protocol: RNA samples were collected after 48h following the first transfection using Qiagen columns.

treatment_protocol: Cells were treated with siRNA against HCF-1 or luciferase, as previously described {Julien, 2003 #4}, twice 12h apart using oligofectamine (Invtrogen).

tag: treatment

value: HeLa


title: HeLa_treated_with_siRNA_against_HCFC1_rep3

description: HeLa, cycling


title: MM 81

description: Uveal melanoma from enucleation 81


title: MM 77

description: Uveal melanoma from enucleation 77


title: HeLa_treated_with_siRNA_against_Luciferase_rep3

description: HeLa, cycling

value: Luciferase


title: Klf4WT vom 11/17.12.07

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description: Klf4WT vom 11/17.12.07

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: GCOS software

label_protocol: GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix; manufacturer’s recommendations), amount of RNA labeled: 1µg

extract_protocol: Trizol (Invitrogen; manufacturer’s recommendations)

tag: The following constructs were used

value: Mus musculus  Klf4 full length, (ref|NM_010637.1) cDNA, Mus musculus cyclin-dependent kinase inhibitor 1A (P21) (Cdkn1a), cDNA (ref|NM_007669.3) were fused in frame to the modified oestrogen receptor ERT2 (Feil et al., 1997) and cloned into a retroviral vector (Mieg3) expressing the constructs together with eGFP after an internal ribosomal entry site . (Williams et al., 2000). For Klf4, a mutant comprinsing the zinc- finger domains only  AA 393 – 474 (Klf4 dN) as well as a mutant comprising the entire protein except the zinc fingers AA 1-393 (Klf4-dC) were constructed and fused in frame to the modified oestrogen receptor.

tag: BM cells from 5-FU treated mice were infected with viral constructs, sorted for GFP expression (day8), plated in IMDM , 10% FCS, 2mM Gln, 1% P/S, supplemented with 50ng/ml rSCF, 100ng/ml TPO and 100ng/ml G-CSF and cultured for 72h (day8-day10). On day10 cells were stimulated with 4-OHT (1uM) for 16h. After that time, total RNA was isolated by Trizol method.


title: Klf4WTVaVCre vom 5.12.07

description: Klf4WTVaVCre vom 5.12.07

source_name: Klf4WTVaVCre vom 5.12.07


title: Time point 1 (2.30 pm) subject 12

description: Gene expression at 2.30 pm

tag: tissue


title: HeLa_treated_with_siRNA_against_HCFC1_rep1

description: HeLa, cycling


title: Time point 1 (2.30 pm) subject 13

description: Gene expression at 2.30 pm


title: BM, Ly-6C high, Klf4flfl, MxCRE

description: BM, Ly-6C high, Klf4flfl, MxCRE

source_name: BM, Ly-6C high, Klf4flfl, MxCRE


title: HeLa_treated_with_siRNA_against_Luciferase_rep2

description: HeLa, cycling


title: BM, Ly-6C high, Klf4wt, MxCRE

description: BM, Ly-6C high, Klf4wt, MxCRE

source_name: BM, Ly-6C high, Klf4wt, MxCRE


title: Klf4WTVaVCre vom 5.12.07 HO2

description: Klf4WTVaVCre vom 5.12.07 HO2

source_name: Klf4WTVaVCre vom 5.12.07 HO2


title: Time point 1 (2.30 pm) subject 14

description: Gene expression at 2.30 pm


title: Klf4WTVaVCre vom 11.12.07

description: Klf4WTVaVCre vom 11.12.07

source_name: Klf4WTVaVCre vom 11.12.07


title: MM 10

description: Uveal melanoma from enucleation 10

source_name: Primary uveal melanoma tumor


title: HeLa_treated_with_siRNA_against_Luciferase_rep1

description: HeLa, cycling


title: MM 18

description: Uveal melanoma from enucleation 18


title: Time point 1 (2.30 pm) subject 10

description: Gene expression at 2.30 pm

source_name: Suction blister epidermis


title: MM 88

description: Uveal melanoma from enucleation 88


title: Time point 1 (2.30 pm) subject 9

description: Gene expression at 2.30 pm


title: Time point 1 (2.30 pm) subject 7

description: Gene expression at 2.30 pm


title: Time point 1 (2.30 pm) subject 8

description: Gene expression at 2.30 pm


title: MM 71

description: Uveal melanoma from enucleation 71


title: p21-ERT2, 4-OHT (1uM) 16h

description: p21-ERT2, 4-OHT (1uM) 16h


title: 9_EPC day 7 77E

city: Adelaide

first: Jyotsna

last: Pippal

address: IMVS, Level 3, Frome Road

department: Center for cancer biology

country: Australia

institute: Hanson Research Institute

hyb_protocol: As per affymetrix protocol

scan_protocol: Performed on genechip system 30007G

data_processing: Performed in expression console at gene core level. Robust multi-array analysis (RMA) was applied for normalizing and summarizing probe level intensity measurements from Affymetrix gene chips.

label: Biotin

source_name: Human cord blood derived CD133+ non adherent endothelial progenitor cells

label_protocol: RNA was amplified and labelled using Applause™ WT-Amp ST / WT-Amp Plus ST Systems.

extract_protocol: Total RNA was isolated from natural EPCs and donor matched HUVEC using RNEasy micro plus and RNEasy mini kit respectively (QIAGEN, Hilden, Germany). RNA integrity and quantity was determined using Agilent 2100 bioanalyzer.

tag: group

value: EPC day 7

value: donor blood (20 - 130 ml) was obtained by venipuncture of human umbilical cord veins immediately after delivery and processed within 2h.

value: cord blood was diluted in 1:1 ratio with sterile phosphate buffered saline (PBS) and layered on 15mL of Lymphoprep™ (Axis-Shield, Oslo, Norway).  Mononuclear cells (MNCs) were isolated and washed with HUVE media


title: p21-ERT2, no induction

description: p21-ERT2, no induction

source_name: p21-ERT2, no induction


title: MM 70

description: Uveal melanoma from enucleation 70


title: Time point 1 (2.30 pm) subject 5

description: Gene expression at 2.30 pm


title: KLF4del-ERT2 in MIEG3, 4-OHT (1uM) 16h

description: KLF4del-ERT2 in MIEG3, 4-OHT (1uM) 16h

source_name: KLF4del-ERT2 in MIEG3, 4-OHT (1uM) 16h


title: 6_HUVEC 45H

source_name: Human Umbilical cord vein endothelial cells

value: HUVEC


title: Time point 1 (2.30 pm) subject 6

description: Gene expression at 2.30 pm


title: MM 68

description: Uveal melanoma from enucleation 68

value: eye tumor


title: MM 79

description: Uveal melanoma from enucleation 79


title: Time point 1 (2.30 pm) subject 3

description: Gene expression at 2.30 pm


title: 8_EPC day 7 76E


title: 10_EPC day 7 78E


title: 5_HUVEC 46H


title: Zn-ERT2 in MIEG3, 4-OHT (1uM) 16h

description: Zn-ERT2 in MIEG3, 4-OHT (1uM) 16h

source_name: Zn-ERT2 in MIEG3, 4-OHT (1uM) 16h


title: 7_HUVEC 47H


title: MM 57

description: Uveal melanoma from enucleation 57


title: 2_EPC day 4 45E

value: EPC day 4


title: KLF4-ERT2 in MIEG3, 4-OHT (1uM) 16h

description: KLF4-ERT2 in MIEG3, 4-OHT (1uM) 16h

source_name: KLF4-ERT2 in MIEG3, 4-OHT (1uM) 16h


title: 4_HUVEC 43H


title: MM 74

description: Uveal melanoma from enucleation 74


title: Time point 1 (2.30 pm) subject 2

description: Gene expression at 2.30 pm


title: Time point 1 (2.30 pm) subject 4

description: Gene expression at 2.30 pm


title: MM 53

description: Uveal melanoma from enucleation 53


title: 3_EPC day 4 47E


title: MM 94

description: Uveal melanoma from enucleation 94


title: MM 93

description: Uveal melanoma from enucleation 93


title: Time point 1 (2.30 pm) subject 1

description: Gene expression at 2.30 pm


title: MM 92

description: Uveal melanoma from enucleation 92


title: Time point 0 (9.30 am) subject 18

description: Gene expression at 9.30 am

value: Time point 0 (9.30 am)


title: MIEG3, 4-OHT (1uM) 16h

description: MIEG3, 4-OHT (1uM) 16h

source_name: MIEG3, 4-OHT (1uM) 16h


title: Time point 0 (9.30 am) subject 17

description: Gene expression at 9.30 am


title: Time point 0 (9.30 am) subject 20

description: Gene expression at 9.30 am


title: 1_EPC day 4 43E

value: cord blood was diluted in 1:1 ratio with sterile phosphate buffered saline (PBS) and layered on 15mL of Lymphoprep™ (Axis-Shield, Oslo, Norway).  Mononuclear cells (MNCs) were isolated and washed with HUVE media.


title: MM 90

description: Uveal melanoma from enucleation 90

value: Fresh frozen sample from enucleated eye


title: MM 66

description: Uveal melanoma from enucleation 66


title: Time point 0 (9.30 am) subject 15

description: Gene expression at 9.30 am

value: Epidermis


title: hTERT KGM Biological Replicate 3

city: Boston

first: David

middle: A

last: Sullivan

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: replicate 3

hyb_protocol: cRNA/hybridization buffer mixtures were incubated at 65°C for 5 minutes, followed by brief centrifugation to collect.  The mixtures were added to BeadChips and then BeadChips inserted into hybridization chambers, and hybridization was carried out at 58°C for 16-18 hours at rocking speed set to 5.  BeadChips were washed and stained in the following steps:  1) 55°C for 10 minutes static in HighTemp Wash Buffer in a Hybex waterbath, 2) ambient temperature shaking for 5 minutes in E1BC wash buffer, 3) ambient temperature shaking for 10 minutes in ethanol, 4) ambient temperature shaking for 2 minutes in E1BC buffer, 5) ambient temperature for 10 minutes rocking in Block E1 buffer, 6) ambient temperature for 10 minutes rocking in Block E1 buffer containing 1ug/ml Cy3-streptavidin, and 7) ambient temperature shaking for 5 minutes in E1BC buffer.

scan_protocol: BeadArrays were dried in a centrifuge for 4 minutes and scanned using a BeadArray scanner.  Illumina BeadScan software was used to produce .idat, .xml, and .tif files for each array on a slide and .sdf files for each barcode on a slide of 12 arrays.  Raw data were extracted using Illumina BeadStudio software v 3.   Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction in an Excel report containing the project description (sample key), gene identifiers and corresponding probe IDs, table of detection p-values, tables of normalized data with and without background subtraction, array quality control metrics, and array quality control metric cut-offs and definitions.

data_processing: Data were were cubic spline normalized using Illumina Bead Studio software . After normalization the data were furhter processed by changing all negative values to zero and then adding 16 to each intensity.

source_name: hTERT_KGM_Biological Replicate 3

label_protocol: Biotinylated cRNA were prepared using a MessageAmp™ II-based protocol (Ambion Inc., Austin, TX) and one round of amplification. The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.  Labeled cRNA was used to probe HumanHT-12 v3 Expression BeadChips.

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

value: hTERT immortalized meibomian gland epithelial cells


title: Time point 0 (9.30 am) subject 16

description: Gene expression at 9.30 am


title: Time point 0 (9.30 am) subject 12

description: Gene expression at 9.30 am


title: Time point 0 (9.30 am) subject 14

description: Gene expression at 9.30 am


title: hTERT KGM Biological Replicate 1

description: replicate 1

source_name: hTERT_KGM_Biological Replicate 1


title: hTERT BPE Biological Replicate 2

description: replicate 2

source_name: hTERT_BPE_Biological Replicate 2


title: Time point 0 (9.30 am) subject 11

description: Gene expression at 9.30 am


title: Time point 0 (9.30 am) subject 13

description: Gene expression at 9.30 am


title: MM 38

description: Uveal melanoma from enucleation 38


title: MM 76

description: Uveal melanoma from enucleation 76


title: hTERT KGM Biological Replicate 2

description: replicate 2

source_name: hTERT_KGM_Biological Replicate 2


title: hTERT BPE Biological Replicate 3

description: replicate 3

source_name: hTERT_BPE_Biological Replicate 3


title: MM 64

description: Uveal melanoma from enucleation 64


title: MM 63

description: Uveal melanoma from enucleation 63


title: hTERT BPE Biological Replicate 1

description: replicate 1

source_name: hTERT_BPE_Biological Replicate 1


title: MM 61

description: Uveal melanoma from enucleation 61


title: MM 55

description: Uveal melanoma from enucleation 55


title: MM 60

description: Uveal melanoma from enucleation 60


title: hTERT EGF Biological Replicate 3

description: replicate 3

source_name: hTERT_EGF_Biological Replicate 3


title: Time point 0 (9.30 am) subject 10

description: Gene expression at 9.30 am


title: hTERT EGF Biological Replicate 2

description: replicate 2

source_name: hTERT_EGF_Biological Replicate 2


title: Time point 0 (9.30 am) subject 8

description: Gene expression at 9.30 am


title: hTERT EGF Biological Replicate 1

description: replicate 1

source_name: hTERT_EGF_Biological Replicate 1


title: hTERT basal Biological Replicate 3

description: replicate 3

source_name: hTERT_basal_Biological Replicate 3


title: Time point 0 (9.30 am) subject 6

description: Gene expression at 9.30 am

source_name: Suction blister epidermis


title: MM 48

description: Uveal melanoma from enucleation 48

source_name: Primary uveal melanoma tumor


title: MM 49

description: Uveal melanoma from enucleation 49


title: Time point 0 (9.30 am) subject 7

description: Gene expression at 9.30 am


title: hTERT basal Biological Replicate 2

description: replicate 2

source_name: hTERT_basal_Biological Replicate 2


title: MM 40

description: Uveal melanoma from enucleation 40


title: Time point 0 (9.30 am) subject 4

description: Gene expression at 9.30 am


title: Time point 0 (9.30 am) subject 5

description: Gene expression at 9.30 am


title: Time point 0 (9.30 am) subject 3

description: Gene expression at 9.30 am


title: wild type light WT.L

city: New York

first: Luke

middle: Mackley

last: Noble

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: dark incubated wild-type as reference for 2 hour light exposure (wild-type), biological replicates

hyb_protocol: TIGR protocol M008.

scan_protocol: Axon GenePix 4100, Genepix software with data acquired using morphological opening correction.

data_processing: Raw data were imported into R, lowess normalised and analysed using the limma package with normexp background correction (offset = 50) and duplicateCorrelation for duplicate probe spots, normalised to dark incubated wild-type as reference.

organism: Aspergillus nidulans

source_name: wild-type, dark

label_protocol: RNA was reverse transcribed using the Invitrogen Superscript Indirect Labelling Kit with oligo d(T) primers, and dye-labelled according to the manufacturer’s protocol.

growth_protocol: 46 hours growth at 37C on 1% agar Aspergillus complete medium plates, followed by 2 hours of light exposure or continued dark.

extract_protocol: Total RNA was extracted using Trizol reagent according to protocol.

tag: strain

value: wild type

value: dark

source_name: wild-type, light

value: light


title: kdmA dark KO.D

description: dark incubated wild-type as reference for dark incubated kdmA deletion mutant, single hybridisation

source_name: kdmA deletion, dark

value: kdmA deletion


title: brain_mut3

city: Santa Cruz

first: Manny

last: Ares

address: 1125 High St

department: Molecular and Cellular Biology

institute: UCSC

hyb_protocol: Targets were hybridized to chips in 7% DMSO solution for 16 hrs overnight at 50. Microarrays were washed, processed with anti-biotin antibodies and streptavidin-phycoerythrin according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix procedures

data_processing: Intensity values from the DNA arrays were normalized using a quantile normalization (Bolstad et al., 2003), and probe set summaries were derived using the Robust Multi-chip Analysis (RMA) procedure (Irizarry et al., 2003a; Irizarry et al., 2003b) with two modifications. The first modification was to remove all probes with 17 or more continuous bases that match to any other mouse transcript in order to minimize cross-hybridization issues. The second modification was to use the mode of the probe intensity values of similar GC content probes for the background estimate of a particular probe. For example, if a probe has a GC count of 16, then the mode of the intensity of all the probes with a GC count of 16 was used as a background estimate as opposed to RMA in which the mode of all the probes is used as a background estimate for all the probes.

source_name: mouse brain mutant

label_protocol: Total RNA was primed with random hexamers and reverse transcribed. After the reaction was completed, RNA was removed from the reaction by alkaline hydrolysis and the cDNA was purified using Qiagen PCR Quick Purification Kit. A typical reaction started with 5-6ug of total RNA usually yielded ~3ug of cDNA. The cDNA was then fragmented using DNAseI in an empirically controlled reaction that yields DNA fragments of 50-200 bases. This fragmented cDNA was then end labeled using terminal deoxynucleotidyl transferase and "DNA-Labeling-Reagent-1a (DLR-1a)", which is a biotinylated dideoxynucleoside triphosphat

extract_protocol: Total RNA was extracted using Invitrogen Trizol reagent. RNA samples were quantified using NanoDrop ND-1000 Spectrophotometer.

value: brain

value: FBV


title: 687T SSH

city: Cordoba

first: German

middle: Alexis

last: Gonzalez

state: Cordoba

address: Av. Armada Argentina 3555

department: School of Engineering

country: Argentina

institute: Catholic University of Cordoba

description: pancreatic tumor tissue, replicate 6

hyb_protocol: A pre-hybridization step were carried out. Then, hybridization buffer 2X were added to all samples followed by an incubation at 42°C for 16 h. in an hybridization chamber (InSlide Out, Boekel Scientific, Pennsylvania, PA, USA).

scan_protocol: Scanned on a VersArray ChipReader scanner (Bio-Rad Laboratories, Hercules, CA). Images were quantified using the software SpotReader (versión 1.3.1.0, Niles Scientific, USA)

data_processing: R-2.14 was used for background correction (norm exp with offset=50) and printip LOESS normalization. These functions are implemented in limma package. Flagged genes were considered missing values.

label: Alexa 647

source_name: pancreatic tumor tissue, indirect strategy

label_protocol: 1 µg of total RNA were primed with T7-oligo (dT) primer and reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase (Invitrogen), and dNTP mix 10 mM.  In vitro transcription were carried out with 1.5 µL ATP (100 mM), 1.5 µL CTP (100 mM), 1.5 µL GTP (100 mM), 0.75 µL UTP (100 mM), 2 µL aa-UTP (50 mM), 4 µL T7 Reaction Buffer 10X and 7 µL T7 Enzyme Mix at 37ºC for 14 h.

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

tag: gender

value: M

tag: age

value: pancreatic

tag: disease state

value: advanced

tag: histological subtype

value: ductal adenocarcinoma

tag: differentiation

value: Poor

label: Alexa 555

source_name: Human Universal Reference RNA (Clontech)

tag: reference

value: comercial (normal RNA from many normal human tissues)


title: 687A SSH

description: pancreatic non-tumoral tissue, replicate 6

source_name: adjacent pancreatic non-tumoral tissue, indirect strategy


title: DHT12 [US10173810_251959710400_S01_GE1_107_Sep09_2_2]

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: ovary explants

hyb_protocol: FHM 8 x 15K microarrays were manufactured with Agilent Sure Print Technology in Fall 2010.  RNA labeling, microarray hybridization, and microarray analysis were performed according to Agilent’s One-Color Microarray-Gene Based Expression Analysis protocol (May 2010) using an Agilent kit (Agilent, Mississauga, ON, CAN).  After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

data_processing: Normalized signal intensity provided here is LOESS Normalization

organism: Pimephales promelas

label_protocol: Agilent one color protocol for Cy3

extract_protocol: RNA was extracted from gonad explants according to RNA isolation protocol (TRIzol® Reagent, Invitrogen, Burlington, ON, CAN).  After extraction using 1 ml TRIzol®, nucleic acid pellets were reconstituted in 20-25 µl RNA Secure™ (Ambion, Austin, TX, USA) in order to protect RNA integrity as per manufacturer’s protocol.  RNA quantity was measured using the NanoDrop ND2000 (Thermo Scientific) prior to DNase treatment for real-time PCR and RNA integrity was evaluated according to Agilent 2100 Bioanalyzer protocol (Agilent, Mississauga, ON, CAN).  RNA integrity values were generated and ranged from 6.5-8.3 (RIN average ± SD = 7.45 ± 0.55) for ovary explants.  To clean-up RNA, samples that had RIN numbers below 7.5 were purified using QIAGEN RNeasy® Kit (Toronto, ON) according to the Qiagen RNeasy® Kit protocol.  After purification, only samples with RIN values greater than 7.5 were used for microarray and qPCR analyses.

treatment_protocol: Ovary explants were incubated with 10^-6M for 6, 9, and 12 hours

tag: agent

value: DHT

tag: time point

value: 12 hours

value: ovary

value: female


title: Time point 0 (9.30 am) subject 2

description: Gene expression at 9.30 am

value: Epidermis

value: Time point 0 (9.30 am)


title: 636A SSH

description: pancreatic non-tumoral tissue, replicate 5

value: F

value: Moderate


title: kdmA light KO.L

description: dark incubated wild-type as reference for 2 hour light exposure (kdmA deletion mutant), biological replicates

tag: genotype

value: wild type

value: dark

source_name: kdmA deletion, light

value: kdmA deletion

value: light


title: CON12 [US10173810_251959710400_S01_GE1_107_Sep09_2_1]

description: ovary explants

scan_protocol: After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

value: control


title: Time point 0 (9.30 am) subject 1

description: Gene expression at 9.30 am


title: 617A SSH

description: pancreatic non-tumoral tissue, replicate 4

value: M

value: pancreatic

value: advanced


title: 636T SSH

description: pancreatic tumor tissue, replicate 5

value: ductal adenocarcinoma

value: comercial (normal RNA from many normal human tissues)


title: hTERT basal Biological Replicate 1

description: replicate 1

source_name: hTERT_basal_Biological Replicate 1

tag: cell type

value: hTERT immortalized meibomian gland epithelial cells


title: brain_wt3

source_name: mouse brain wt

value: brain

value: wt

value: FBV


title: brain_mut2


title: DHT12 [US10173810_251959710400_S01_GE1_107_Sep09_1_2]

description: ovary explants

value: DHT

value: 12 hours

value: ovary

value: female


title: CON12 [US10173810_251959710400_S01_GE1_107_Sep09_1_1]

description: ovary explants


title: brain wt2


title: 558A SSH

description: pancreatic non-tumoral tissue, replicate 3

value: F

value: Moderate


title: 617T SSH

description: pancreatic tumor tissue, replicate 4


title: brain_wt1


title: CON12 [US10173810_251959710399_S01_GE1_107_Sep09_2_1]

description: ovary explants


title: HSY3

city: Atlanta

first: Jeremy

last: Boss

state: GA

address: 1510 Clifton Rd

department: Micobiology and Immunology

institute: Emory University

hyb_protocol: Applied Biosystem mouse genome survey

scan_protocol: Standard ABI protocol, performed by the Emory Biomarker Core Center (http://www.biomarker.emory.edu/)

data_processing: Sigle color cDNA microarray was used to analyze absoulte amount of RNA level from each sample. And Fold change data was used to reflects the level in IL2, IL5, LPS stimulated cell divided by control (unstimulated cell).

label: digoxigenin

source_name: unstimulated primary murine B cell

growth_protocol: RPMI supplemented with 10% FBS

extract_protocol: Total RNA was extracted using RNAeasy kit from Qiagen.

treatment_protocol: For B cell differentiation, purified murine B cell were treated with IL2, IL5, LPS for 24 hours.

value: spleen B cell

value: 5 weeks


title: DHT12 [US10173810_251959710398_S01_GE1_107_Sep09_2_1]

description: ovary explants


title: HSY2

source_name: IL2, IL5, LPS treated B cell

label_protocol: Standard ABI protocol, performed by the Emory Biomarker Core Center (http://www.biomarker.emory.edu/)

value: IL2, IL5, LPS


title: HSY4


title: 558T SSH

description: pancreatic tumor tissue, replicate 3

value: pancreatic


title: MM 23

description: Uveal melanoma from enucleation 23

tag: collection

value: Fresh frozen sample from enucleated eye

value: eye tumor


title: DHT12 [US10173810_251959710398_S01_GE1_107_Sep09_1_2]

description: ovary explants


title: 271A SSH

description: pancreatic non-tumoral tissue, replicate 2

value: M

value: advanced

value: ductal adenocarcinoma

value: comercial (normal RNA from many normal human tissues)


title: 56A SSH

description: pancreatic non-tumoral tissue, replicate 1

value: Poor


title: DHT9 [US10173810_251959710397_S01_GE1_107_Sep09_2_2]

description: ovary explants

value: DHT

value: 9 hours


title: CON6 [US10173810_251959710397_S01_GE1_107_Sep09_2_1]

description: ovary explants

value: control

value: 6 hours

value: ovary


title: quad_mut3

source_name: mouse quad mutant

value: quad

value: FBV


title: HSY1

value: spleen B cell

value: 5 weeks


title: bile+1

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: O157:H7 mid-log phase cells grown in Luria broth with 0.8% bile salts, replicate 1

hyb_protocol: cDNA was hybridized for 16 hr at 45C on GeneChip E.coli Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix scanner 7G.

data_processing: The data were imported into FlexArray using gc-RMA preprocessing for analysis.

organism: Escherichia coli

source_name: E.coli O157:H7 in LB at mid-log phase

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

growth_protocol: O157:H7 cells were grown to mid-log phase in Luria broth with or without 0.8% bile salts.

extract_protocol: Hot phenol extraction of total RNA.

value: strain O157:H7

tag: growth phase

value: mid-log phase

tag: growth media

value: LB; 0.8% bile salts


title: CON12 [US10173810_251959710398_S01_GE1_107_Sep09_1_1]

description: ovary explants

value: 12 hours

value: female


title: 56T SSH

description: pancreatic tumor tissue, replicate 1

value: F

value: pancreatic

value: advanced

value: ductal adenocarcinoma


title: bile+3

description: O157:H7 mid-log phase cells grown in Luria broth with 0.8% bile salts, replicate 3


title: bile+2

description: O157:H7 mid-log phase cells grown in Luria broth with 0.8% bile salts, replicate 2


title: 271T SSH

description: pancreatic tumor tissue, replicate 2

value: M

value: Moderate

value: comercial (normal RNA from many normal human tissues)


title: ctrl3

description: O157:H7 mid-log phase cells grown in Luria broth, replicate 3

value: LB


title: quad_wt3

source_name: mouse quad wt

value: quad

value: wt


title: CON9 [US10173810_251959710397_S01_GE1_107_Sep09_1_4]

description: ovary explants

value: control

value: 9 hours

value: ovary


title: ctrl2

description: O157:H7 mid-log phase cells grown in Luria broth, replicate 2

value: strain O157:H7

value: mid-log phase


title: quad_mut2

value: FBV


title: Time point 0 (9.30 am) subject 9

description: Gene expression at 9.30 am

source_name: Suction blister epidermis

value: Epidermis

value: Time point 0 (9.30 am)


title: 687A direct

source_name: adjacent pancreatic non-tumoral tissue, direct strategy

value: pancreatic

value: Poor


title: CON6 [US10173810_251959710397_S01_GE1_107_Sep09_1_3]

description: ovary explants

value: 6 hours

value: female


title: Microcystin-LR 25MC10

city: Nanjing

first: Lizhi

last: Xu

state: Jiangsu

address: 22 Hankou Road

department: School of Medicine

country: China

institute: Nanjing University

hyb_protocol: Samples were sent to Exiqon where they were labeled and hybridized into the miRCURY LNA microarray (miRbase 11.0 human array)

scan_protocol: The processed slides were scanned by using an Axon 4000B microarray Scanner, with the laser set at 635 nm and Power 80% and the photomultiplier set at 70% with a scan resolution of 10 µm.

data_processing: The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data=(Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.   The profiling identified a subset of the total number of miRNAs analyzed by the miRCURY™ array that are differentially expressed. Unsupervised hierarchical clustering was performed on miRNA expression profiling. We also show the scatter plot comes with Correlation R-value in the Correlation & Scatter Plot sheet in miRNA_Data_Analysis_Report.

source_name: WRL-68 treated with MC-LR

label_protocol: WRL-68 cells were seeded on 25 cm2 flasks at a density of 2×104 cells/mL and incubated for 72 h. The cells were then passaged and exposed to 10 µg/L MC-LR (final concentration). The cells were labeled 25MC10, following the passage number and the final concentration of MC-LR used. The control cells were simultaneously treated with phosphate-buffered saline (PBS). All treatments were performed in triplicate.

growth_protocol: Human cell line WRL-68 (CL-48 from ATCC, Manassas, VA, USA) was grown in 25 cm2 flasks with Dulbecco’s modified Eagle’s minimal essential medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% heat-inactivated certified fetal calf serum (FCS; Sijiqing Biological Engineering Materials Co., Ltd., Hangzhou, Zhejiang, PR China), 100 U/mL penicillin, and 100 mg/mL streptomycin at 37 °C in a humidified chamber with 5% CO2. The cells were passaged at the estimated log growth phase until a sufficient number of 80%–90% confluent 25 cm2 flasks were obtained for each experiment.

extract_protocol: Total RNA from the control cells (n=3) and that from the 25MC10 cells (n=3) were isolated using TRIzol reagent (Invitrogen) following the manufacturer’s instructions.

treatment_protocol: WRL-68 cells were seeded on 25 cm2 flasks at a density of 2×104 cells/mL (2×105 cells per flask) and exposed to 10 µg/L MC-LR (final concentration) and incubated. After 72 h, the cells were then passaged and exposed to another 10 µg/L MC-LR. The same treatment with every passage for 25 passages and the cells were labeled 25MC10. The control cells were simultaneously treated with phosphate-buffered saline (PBS). All treatments were performed in triplicate.

tag: cell name

tag: treatment

value: Microcystin-LR


title: 636A direct

value: F

tag: tissue

value: advanced

value: ductal adenocarcinoma

value: Moderate

value: comercial (normal RNA from many normal human tissues)


title: 687T direct

description: pancreatic tumor tissue, replicate 6

source_name: pancreatic tumor tissue, direct strategy

value: M


title: heart_mut3

source_name: mouse heart mutant

value: heart

tag: strain


title: ctrl1

description: O157:H7 mid-log phase cells grown in Luria broth, replicate 1

value: strain O157:H7

value: LB


title: DHT9 [US10173810_251959710396_S01_GE1_107_Sep09_2_4]

description: ovary explants

value: DHT

value: 9 hours

value: ovary

tag: gender


title: brain_mut1

source_name: mouse brain mutant

value: brain

value: FBV


title: quad_mut1

value: quad


title: PBS control

description: The control cells were seeded on 25 cm2 flasks at a density of 2×104 cells/mL (2×105 cells per flask) treated with phosphate-buffered saline (PBS). After 72 h, the cells were then passaged. The same treatment with every passage for 25 passages.

source_name: WRL-68 treated with PBS

value: control


title: quad_wt2

value: wt


title: 636T direct

description: pancreatic tumor tissue, replicate 5

value: F

tag: age

value: pancreatic

source_name: Human Universal Reference RNA (Clontech)


title: CON9 [US10173810_251959710396_S01_GE1_107_Sep09_1_4]

description: ovary explants

value: female


title: 617A direct

tag: disease state

value: advanced

value: ductal adenocarcinoma

value: Moderate


title: heart_mut2

source_name: mouse heart mut

value: heart


title: quad_wt1


title: heart_wt3

source_name: mouse heart wt


title: DHT6 [US10173810_251959710396_S01_GE1_107_Sep09_1_2]

description: ovary explants

value: 6 hours


title: DHT9 [US10173810_251959710396_S01_GE1_107_Sep09_2_2]

description: ovary explants


title: heart_mut1


title: heart_wt1


title: 617T direct

description: pancreatic tumor tissue, replicate 4

value: M

tag: histological subtype

value: comercial (normal RNA from many normal human tissues)


title: 558A direct

tag: differentiation


title: DHT6 [US10173810_251959710395_S01_GE1_107_Sep09_2_2]

description: ovary explants

value: DHT


title: DHT6 [US10173810_251959710395_S01_GE1_107_Sep09_2_3]

description: ovary explants

value: ovary


title: CON9 [US10173810_251959710395_S01_GE1_107_Sep09_2_4]

description: ovary explants

value: 9 hours


title: 558T direct

description: pancreatic tumor tissue, replicate 3

tag: reference


title: NF 46 sample 4

hyb_protocol: Microarrays were hybridized for 17 h and washed according to Agilent protocol.

scan_protocol: Microarrays were scanned at 5 μm with the Agilent G2505 B Microarray Scanner and Agilent Feature Extraction Software (v. 9.5) was used to extract raw signal intensities from microarray images.  The quality of microarray data was evaluated by manual inspection and each microarray was deemed to be of high quality.

organism: Xenopus tropicalis

source_name: whole animal

extract_protocol: Total RNA extraction for microarray analysis was done using TRIzol® Reagent (Life Technologies Corporation, Invitrogen, Burlington, CAN) . RNA was resuspended in 20-30 µl RNAsecure™ Reagent (Ambion®).  Total RNA integrity was evaluated using the RNA 6000 Nano Assay Kit with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA samples were purified using the RNeasy Mini Kit (Qiagen, Mississauga, ON) and RNA concentrations were determined using the NanoDrop-2000 spectrophotometer (Thermo Scientific).

treatment_protocol: Gene expression analysis was performed with four biological replicates for four developmental stages (n = 16). Stages were NF stages 2, 16, 34, and 46.

value: embryo

tag: developmental stage

value: NF 46


title: DHT6 [US10173810_251959710395_S01_GE1_107_Sep09_2_1]

description: ovary explants

tag: agent

tag: time point


title: 56A direct

value: Poor


title: TK2 KO heart, biological rep1

city: Huddinge

first: João

middle: Amorim

last: Paredes

state: Stockholm

address: Karolinska Universitetssjukhuset Huddinge, F68

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

description: Gene expression data from heart muscle of 11 days-old TK2 knockout mouse

hyb_protocol: Automated with GeneTitan Instrument and Affymetrix GeneChip Command software (AGCC)

data_processing: Affymetrix Expression Console Software; Summarization: PLIER,  Normalization: Global Median

source_name: Heart from TK2 KO 11 days-old mice

label_protocol: Labelling was done using Ambion WT Expression kit (Life Technologies), according to manufacturer's instructions.

growth_protocol: Official Swedish regulations for use and care of laboratory animals were followed throughout and the experimental protocol was approved by the local ethical commitee (S104-09, S135-11)

extract_protocol: Muscle tissues were harvested immediatelly after we have sacrificed the mice. Total RNA was extracted using Rneasy kit (QIAGEN), according to manufacturer's instructions.

value: 11 days-old

tag: genotype

value: TK2 knockout, TK2-/-


title: TK2 KO heart, biological rep3

scan_protocol: Automated with GeneTitan Instrument and Affymetrix GeneChip Command software (AGCC)


title: NF 46 sample 2


title: 271A direct

value: pancreatic


title: wt heart, biological rep3

description: Gene expression data from heart muscle of 11 days-old wild-type mouse

source_name: Heart from wt 11 days-old mice

value: wild-type, TK2+/+


title: 271T direct

description: pancreatic tumor tissue, replicate 2

value: advanced


title: NF 46 sample 1


title: heart_wt2

source_name: mouse heart wt 2

value: wt

value: FBV


title: CON6 [US10173810_251959710394_S01_GE1_107_Sep09_2_4]

description: ovary explants

value: control

value: female


title: wt heart, biological rep1

value: heart


title: DHT9 [US10173810_251959710395_S01_GE1_107_Sep09_1_2]

description: ovary explants


title: DHT6 [US10173810_251959710395_S01_GE1_107_Sep09_1_3]

description: ovary explants

value: 6 hours


title: NF 46 sample 3


title: CON6 [US10173810_251959710395_S01_GE1_107_Sep09_1_1]

description: ovary explants


title: NF 34 sample 4

value: NF 34


title: Low leaf Cd pool

type: genomic

city: Shanghai

first: Daiyin

last: Chao

address: 300 Fenglin Road

department: Shanghai Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences

description:
CS28181-F2-LCd
Hybridized to the Affymetrix SNP-tiling array AtSNPtile.

hyb_protocol: Labelled DNA was hybridized to each array according to the manufacturer's instructions, and then washed using Affymetrix Fluidics Stations.

scan_protocol: The arrays were scanned using the GeneChip Scanner (Type M10 with Filter 570 and Pixel Size 0.7).

data_processing: The CEL files containing raw data of signal intensity for all probes were read and spatially corrected using R scripts from Borevitz et al. (2003, Genome Research, PMID 12618383) with the R program and the Bioconductor affymetrix package. Polymorphic SNPs between the two parents identified previously by Borevitz et al. (2003, Genome Research) were used for further analysis. There are 4 probes for each SNP, antisense and sense probes for two alleles. The allele frequency signal difference between the two pools for each SNP was then assessed based on the signal intensity difference of the 4 probes. The whole process can be carried out using R scripts that are available at http://ars.usda.gov/mwa/bsasnp .

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: low leaf Cd pool

label_protocol: As described by the manufacturer of the BioPrime DNA labeling system (Invitrogen).

growth_protocol: Plants were grown in a controlled common garden (photoperiod of 10 h light (90 µmol•m-2•s-1)/ 14 h dark, humidity of 60% and temperature ranging from 19 to 22 ºC) in potting mix soil with Cd supplied in the soil at a sub-toxic concentration. Plants were bottom-watered twice a week with modified 0.25 × Hoagland solution in which Fe was replaced by 10 µM Fe-HBED (N,N'-di(2-hydroxybenzyl)ethylenediamine- N,N'-diacetic acid monohydrochloride hydrate; Strem Chemicals, Inc.)

extract_protocol: Genomic DNA was extracted from leaf pools using the Qiagen DNeasy Plant Mini Kit. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: accessions

value: leaf

tag: cd level

value: low


title: wt heart, biological rep2


title: High leaf Cd pool

description:
CS28181-F2-HCd
Hybridized to the Affymetrix SNP-tiling array AtSNPtile.

source_name: high leaf Cd pool

value: high


title: TK2 KO heart, biological rep2


title: CON9 [US10173810_251959710394_S01_GE1_107_Sep09_2_1]

description: ovary explants

value: 9 hours

value: ovary


title: CON9 [US10173810_251959710394_S01_GE1_107_Sep09_1_3]

description: ovary explants


title: 56T direct

description: pancreatic tumor tissue, replicate 1

value: F

value: ductal adenocarcinoma

value: Poor

value: comercial (normal RNA from many normal human tissues)


title: NF 34 sample 2

value: embryo


title: Serum-induced brain tumor cell_316_rep2

city: Nagoya

first: Keisuke

last: Katsushima

address: 1-1 Kanokoden

country: Japan

institute: Aichi Cancer Center Research Institute

hyb_protocol: Labeled samples were purified with MicroBio-Spin 6 columns (Bio-Rad) and hybridized to microarray at 55 °C with rotation at 20 rpm for 20 hours.

scan_protocol: Microarrays were scanned by an Agilent Scanner (Agilent Scan Control 7.0 software) and analyzed using Agilent Feature Extraction 10.7 software for miRNA microarray.

data_processing: Raw data were normalized and analyzed with the use of GeneSpring software (version 11.5).

source_name: Serum-induced brain tumor cell

label_protocol: One hundred ng of total RNA was labeled with pCp-Cy3 (Agilent Technologies) and 15 units of T4 RNA ligase (GE Healthcare, Little Chalfont, Buckinghamshire, UK) at 16°C for 2 hours.

extract_protocol: MicroRNA was isolated with TRIzol reagent (Invitrogen).

treatment_protocol: GSC were established from Glioblastoma tissue sample. Briefly, dissociated tumor cells were cultured in NBE media comprising neurobasal media, with N2 and B27 supplements (Invitrogen, Carlsbad, CA), along with human recombinant basic fibroblast growth factor and epidermal growth factor (20 ng/ml each; R&D Systems, Minneapolis). Serum-induced brain tumor cells (S-BTC) were established by culturing GSC in DMEM media containing 10% fetal bovine serum .

tag: cell type

value: Serum-induced brain tumor cell


title: TK2 KO skel muscle, biological rep1

description: Gene expression data from skeletal muscle of 11 days-old TK2 knockout mouse

source_name: Hind limb skeletal muscle from TK2 KO 11 days-old mice

value: 11 days-old

value: skeletal muscle

value: TK2 knockout, TK2-/-


title: NF 34 sample 3


title: TK2 KO skel muscle, biological rep3


title: TK2 KO skel muscle, biological rep2


title: NF 16 sample 4

value: NF 16


title: wt skel muscle, biological rep3

description: Gene expression data from skeletal muscle of 11 days-old wild-type mouse

source_name: Hind limb skeletal muscle from wt 11 days-old mice

value: wild-type, TK2+/+


title: Glioma stem-like cell_316_rep1

source_name: Glioma stem-like cell

value: Glioma stem-like cell


title: DHT9 [US10173810_251959710394_S01_GE1_107_Sep09_1_1]

description: ovary explants

value: DHT

value: female


title: Serum-induced brain tumor cell_1228_rep1


title: NF 34 sample 1

value: NF 34


title: NF 16 sample 2


title: Glioma stem-like cell_1228_rep1


title: Desulfovibrio vulgaris Hildenborough strain JW9009 (deletion mutant in DVU2097) on pyruvate-sulfate with carbon monoxide

type: mixed

city: Berkeley

first: Lara

last: Rajeev

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

description: This sample was used to investigate the gene expression changes upon exposure to carbon monoxide in D. vulgaris JW9009 strain deleted for the cooA gene (DVU2097) during growth on pyruvate-sulfate. Control is JW9009 grown on pyruvate-sulfate without CO

hyb_protocol: Sample hybridization was carried out as described in He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: Imagene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A.P. Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Total RNA from mid-log phase cells of Desulfovibrio vulgaris Hildenborough JW9009 (deletion mutant in DVU2097) grown on pyruvate-sulfate with 1% carbon monoxide in headspace

label_protocol: Sample labeling was carried out as described in He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

growth_protocol: Inoculate 1 ml of log-phase inoculum culture in 100 ml of defined CCMA medium with pyruvate as electron donor and sulfate as electron acceptor in sealed glass bottles with nitrogen/CO2 and 1% CO as headspace. Grow culture at 37°C till mid log phase (OD of ~0.3) and harvest cells. Three replicates were grown with CO and three were grown as control without CO.

extract_protocol: Total RNA was extracted as described in He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

value: Hildenborough

value: Deletion in DVU2097 (cooA)

tag: growth condition

source_name: Desulfovibrio vulgaris Hildenborough, genomic DNA

extract_protocol: Genomic DNA was extracted as described in Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316Ð322.


title: ymoA mutant vs. YPIII wild type, replicate 2

city: Braunschweig

first: Ann

middle: Kathrin

last: Heroven

state: Niedersachsen

address: Inhoffenstr. 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

hyb_protocol: 300ng of each Cy3- and Cy5-labelled RNA were mixed, fragmented and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions.

scan_protocol: Data were scanned at a resolution of 5μm using Axon GenePix Personal 4100A scanner 14, and features were extracted using the software package GenePix Pro 6.015.

data_processing: The processing was done using the software package "R" in combination with the “Bioconductor” software framework (www.bioconductor.de) (Gentleman et al., 2004). Preprocessing based on the marray package employing the read.GenePix function. Control code for probe selection was adapted to the custom-made Agilent microarray system and a quality control was performed to check for hybridization artifacts and large-scale differences between the microarrays of one experiment. A two-color intensity-dependent normalization (“Lowess” normalization) was applied.

organism: Yersinia pseudotuberculosis YPIII

source_name: ymoA knockout mutant

label_protocol: RNA samples were labelled with Cy3 using the ULS fluorescent labelling kit (Kreatech, Germany).

extract_protocol: RNA extraction was performed using the SV Total RNA Isolation System (Promega).

tag: background strain

value: YPIII

value: ymoA null mutant

source_name: wild type

label_protocol: RNA samples were labelled with Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).

value: wild type


title: ymoA mutant vs. YPIII wild type, replicate 3


title: NF 2 sample 4

tag: tissue

value: NF 2


title: NF 16 sample 1

value: embryo


title: Desulfovibrio vulgaris Hildenborough wild type on pyruvate-sulfate with carbon monoxide

description: This sample was used to investigate the gene expression changes upon exposure to carbon monoxide in D. vulgaris Hildenborough wild type strain during growth on pyruvate-sulfate. Control is wild type cells grown on pyruvate-sulfate without CO.

source_name: Total RNA from mid-log phase cells of Desulfovibrio vulgaris Hildenborough wild type grown on pyruvate-sulfate with 1% carbon monoxide in headspace

growth_protocol: Inoculate 1 ml of log-phase inoculum culture in 100 ml of defined CCMA medium with pyruvate as electron donor and sulfate as electron acceptor in sealed glass bottles with nitrogen/CO2 and 1% CO as headspace. Grow culture at 37°C till mid log phase (OD of ~0.3) and harvest cells. Three replicates were grown with CO in the headspace, and three replicates were grown as control with no CO.

tag: strain

value: Desulfovibrio vulgaris Hildenborough, genomic DNA


title: ymoA mutant vs. YPIII wild type, replicate 4


title: NF 16 sample 3


title: K96243vsH307

city: Maung

first: THANATCHAPORN

last: BARTPHO

state: Khon Kaen

address: 123 Mitthaphap

country: Thailand

institute: Meliodosis Research Center, Faculty of Medicine, Khon Kaen University

description: raw data file=K96243vsH307.gpr

hyb_protocol: DNA probe was prepared by mixed 2 µg each of Cy5 labeled gDNA of the K96243 and Cy3 labeled of a selected isolate and then dry in a SpeedVac concentrator for about 30 min. The probe was resuspended in 50 µl hybridization solution (50% formamide, 5x SSC, 0.1% SDS) and hybridized onto the post-processed slides while the LifterSlip Microarray Coverslips was placed over the array slide and incubated at 42°C in a water bath for 16-20 h.

scan_protocol: The slides were scanned by a GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA, USA) and initially analyzed with GenePix Pro 6.1 software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal and across arrays using the Aroma package, R software was used.

organism: Burkholderia pseudomallei

source_name: Reference strain

label_protocol: Genomic DNA of B. pseudomallei was labeled by nick translation. The 10-15 µg gDNA of B. pseudomallei K96243 used as reference strain was labeled with Cy5-dCTP whereas each B. pseudomallei tested strain (BP45s, BP28L, H307, P54, P82) was labeled with Cy3-dCTP fluorescent dye using a standard nick-translation reaction to generate randomly labeled DNA fragments according to the manufacturer's protocol (Promega, Madison, WI, USA). After the labeling reaction was completed, unincorporated nucleotides were removed by passage over a gel filtration spin column (illustra MicroSpin™ G-50 Columns, GE Healthcare Bio-Sciences, NJ, USA) according to the manufacturer's recommendations.

growth_protocol: Bacteria were grown overnight in Luria Bertani broth (LB broth) and incubated at 37oC with shaking at 200 rpm.

extract_protocol: The overnight culture of all B. pseudomallei strains in LB broth were used for genomic DNA (gDNA) extraction according to manufacturer's protocol (Generation capture column, QIAGEN Sciences, MD, USA).

source_name: Clinical

tag: isolate


title: wt skel muscle, biological rep2

tag: age

value: 11 days-old


title: K96243vsP54

description: raw data file=K96243vsP54.gpr


title: K96243vsP82

description: raw data file=K96243vsP82.gpr


title: Desulfovibrio vulgaris Hildenborough strain JW9009 (deletion mutant in DVU2097) on pyruvate-sulfate

description: This sample was used to investigate the gene expression differences at mid-log phase between WT D. vulgaris and a strain deleted for the cooA gene (DVU2097) when grown on pyruvate-sulfate. Control is the WT D. vulgaris cells grown under same conditions.

source_name: Total RNA from mid-log phase cells of Desulfovibrio vulgaris Hildenborough JW9009 (deletion mutant in DVU2097) grown on pyruvate-sulfate

growth_protocol: Inoculate 1 ml of log-phase inoculum culture in 100 ml of defined CCMA medium with pyruvate as electron donor and sulfate as electron acceptor in sealed glass bottles with nitrogen/CO2 as headspace. Grow culture at 37°C till mid log phase (OD of ~0.3). Three replicates of JW9009 were grown along with three replicates of WT as control.

value: grown on pyruvate-sulfate


title: K96243vsBP28L

description: raw data file=K96243vsBP28L.gpr

source_name: Environment


title: wt skel muscle, biological rep1

value: skeletal muscle


title: ymoA mutant vs. YPIII wild type, replicate 1


title: NF 2 sample 3

source_name: whole animal


title: NF 2 sample 2


title: K96243vsBP45S

description: raw data file=K96243vsBP45s.gpr


title: Wound tissue day70 vs. day0 uninjured skin rep.3 low int. scan

status: Public on Jul 30 2012

city: Dolni Dobrouc

first: Rastislav

last: Slavkovský

address: Dolni Dobrouc 401

department: R&D

country: Czech Republic

institute: Contipro Biotech

description: Biological replicate 3 of 4. Wound tissue day 70 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.

hyb_protocol: Samples from skin and wound from the same animal, labeled with opposite color were hybridized. After 30 min/60  C fragmentation of samples with fragmentation buffer and blocking agent (Agilent), Hi-RPM Hybridization buffer (Agilent) was added and mixed. Mixture was applied to microarrays and enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential. Hybridization was performed at 65°C for 17h. Slide were washed thoroughly using  GE Wash Buffer 1 at RT, Wash Buffer 2 at 37°C and HPLC acetonitril (Sigma), followed by stabilization using Stabilization and drying solution (Agilent)

scan_protocol: Slides were scanned using Molecular Device Axon Gene Pix 4000B (ver. 2010) at 5 um resolution, with 3 passages  at low PMT settings (L-samples) and  3 passages high PMT settings (H-samples), in order to detect wide range of expressions.

data_processing: Gene Pix Pro 7.2 was used for image analysis and bad spots removal (low intensity, saturated, control array spots). Acuity 4.1 was used for data compilation, LOWESS normalization and data analysis. Where applicable, flip dye function was applied on flip dye data (logR => -logR). Values, in the Sample tables, are not merged (high and low intensity scan). Positive values signify increase of transcript in wound sample in comparison to skin. Negative values signify decrease in skin. Hi and Low intensity scans data were merged using average of LOWESS logR, for further analysis.

organism: Sus scrofa

source_name: D70 wound tissue

label_protocol: 0.5 µg of total RNA was amplified labeled with Cy3 and Cy5-CTPs using Low Input QuickAmp Labeling Kit (Agilent) according to manufactuers's instructions. In two animals, skin samples were labeled Cy3 and wound sample Cy5, in other two animals, samples were labeled inversly using flip dye.

extract_protocol: Total RNA extracted from tissue stabilized in RNALatter using QIAGEN RNeasy Lipid Tissue Mini kit and automatic isolator QIAcube according to supplier standard protocol and instructions.

tag: scan method

value: low int. scan

value: wound scar tissue

tag: sample day

source_name: D0 skin

value: skin


title: Wound tissue day70 vs. day0 uninjured skin rep.3 high int. scan

description: Biological replicate 3 of 4. Wound tissue day 70 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.

value: high int. scan


title: NF 2 sample 1


title: Wound tissue day70 vs. day0 uninjured skin rep.2 (dye flip) high int. scan

description: Biological replicate 2 of 4. Wound tissue day 70 vs day 0 uninjured skin. High intensity scan. Scan 2 of 2.


title: Wound tissue day70 vs. day0 uninjured skin rep.1 high int. scan

description: Biological replicate 1 of 4. Wound tissue day 70 vs day 0 uninjured skin.High intensity scan.  Scan 2 of 2.


title: Wound tissue day70 vs. day0 uninjured skin rep.4 (dye flip) high int. scan

description: Biological replicate 4 of 4. Wound tissue day 70 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.


title: Wound tissue day70 vs. day0 uninjured skin rep.1 low int. scan

description: Biological replicate 1 of 4. Wound tissue day 70 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day70 vs. day0 uninjured skin rep.2 (dye flip) low int. scan

description: Biological replicate 2 of 4. Wound tissue day 70 vs day 0 uninjured skin. Low intensity scan. Scan 1 of 2.


title: Wound tissue day70 vs. day0 uninjured skin rep.4 (dye flip) low int. scan

description: Biological replicate 4 of 4. Wound tissue day 70 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day35 vs. day0 uninjured skin rep.4 (dye flip) high int. scan

description: Biological replicate 4 of 4. Wound tissue day 35 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.

source_name: D35 wound tissue


title: Wound tissue day35 vs. day0 uninjured skin rep.2 (dye flip) high int. scan

description: Biological replicate 2 of 4. Wound tissue day 35 vs day 0 uninjured skin. High intensity scan. Scan 2 of 2.


title: Wound tissue day35 vs. day0 uninjured skin rep.3 high int. scan

description: Biological replicate 3 of 4. Wound tissue day 35 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.


title: Wound tissue day35 vs. day0 uninjured skin rep.3 low int. scan

description: Biological replicate 3 of 4. Wound tissue day 35 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day21 vs. day0 uninjured skin rep.4 (dye flip) high int. scan

description: Biological replicate 4 of 4. Wound tissue day 21 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.

source_name: D21 wound tissue


title: Wound tissue day21 vs. day0 uninjured skin rep.1 high int. scan

description: Biological replicate 1 of 4. Wound tissue day 21 vs day 0 uninjured skin.High intensity scan.  Scan 2 of 2.


title: Wound tissue day21 vs. day0 uninjured skin rep.2 (dye flip) high int. scan

description: Biological replicate 2 of 4. Wound tissue day 21 vs day 0 uninjured skin. High intensity scan. Scan 2 of 2.


title: Wound tissue day35 vs. day0 uninjured skin rep.1 high int. scan

description: Biological replicate 1 of 4. Wound tissue day 35 vs day 0 uninjured skin.High intensity scan.  Scan 2 of 2.


title: Wound tissue day21 vs. day0 uninjured skin rep.3 high int. scan

description: Biological replicate 3 of 4. Wound tissue day 21 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.


title: Wound tissue day21 vs. day0 uninjured skin rep.3 low int. scan

description: Biological replicate 3 of 4. Wound tissue day 21 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day35 vs. day0 uninjured skin rep.1 low int. scan

description: Biological replicate 1 of 4. Wound tissue day 35 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day35 vs. day0 uninjured skin rep.2 (dye flip) low int. scan

description: Biological replicate 2 of 4. Wound tissue day 35 vs day 0 uninjured skin. Low intensity scan. Scan 1 of 2.


title: Wound tissue day35 vs. day0 uninjured skin rep.4 (dye flip) low int. scan

description: Biological replicate 4 of 4. Wound tissue day 35 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day21 vs. day0 uninjured skin rep.4 (dye flip) low int. scan

description: Biological replicate 4 of 4. Wound tissue day 21 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day14 vs. day0 uninjured skin rep.2 (dye flip) high int. scan

description: Biological replicate 2 of 4. Wound tissue day 14 vs day 0 uninjured skin. High intensity scan. Scan 2 of 2.

source_name: D14 wound tissue

value: granulation wound tissue


title: Wound tissue day14 vs. day0 uninjured skin rep.2 (dye flip) low int. scan

description: Biological replicate 2 of 4. Wound tissue day 14 vs day 0 uninjured skin. Low intensity scan. Scan 1 of 2.


title: medium treatment day28 replicate 3

city: St Lucia

first: Paulina

last: Kaniewska

address: Gehrman Building

department: School of Biological Sciences

institute: University of Queensland

hyb_protocol: Samples were hybridized using the Genisphere 900 3DNA kit components (vial 7 buffer) plus human Cot DNA (for blocking) at 42 degrees overnight.  Wash: 15 min (2X SSC/ 0.1% SDS at 65 degrees), 15 min 2X SSC RT, 15 min 0.2X SSC .

scan_protocol: Slides were scanned using AXON GenePix4000B, and and image acquisition and quality control was performed using the software GenePix ® Pro 5.

data_processing: Normexp background corrected signal intensities were used, also print-tip loess normalization was applied within slides, while scale normalization was applied between slides, in order to ensure that distributions were similar between arrays. As the experimental design for this experiment was a reference microarray design the value represents the normalized log (Channel 1/channel 2).

organism: Acropora millepora

source_name: Coral after 28 days of medium treatment exposure replicate 3

label_protocol: cDNA probe synthesis was performed from 1000ng total RNA using Superscript Reverse Transcripase (Invitrogen) and the Genisphere 900 3DNA Dendrimer from a Genisphere 3DNA-900 microarray kit according to the manufacturers’ instructions.

extract_protocol: Total RNA was extracted from each sample using Trizol (Invitrogen) following manufacturer’s instructions.  The integrity and quality of total RNA was assessed using a Bioanalyzer (Agilent Technology).  Only samples showing intact RNA were used for probe construction.

tag: sample type

value: adult coral in symbiosis with dinoflagellate

tag: acidification treatment

tag: time

value: 28 days

source_name: reference sample for coral

value: reference sample of pooled control and time zero adult corals


title: Wound tissue day21 vs. day0 uninjured skin rep.1 low int. scan

description: Biological replicate 1 of 4. Wound tissue day 21 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day14 vs. day0 uninjured skin rep.3 high int. scan

description: Biological replicate 3 of 4. Wound tissue day 14 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.


title: Wound tissue day21 vs. day0 uninjured skin rep.2 (dye flip) low int. scan

description: Biological replicate 2 of 4. Wound tissue day 21 vs day 0 uninjured skin. Low intensity scan. Scan 1 of 2.


title: Wound tissue day14 vs. day0 uninjured skin rep.4 (dye flip) low int. scan

description: Biological replicate 4 of 4. Wound tissue day 14 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day14 vs. day0 uninjured skin rep.1 high int. scan

description: Biological replicate 1 of 4. Wound tissue day 14 vs day 0 uninjured skin.High intensity scan.  Scan 2 of 2.


title: high treatment day28 replicate 1

source_name: Coral after 28 days of high treatment exposure replicate 1


title: high treatment day28 replicate 3

source_name: Coral after 28 days of high treatment exposure replicate 3


title: Wound tissue day14 vs. day0 uninjured skin rep.1 low int. scan

description: Biological replicate 1 of 4. Wound tissue day 14 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day7 vs. day0 uninjured skin rep.4 (dye flip) high int. scan

description: Biological replicate 4 of 4. Wound tissue day 7 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.

source_name: D7 wound tissue


title: high treatment day28 replicate 2

source_name: Coral after 28 days of high treatment exposure replicate 2


title: Wound tissue day7 vs. day0 uninjured skin rep.1 high int. scan

description: Biological replicate 1 of 4. Wound tissue day 7 vs day 0 uninjured skin.High intensity scan.  Scan 2 of 2.


title: Wound tissue day7 vs. day0 uninjured skin rep.3 high int. scan

description: Biological replicate 3 of 4. Wound tissue day 7 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.


title: Wound tissue day14 vs. day0 uninjured skin rep.3 low int. scan

description: Biological replicate 3 of 4. Wound tissue day 14 vs day 0 uninjured skin.Low intensity scan. Scan 1 of 2.


title: Wound tissue day14 vs. day0 uninjured skin rep.4 (dye flip) high int. scan

description: Biological replicate 4 of 4. Wound tissue day 14 vs day 0 uninjured skin.High intensity scan. Scan 2 of 2.


title: Wound tissue day7 vs. day0 uninjured skin rep.2 (dye flip) high int. scan

description: Biological replicate 2 of 4. Wound tissue day 7 vs day 0 uninjured skin. High intensity scan. Scan 2 of 2.


title: medium treatmentday28 replicate 2

source_name: Coral after 28 days of medium treatment exposure replicate 2


title: control treatment day28 replicate 2

source_name: Coral after 28 days of control treatment exposure replicate 2


title: control treatment day28 replicate 3

source_name: Coral after 28 days of control treatment exposure replicate 3


title: medium treatmentday28 replicate 1

source_name: Coral after 28 days of medium treatment exposure replicate 1


title: Wound tissue day7 vs. day0 uninjured skin rep.2 (dye flip) low int. scan

description: Biological replicate 2 of 4. Wound tissue day 7 vs day 0 uninjured skin. Low intensity scan. Scan 1 of 2.


title: Wound tissue day7 vs. day0 uninjured skin rep.1 low int. scan

description: Biological replicate 1 of 4. Wound tissue day 7 vs day 0 uninjured skin. Low intensity scan. Scan 1 of 2.


title: Wound tissue day3 vs. day0 uninjured skin rep.3 high int. scan

description: Biological replicate 3 of 4. Wound tissue day 3 vs day 0 uninjured skin. High intensity scan. Scan 2 of 2.

source_name: D3 wound tissue


title: Wound tissue day3 vs. day0 uninjured skin rep.4 (dye flip) low int. scan

description: Biological replicate 4 of 4. Wound tissue day 3 vs day 0 uninjured skin. Low intensity scan. Scan 1 of 2.