title: KLF5 study_Cre- mice_no radiation

city: Suzhou

first: Ming

address: No. 199 Ren'ai Road

institute: Soochow University

description:
con-cre-
This sample is of pooled intestine tissues from non-irradiated Cre- mice. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System. Hybridization was performed by Shanghai KangChen Bio-tech Inc., Shanghai, China, following NimbleGen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation). Scanning was performed by Shanghai KangChen Bio-tech Inc., Shanghai, China.

data_processing:
Images were quantified using Nimblescan V2.5. The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 2003;4(2):249), quantile normalization (Bolstad et al. Bioinformatics 2003;19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).
Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. All gene level files were imported into Agilent GeneSpring GX software (version 12.0) for further analysis. Genes that have values greater than or equal to lower cut-off: 50.0 (i.e. low intensity filtering) were chosen for differentially expressed gene screening.

source_name: non-radiated Cre- mice

label_protocol: ds-cDNA labeling with NimbleGen one-color DNA labeling kit. Labeling was performed by Shanghai KangChen Bio-tech Inc., Shanghai, China, following NimbleGen's standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted from small intestine tissues with Trizol reagent (Invitrogen, Carlsbad, CA, USA) and quantified using a NanoDrop ND-1000 (Thermo Scientific Inc., Waltham, MA, USA). RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Extraction was performed by Shanghai KangChen Bio-tech Inc., Shanghai, China

value: Cre-

value: none (non-irradiated control)

tag: tissue

value: small intestine


title: TCCSUP vs. KSHV-infected TCCSUP

status: Public on Mar 10 2015

type: RNA

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

country: South Korea

institute: Eulji University School of Medicine

description: TCCSUP vs. KSHV-infected TCCSUP

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

molecule: total RNA

organism: Homo sapiens

source_name: TCCSUP

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Cultured in DMEM with 10~20% FBS and 200ug/ml of hygromycin

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

treatment_protocol: KSHV BAC16 was infected and culture for 2 weeks with 200ug/ml of hygromycin

tag: cell line

value: TCCSUP

tag: cell type

value: bladder cancer

source_name: KSHV TCCSUP


title: Ventral midbrain lysates, 3wks, Control dopaminergic neurons 2

status: Public on Mar 11 2015

city: Durham

first: Pavle

last: Matak

state: North Carolina

address: 450 Research Drive, LSRC C-125

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University

description: SAMPLE 2

hyb_protocol: Targets were hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA).  Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0  Array in the Affymetrix Hybridization Oven.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on each dataset separately, 3 week old mice were RMA normalized together and then the 10 week old mice were normalized together. Multi-way ANOVA and fold change were performed to select target genes that were differentially expressed between Tfr1fl/+ CRE; Rpl22+/- and Tfr1fl/fl CRE; Rpl22+/- mice. Differentially expressed genes were selected with a p-value cut-off of 0.05 based on the ANOVA test and a fold change cut-off of 2.   Gene Set Enrichment Analysis [(GSEA/MSigDB v4.5) was performed on genes with >2-fold change.

label: Biotin

organism: Mus musculus

source_name: 3 wks_Control dopaminergic neurons

label_protocol: 50 ng of total RNA was amplified according to the NuGEN Ovation RNA Amplification System V2. Affymetrix GeneChip analysis was performed according to the manufacturer’s instructions,

growth_protocol: Tfr1ΔDN and CTR mice were maintained until 3 and 10 wks of age after which they were sacrificed

extract_protocol: Fresh ventral midbrains from mice were isolated and actively translated mRNAs from dopaminergic neurons immunoprecipitated accroding to prevoiously published protocol (Sanz et al, PNAS, 2009, Cell-type-specific isolation of ribosome-associated mRNA from complex tissues).

treatment_protocol: Tfr1ΔDN condiitonal knockout mice carry a deletion of Transferrin receptor 1 specifically in dopaminergic neurons. These mice and respective controls (heterozygotes for Tfr1 allele) were bred onto a Ribotag mouse background to enable subsequent mRNA extraction

tag: strain background

value: F2 mice of 129Sv and C57BL/6

tag: genotype/variation

value: CTR; control

tag: age

value: 3 wks

value: ventral midbrain

value: dopaminergic neurons


title: KLF5 study_Cre+ mice_no radiation

last: Li

country: China

description:
con-cre+
This sample is of pooled intestine tissues from non-irradiated Cre+ mice. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group.

source_name: non-radiated Cre+ mice

value: Cre+

tag: treated with


title: 01-254-N

type: genomic

city: Detroit

first: Maria

last: Worsham

state: MI

address: 1 Ford Place

department: Otolaryngology

institute: Henry Ford Health System

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio V2011.1
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Normal

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from breast cancer samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: Normal

tag: disease state


title: KLF5 study_Cre- mice_6h post 15 Gy TBI

description:
6h-cre-
This sample is of pooled intestine tissues from Cre- mice at 6 h post 15Gy TBI. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group.

source_name: Cre- mice 6h post 15 Gy TBI

value: 15 Gy total body irradiation (TBI)

tag: time point

value: 6h post 15Gy TBI


title: KLF5 study_Cre+ mice_6h post 15 Gy TBI

description:
6h-cre+
This sample is of pooled intestine tissues from Cre+ mice at 6 h post 15Gy TBI. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group.

source_name: Cre+ mice 6h post 15 Gy TBI


title: 1mic-30min-repeat 2

city: Beijing

first: Hua

last: Fu

address: 6#, Rongjing East Street

institute: Institute of pathogen biology

description: S. flexneri 2a strain 301 (Sf301) was used in our study , The germ was routinely grown at 37°C with shaking (200 rpm) on cation-adjusted MUELLER-HINTON broth (caMHB) containing 20 mg of calcium and 10 mg of magnesium per liter. Furazolidone obtained from Sigma Company was resolved in dimethyl sulfoxide (DMSO)  diluted with caMHB to final concentrations. Minimal inhibitory concentration of Furazolidone for Sf301 was determined by using the broth microdilution technique according to NCCLS guidelines

hyb_protocol: Prior to hybridization, the labeled cDNA was purified with QIAquick PCR purification kit (Qiagen), and then each pair of labeled cDNA: one is drug treated sample and the other is corresponding control sample, were mixed and dried by vacuum centrigugation.   1.  Mark positions of array grids using a diamond tipped pen. Bake slides for 2-4h at 80°C or UV crosslink twice using the autocrosslink program of a Stratalinker (Stratagene) Slides are then blocked using the method of Diehl et al in Nucleic Acids Research, 2001, Vol 29, No.7 e38 except slides were incubated in water at 95°C instead of boiling for 2 minutes, then rinsed in 95% ethanol for 1 minute and centrifuged dry at 1200 rpm for 5 minutes at room temp, preferably in an enclosed slide chamber (with bottom lined with blotting paper), otherwise ensure the centrifuge bowl and rotor are as dust free as possible. Place the slides in a 5-position plastic slide cassette or slide chamber until ready for use.    2. To 10 µl of dried down labelling reactions add 1.5 µl of 50 X Denhardts solution, 2.25 µl of 20 X SSC, 1.125 µl of E. coli tRNA (10 µg/µl) and 0.375 µl of 1M HEPES, pH7.0. Add 0.375 µl of 10% SDS to the mixture. The hyb components (except SDS) can be mixed together as a stock solution and added to labelling reactions.    3. Incubate 100 °C X 2 min. Let stand on the bench for 5 - 10 min. Do not place on ice or the SDS will precipitate.    4. Spin in a microfuge at full speed for 5 min, transfer to clean tube and repeat spin    5. Place array slide in the hyb chamber.    6. Pipette hyb. solution towards one edge of an array.    7. Place edge of a clean coverslip on the edge of the array.    8. Position fine nosed forceps under the coverslip.    9. Using the forceps slowly lower the coverslip down onto the hyb. solution and the array.   10. Apply 20 µl of 3 X SSC around the 4 corners of the slide using a pipette (approximately 5 µl per corner). This will maintain the correct humidity in the hybridisation chamber.   11. Place the chambers at the bottom of a water bath at 63°C overnight.   12. Place the slides directly into the heated wash solution, 2 X SSC, 0.1% SDS at 63°C and agitate to remove the cover slips (5 mins.). We use a thermocouple attached to a hot-plate stirrer for this step. Repeat.   13. Transfer slide rack to a solution of 1 X SSC at room temp. and agitate for 5 min. Repeat.   14. Wash in 0.2 X SSC for 5 min. Repeat.   15. Spin dry 1200 rpm for 5 min at room temp in an enclosed slide chamber (with blotting paper lining the bottom of the chamber).   16. Scan.

scan_protocol: The slides were scanned by using a GenePix 4000B scanner (Axon Instruments). The lasers of the scanner produce wavelengths of 532 nm for Cy3- and 635 nm for Cy5-labeled cDNA. Fluorescent spots and local background intensities were quantified using GenePix Pro 6.0 software (Axon).Signal intensities were corrected by subtracting the local background value.

data_processing: the data set were filtered so that spots designated as Not Found flagged features, as well as Bad and Empty features were excluded from further analysis. Moreover, spots either with signal-to-noise ratio below the detection limit of 3 or containing less than 55 percents of pixels which were two standard deviations above background in both channels were discarded from the dataset. After filtration, Lowess normalizations were performed with the fluorescent signal ratios (Cy5/Cy3) by using Tiger MIDAS V2.19 software (Tiger). VALUEs indicates the log2 ratio of cy5/Cy3 of  genes.

organism: Shigella flexneri

label_protocol: According to the manufacturer’s instructions, the cDNA was labeled with incorporation of fluorescent dyes (Amersham) except that a different dNTP mix was used (10× mix: 1.2 mM each dATP, dGTP, and dTTP;0.6 mM dCTP;10 mM Tris, pH 8.0;1 mM EDTA). Cy5-dCTP was used.

extract_protocol: Total RNA was extracted by using SV RNA Isolation System .Totle RNA was extracted according to the manufacturer’s instructions.

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 1× MIC. At 30 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.

label_protocol: According to the manufacturer’s instructions, the cDNA was labeled with incorporation of fluorescent dyes (Amersham) except that a different dNTP mix was used (10× mix: 1.2 mM each dATP, dGTP, and dTTP;0.6 mM dCTP;10 mM Tris, pH 8.0;1 mM EDTA). Cy3-dCTP was used.

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3),  DMSO without the antimicrobial was added to control cultures at a final concentration of 0.25% (vol/vol) .At 30 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.


title: 1mic-90min-repeat 2

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 1× MIC. At 90 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3),  DMSO without the antimicrobial was added to control cultures at a final concentration of 0.25% (vol/vol) .At 90 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.


title: 1mic-30min-repeat 3


title: 0.25mic-90min-repeat 3

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 0.25× MIC. At 90 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.


title: 1mic-30min-repeat 1


title: U937_vec cells, control, biological replicate 1

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

label: biotin

source_name: U937_vec cells, no treatment, 48 h

label_protocol: Affymetrix standard protocol

growth_protocol: RPMI1640, 10% FCS, 1% penicillin/streptomycin/glutamine

extract_protocol: RNeasy Plus Mini kit (Quiagen)

treatment_protocol: Logarithmically growing cells were treated or not with 400 nM etoposide for 48 h

tag: vector

value: empty vector

tag: treatment


title: 0.25mic-30min-repeat 3

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 0.25× MIC. At 30 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.


title: 1mic-90min-repeat 3


title: 0.25mic-30min-repeat 2


title: 0.25mic-90min-repeat 2


title: 1mic-90min-repeat 1


title: 0.5mic-30min-repeat 3

description: S. flexneri 2a strain 301 (Sf301) was used in our study , The germ was routinely grown at 37°C with shaking (200 rpm) on cation-adjusted MUELLER-HINTON broth (caMHB) containing 20 mg of calcium and 10 mg of magnesium per liter. Furazolidone obtained from Sigma Company was resolved in dimethyl sulfoxide (DMSO)  diluted with caMHB to final concentrations. Minimal inhibitory concentration of Furazolidone for Sf301 was determined by using the broth microdilution technique according to NCCLS guidelines.

data_processing: The data set were filtered so that spots designated as Not Found flagged features, as well as Bad and Empty features were excluded from further analysis. Moreover, spots either with signal-to-noise ratio below the detection limit of 3 or containing less than 55 percents of pixels which were two standard deviations above background in both channels were discarded from the dataset. After filtration, Lowess normalizations were performed with the fluorescent signal ratios (Cy5/Cy3) by using Tiger MIDAS V2.19 software (Tiger). VALUEs indicates the log2 ratio of cy5/Cy3 of  genes.

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 0.5× MIC. At 30 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation

extract_protocol: Total RNA was extracted by using SV RNA Isolation System.Totle RNA was extracted according to the manufacturer’s instructions.

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3),  DMSO without the antimicrobial was added to control cultures at a final concentration of 0.25% (vol/vol) .At 30 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation


title: 0.25mic-90min-repeat 1


title: 0.25mic-30min-repeat 1


title: 0.5mic-90min-repeat 3

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 0.5× MIC. At 90 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3),  DMSO without the antimicrobial was added to control cultures at a final concentration of 0.25% (vol/vol) .At 90 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation


title: 0.5mic-90min-repeat 2


title: 0.5mic-30min-repeat 1

tag: Overnight cultures were diluted in freshly prepared cation-adjusted MHB to optical density at 600 nm (OD600) of about 0.05.Then the diluted cultures were allowed to continue growing at 37°C with shaking (200 rpm).When they were grown to early exponential growth phase (an OD600 of about 0.3), furazolidone was added from the 400×stock dissolved in DMSO into the cultures to give final concentrations of 0.5× MIC. At 30 min after treatment, samples were collected and washed twice with PBS for subsequent RNA isolation.


title: 0.5mic-30min-repeat 2

tag: Channel 1 characteristics


title: Sa_8h_D1 (sample 7)

city: Jena

first: Andreas

last: Dix

address: Beutenbergstraße 11a

country: Germany

institute: Hans-Knöll-Institut

description:
SAMPLE 7
donor 1, Staphylococcus aureus-infected blood, 8h post infection

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was read in, background corrected, and log2-transformed using the “lumi” package in R

source_name: Whole blood

label_protocol: A total of 500 ng isolated RNA was immediately further processed to synthesize biotin-labeled complementary RNA (cRNA) using the Illumina® TotalPrep™ RNA Amplification Kit (Ambion). All procedures were carried out as proposed in the manufacturer’s protocol. Concentration as well as quality of cRNA were verified via the NanoDrop™ 1000 Spectrophotometer system (Thermo Scientific).

extract_protocol: Blood was collected and stored in PAXgene Blood RNA Tubes (PreAnalytiX) to stabilize intracellular RNA until further use. RNA isolation was performed using the PAXgene Blood RNA Kit (PreAnalytiX) corresponding to the manufacturer’s instruction. High quality of isolated RNA was proven by RNA integrity numbers (RIN) ranging from 8.2 to 9.5.

tag: individual

value: donor 1

tag: infection

value: Staphylococcus aureus

tag: time

value: 8h post infection

tag: gender

value: male

tag: tissue

value: blood


title: Lamin chromatin profile_2

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

description: Wash DamID chromatin profiling

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and resuspended in 12.3 ml H2O. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction to generate the pair files for each channel. 635 vs 532 ratios were LOESS normalized.All data processing and analysis was performed using the R package for statistical computing (http://www.r-project.org). Data was LOESS normalized and a custom R script was implemented to define overlapping domains, using a minimum 80% overlap threshold, where at least one domain had to have at least 80% overlap with the other. We used parameter optimization functions within CGTools to determine the transition threshold and proportion of positive probe thresholds. In short, sharp transitions in the DamID signal were identified using a sliding edge filter (window size 199 probes), and adjacent transitions exceeding a threshold (here 0.3) were combined into domains if at least 70% of the enclosed probes had a positive log2 ratio.
Processed data files include: Triplicate average in Log 2 scale (text file) and Chromatin profile domains (wig file).

organism: Drosophila melanogaster

label_protocol: 1 mg of DpnI-digested DNA was label with Cy3 or Cy5-labeled random primers using Klenow for 2 h at 37C.

growth_protocol: In CCM3 media at 25C for 48h post-transfection

extract_protocol: Genomic DNA was recoveredby standard methods and digested with DpnI overnight at 37C. A 5-30% sucrose gradient was used to recover a DNA fragments range between 0.3-2.5Kb.

treatment_protocol: DNA electroporation of WT Kc167 cells

tag: cell line

source_name: Dam only


title: H3K9me2_B

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL.files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. Two sample comparisons of immunoprecipitated (strain 1) vs. immunoprecipitated (strain 2), quantile normalization (separate) and linear scaling to 100 was applied. Probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2004) and reported in BAR files.
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for relative enrichment (spt16-myc vs WT or H3K4me2 vs. input) for each probe.

organism: Schizosaccharomyces pombe

source_name: ChIP DNA, WT

label_protocol: A specific sequence tag was attached to immunoprecipitated DNA fragments by PCR using sequenase and random primers (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'). This DNA was amplified using Taq polymerase and a primer recognizing the specific sequence tag (5'-GTTTCCCAGTCACGATC-3') in the precence of 5 mM dUTP. PCR products were purified using Qiaquick PCR purification kit. DNA was fragmented by UDG and APE nuclease treatment and labelled with biotin by Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols. Immunoprecipitation Assay Protocol

growth_protocol: Liquid cultures were grown in YES media shaking at 180 rpm at 30 °C.

extract_protocol: Immunoprecipitation was done using indicated antibody from chromatin extracts prepared from mid-logarithmic phase cells. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine, and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 600 bp were collected. Chromatin was immunoprecipitated with indicated antibody for 2 hours and incubated with protein A agarose beads for 1 hour. The beads were washed, chromatin eluted at with TES at 65C and crosslinks reversed at 65C over night, together with input samples. Proteins were digested with proteinase K and immunoprecipitated DNA recovered using QIAquick PCR Purification kit.

tag: strain

tag: genotype

value: WT

tag: chip antibody

value: ab7766 anti-h3k4me3 (abcam)

tag: sample type

value: ChIP DNA


title: H3K4me2_A

value: ab7766 anti-h3k4me2 (abcam)

tag: treatment


title: spt16-myc_A

source_name: ChIP DNA, spt16-myc

value: 9E10 mouse anti-Myc (abcam)


title: Lamin chromatin profile_1

description: Wash DamID chromatin profiling


title: untagged_myc


title: spt16-myc_B


title: Wash chromatin profile_2

description: Wash DamID chromatin profiling


title: Wash chromatin profile_1

description: Wash DamID chromatin profiling


title: 0.5mic-90min-repeat 1


title: Lamin chromatin profile_3

description: Wash DamID chromatin profiling


title: WIGMOR-NonInfected-20d-sample4

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

country: France

institute: UMR 177 IRD-CIRAD

description: Total RNA, 20 days, uninfected sample, sample 4

hyb_protocol: 800 ng of Cy3-labelled cRNA (specific activity > 15 pmol Cy3/ug cRNA) hybridized to Agilent Wigglesworthia_v1 custom Oligo Microarrays (earray Design ID = 050087; earray Slide Layout =  IS-15744-8-V1) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Feature Extraction 11.0.1 (Agilent technologies) using protocol GE1_1100_Jul11 and Grid 050087_D_F_20130611 to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization and by median of all samples for each probe.

organism: Wigglesworthia glossinidia endosymbiont of Glossina morsitans

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared using the Low Input Quick Amp WT Labeling Kit (One color) according to the manufacturer's instructions

extract_protocol: not provided

tag: status

value: Uninfected

tag: timepoint

value: 20 days

value: Uninfected at 20 days


title: Wash chromatin profile_3

description: Wash DamID chromatin profiling


title: WIGMOR-NonInfected-20d-sample2

description: Total RNA, 20 days, uninfected sample, sample 2


title: WIGMOR-NonInfected-20d-sample3

description: Total RNA, 20 days, uninfected sample, sample 3


title: WIGMOR-NonInfected-20d-sample1

description: Total RNA, 20 days, uninfected sample, sample 1


title: WIGMOR-NonInfected-10d-sample2

description: Total RNA, 10 days, uninfected sample, sample 2

value: 10 days

value: Uninfected at 10 days


title: WIGMOR-NonInfected-10d-sample3

description: Total RNA, 10 days, uninfected sample, sample 3


title: Cancer and normal tissue from patient 3

city: Nanjing

first: Mantang

last: Qiu

state: Jiangsu

address: 42 Baiziting

department: Thoracic Surgery

institute: Cancer Institute of Jiangsu Province

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: After a filtering procedure, 8900 human lncRNAs (annotated by GENCODE(V13) data base, lincRNAs from Cabili et al, and the UCSC data base) were selected for the following analysis. We first did quantile normalization for the microarray data (containing the 8900 lncRNAs and all mRNAs in the microarray) of 5 paired tumor-normal samples. Then, the data was log2-scale transformed. Missing values were imputed using the random forest unsupervised classification algorithm.

source_name: Cancer tissue

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: subject status

value: lung adenocarcinoma (LUAD) patient

tag: subject id

value: patient 3

value: female

tag: age

tag: smoking

value: never-smoker

tag: tissue type

value: Cancer tissue

tag: tumor stage

value: Ia

source_name: Adjacent normal tissue

tag: age (yrs)

value: Adjacent normal tissue


title: WIGMOR-NonInfected-10d-sample1

description: Total RNA, 10 days, uninfected sample, sample 1


title: WIGMOR-NonInfected-3d-sample4

description: Total RNA, 3 days, uninfected sample, sample 4

value: 3 days

value: Uninfected at 3 days


title: WIGMOR-NonInfected-3d-sample2

description: Total RNA, 3 days, uninfected sample, sample 2


title: Cancer and normal tissue from patient 5

value: patient 5

tag: gender

value: IIIa


title: Cancer and normal tissue from patient 4

value: patient 4


title: WIGMOR-NonInfected-10d-sample4

description: Total RNA, 10 days, uninfected sample, sample 4

value: Uninfected


title: Cancer and normal tissue from patient 2

value: patient 2


title: WIGMOR-NonInfected-3d-sample1

description: Total RNA, 3 days, uninfected sample, sample 1


title: Cancer and normal tissue from patient 1

value: patient 1


title: WIGMOR-Infected-20d-sample4

description: Total RNA, 20 days, infected sample, sample 4

value: Infected

value: 20 days

value: Infected at 20 days


title: WIGMOR-Infected-20d-sample3

description: Total RNA, 20 days, infected sample, sample 3


title: WIGMOR-Infected-20d-sample2

description: Total RNA, 20 days, infected sample, sample 2


title: WIGMOR-Infected-10d-sample4

description: Total RNA, 10 days, infected sample, sample 4

value: 10 days

value: Infected at 10 days


title: U937_vec cells, control, biological replicate 2

tag: vector

value: empty vector


title: WIGMOR-Infected-10d-sample3

description: Total RNA, 10 days, infected sample, sample 3


title: WIGMOR-Infected-10d-sample2

description: Total RNA, 10 days, infected sample, sample 2


title: Sample_108: Subject 6

type: protein

city: Irvine

first: Johannes

middle: S.

last: Gach

state: CA

address: 843 Health Sciences Rd

department: Medicine

institute: University of California Irvine

description: Total IgG

hyb_protocol: For array probing, HIV-1 specific mAbs and plasma samples of HIV-1 infected subjects were diluted in Protein Array Blocking Buffer (Whatman, GE Healthcare), supplemented with 10% (vol/vol) DH5α E. coli lysate and incubated on arrays over-night (o/n) at 4°C with constant agitation. Antibody concentrations for the probing ranged from 10 μg/mL to 0.003 μg/mL using serial half-log dilution steps. Plasma samples were probed at a dilution of 1:100.  Following o/n incubation, slides were washed five times in washing buffer (10 mM Tris (pH 8.0), 150 mM NaCl), containing 0.05% Tween 20, and bound human antibodies were detected by biotin SP-conjugated affini-pure goat anti-human IgG Fc fragment specific secondary antibody (Jackson ImmunoResearch, West Grove, PA), diluted 1/200 in blocking buffer. After 1 h at room temperature (RT), slides were washed three times, and bound antibodies were detected with streptavidin-conjugated SureLight® P-3 tertiary reagent (Columbia Biosciences, Columbia, MD), diluted 1/200 in blocking buffer, for 1 h at RT. Slides were then washed 5 times, air dried under brief centrifugation, and stored at 18°C in a desiccator. The arrays were examined with a Perkin Elmer ScanArray Express HT confocal laser scanner at a wavelength of 670 nm and signal intensities were quantified using ProScanArray Express software (Perkin Elmer, Waltham, MA)

scan_protocol: Probed array slides were scanned with a GenePix 4200AL (Molecular Devices, LLC, Sunnyvale, CA) at a wavelength of 635 nm, at 36% laser power and 360 PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to HIV-1 envelope proteins and peptides on the microarray the following steps were taken: (i) the mean background signal of antibody binding to 24 control spots of in vitro transcription/translation reaction without DNA template (noDNA spots) were removed from each sera’s raw values of antibody binding measured as the mean pixel intensity of spots of printed protein.

molecule: protein

source_name: serum

tag: specificity

value: HIV-1 specific

tag: epitope

tag: concentration (ug/ml)

value: 1/100 dilution

value: ART treated

tag: hiv status

value: positive


title: Sample_109: Subject 7

description: Total IgG


title: Sample_106: Subject 4

description: Total IgG


title: Sample_110: Subject 8

description: Total IgG


title: WIGMOR-Stimulated-3d-sample4

description: Total RNA, 3 days, Stimulated sample, sample 4

value: Stimulated

value: 3 days

value: Stimulated at 3 days


title: Sample_104: Subject 2

description: Total IgG


title: WIGMOR-Stimulated-3d-sample3

description: Total RNA, 3 days, Stimulated sample, sample 3


title: WIGMOR-NonInfected-3d-sample3

description: Total RNA, 3 days, uninfected sample, sample 3

value: Uninfected at 3 days


title: WIGMOR-Infected-10d-sample1

description: Total RNA, 10 days, infected sample, sample 1


title: WIGMOR-Stimulated-3d-sample2

description: Total RNA, 3 days, Stimulated sample, sample 2


title: WIGMOR-Stimulated-3d-sample1

description: Total RNA, 3 days, Stimulated sample, sample 1


title: Sample_107: Subject 5

description: Total IgG


title: Sample_103: Subject 1

description: Total IgG


title: Sample_102: F105

description: IgG

source_name: monoclonal antibody

value: Exposed


title: Sample_101: F105

description: IgG


title: WIGMOR-Infected-20d-sample1

description: Total RNA, 20 days, infected sample, sample 1


title: Sample_98: F105

description: IgG


title: Sample_99: F105

description: IgG


title: Sample_100: F105

description: IgG


title: Sample_97: F105

description: IgG


title: Sample_95: 4E10_

description: IgG


title: Sample_96: 4E10_

description: IgG


title: Sample_94: 4E10_

description: IgG


title: Sample_90: 4E10_

description: IgG


title: Sample_91: 4E10_

description: IgG


title: Sample_93: 4E10_

description: IgG


title: Sample_89: 4E10_

description: IgG


title: Sample_88: 2F5

description: IgG


title: Sample_87: 2F5

description: IgG


title: Sample_105: Subject 3

description: Total IgG


title: Sample_92: 4E10_

description: IgG


title: Sample_86: 2F5

description: IgG


title: Sample_85: 2F5

description: IgG


title: DnRARa_Th1_biological rep1

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K (AMADID 028005) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1) was used to read out and process the microarray image files.

source_name: primary CD4+ T cells from spleen, polarised under Th1 conditions for 6 d

label_protocol: 40 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Control and dnRara expressing naïve CD4+CD25negCD44loCD62Lhi T cells were isolated by flow cytometry. Cells were cultured with T-cell depleted irradiated splenocytes with anti CD3 (5ug/ml), IL-2 (100U/ml), IL-12  (10ng/ml) and anti IL-4 (10ug/ml) for 3 days followed by IL-2 (50U/ml) for 3 days.

extract_protocol: RNA was extracted using Trizol following manufacturer's instructions

treatment_protocol: Dead cells were removed using a dead cell removal kit (Miltenyi Biotec)

tag: strain

tag: genotype/variation

value: dnRara


title: DnRARa_Th1_biological rep2


title: WT_Th1_biological rep3

value: Wild Type


title: WT_Th1_biological rep2


title: WT_Th1_biological rep1


title: Sample_83: 2F5

description: IgG


title: DnRARa_Th1_biological rep3


title: Sample_82: 2F5

description: IgG


title: Sample_84: 2F5

description: IgG


title: Sample_81: 2F5

description: IgG


title: Sample_80: 240-D

description: IgG


title: LM8_91_3

city: Zurich

first: Ram Mohan

last: Ram Kumar

address: Forchstrasse 340

department: Orthopaedics

country: Switzerland

institute: University Hospital Balgrist, University of Zurich, Zurich, Switzerland

description: Mouse osteosarcoma cell line

hyb_protocol: Mouse GE 4x44K v2  Microarrays were incubated for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then  immediately air dried prior scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent  DNA  Microarray C reader  using using a scan Control software version A.8.4.1 and one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Osteosarcoma commercial human cell lines

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the low input quick amplification labeling kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Dunn, LM8  cells were cultured at same conditions and at 75% confulence the RNAs were isolated

extract_protocol: Total RNA was isolated using Rneasy MiniKit from Qiagen ( Valencia, CA, USA) following manufacturers instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Dunn, LM8 cells were cultured in in Dulbecco’s Modified Eagle Medium (DMEM containing 4.5 g/l glucose)/Ham F12 (Invitrogen, Carlsbad, CA, USA) (1:1) supplemented with 10% fetal calf serum (FCS), 1 unit/ml penicillin G, and 1 μg/ml streptomycin. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2

tag: cell line

tag: properties

value: Osteoblastic

tag: replicates

value: Passage number 91


title: Sample_78: 240-D

description: IgG


title: LM8_91_2

description: Mouse osteosarcoma cell line


title: Dunn_86_2

description: Mouse osteosarcoma cell line

value: Dunn

value: Passage number 86


title: Dunn_25_2

description: Mouse osteosarcoma cell line

value: Passage number 25


title: LM8_24_2

description: Mouse osteosarcoma cell line

value: Passage number 24


title: Dunn_25_3

description: Mouse osteosarcoma cell line


title: Dunn_86_3

description: Mouse osteosarcoma cell line


title: Sample_77: 240-D

description: IgG

value: HIV-1 specific


title: LM8_91_1

description: Mouse osteosarcoma cell line


title: Sample_75: 240-D

description: IgG


title: Sample_76: 240-D

description: IgG


title: LM8_24_1

description: Mouse osteosarcoma cell line


title: Sample_74: 240-D

description: IgG


title: mocki chromatin profile_1

description: Wash RNAi chromatin Accessibility profiling

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction to generate the pair files for each channel. To standardize for dynamic range differences, each Tukey-biweight normalized data set was transformed to a normalized z-score scale by converting the individual probe log2(IP/fully methylated DNA IP) values to standard deviates; z = (x - m)/s, where x = the log2 ratio of the probe, m = the mean of the data set, and s = the standard deviation of the data set.All data processing and analysis was performed using the R package for statistical computing (http://www.r-project.org).
Ratios are shown in Log 2 scale (GFF). Chromatin accessibility averages are given as the mean of the z-scores of the biological replicates (BigWig).

source_name: MssI-treated nuclei_Mock RNAi cells

label_protocol: 3 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers ( DNA isolated from RNAi-treated nuclei) or with Cy3 nonamers (in vitro M.SssI fully methylated DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: In Schneider media at 25C for 7 days

extract_protocol: After treating the nuclei with the methylase M.SssI, high molecular weight genomic DNA was isolated by standard methods and fragmented using a Bioruptor (Diagenode) to obtain an average fragment size of 500 bp. Methylated DNA immunoprecipitation (MeDIP) was performed by incubating 2 μg of fragmented DNA was denatured and immunoprecipitated with 2 μg of anti-5-methylcytosine (clone 33A3; Cat. No. 39649; Active Motif) for 2 hr at 4°C.  Goat anti-mouse IgG-linked magnetic beads (Invitrogen) were used to recover the DNA/antibody complex and eluted in 0.1 mM Na2HCO3, 0.1% SDS and 2 μg of Proteinase K at 55°C overnight. Immunoprecipitated DNA was recovered with mini-elute PCR columns (Qiagen). DNA was amplified with WGA2 according to manufacturer’s instructions (Sigma-Aldrich). Fully methylated DNA was obtained by recovering genomic DNA, sonicated to an average fragment size of 500 bp, treated twice with M.SssI in vitro and, for each biological replicate, an independent MeDIP with fully methylated DNA was performed as a control.

treatment_protocol: dsRNAi added twice for 7 days

tag: antibody

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog number

value: clone 33A3; Cat. No. 39649

source_name: MssI-treated genomic S2R+ DNA

growth_protocol: In Schneider media at 25C

treatment_protocol: M.SssI-fully methylated genomic DNA


title: Sample_79: 240-D

description: IgG


title: Dunn_25_1

description: Mouse osteosarcoma cell line


title: Lamini chromatin profile_2

source_name: MssI-treated nuclei_Lam RNAi cells


title: nps1-13_YPEG_4hr_rep2

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

country: Japan

institute: National Research Institute of Brewing

description: Gene expression data from nps1-13 mutant in YPEG medium.

hyb_protocol: 5 ug of cRNA were hybridized for 4 hr at 45℃ on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in GeneChip 3' IVT Express Kit Assay (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with Operating Software(GCOS) v1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Saccharomyces cerevisiae

source_name: nps1-13 for 4hr in YPEG medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: WT (BY4743) and nps1-13 strains were grown at 28℃ in YPD medium.

extract_protocol: Total RNA were purified by using RNeasy MiniKit (Qiagen) following manufacture's instruction.

treatment_protocol: WT (BY4743) and nps1-13 cells pregrown in YPD medium were inoculated in YPEG medium for 4hr.


title: Sample_73: 240-D

description: IgG


title: nps1-13_YPEG_4hr_rep1


title: Sample_72: 5F3

description: IgG


title: Dunn_86_1

description: Mouse osteosarcoma cell line


title: Sample_70: 5F3

description: IgG


title: Sample_69: 5F3

description: IgG


title: WT_YPEG_4hr_rep2

description: Gene expression data from BY4743 in YPEG medium.

source_name: BY4743 for 4hr in YPEG medium


title: WT_YPEG_4hr_rep1


title: Sample_68: 5F3

description: IgG


title: Washi chromatin profile_2

source_name: MssI-treated nuclei_Wash RNAi cells


title: Sample_71: 5F3

description: IgG


title: HeLa control for 48h, biological rep2

city: Heidelberg

first: Martin

last: Beck

state: Baden-Wurttemberg

address: Meyerhofstraße 1

department: Structural and Computational Biology

institute: European Molecular Biology Laboratory

description:
Sample name: Control_Rep2_48h
Gene expression data Untreated HeLa cells, control 48h

hyb_protocol: Following fragmentation and labeling (WT Terminal Labeling and Controls Kit, Affymetrix, # 901524), cDNA was hybridized for 16 hr at 45°C on GeneChip Human Gene 2.0 ST Array

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: All microarray samples were pre-processed with Affymetrix Power Tools (APT) and Robust Microarray Analysis (RMA) normalization procedure was applied to generate log2-transformed expression values for ‘meta’ probe sets. Detected above background (DABG) method was used to identify probe sets with signals higher than the background distribution. The ‘meta’ probe sets were retained using a simple criterion of whether more than half of the associated probes were detected (DABG, P value <0.05) in more than half of the replicates in any of the experimental conditions. Differentially expressed genes were identified for the comparisons of TSA and NaB treatments with the corresponding controls in 12 and 48 hours using the Limma package available from R, Bioconductor.

source_name: Untreated HeLa cells

label_protocol: Biotinylated cDNA was synthesized from 500ng of total RNA using the Ambion WT Expression Kit (#4491974) according to manufacturer’s instructions.

growth_protocol: HeLa cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) – low glucose 1g/l (Sigma-Aldrich) supplemented with 10% heat inactivated fetal bovine serum (FBS), Penicillin Streptomycin (PS) and 2mM L-Glutamine.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Cells were allowed to attach to the culture dish for 24h, then the drug, TSA or sodium butyrate was added and cells were treated for 12 or 48 hours.

value: cervical cancer (HeLa) cells

tag: treatment

value: control

tag: time


title: Sample_67: 5F3

description: IgG


title: Lamini chromatin profile_1


title: Lamini chromatin profile_3


title: Sample_66: 5F3

description: IgG


title: HeLa treated with sodium butyrate for 48h, biological rep3

description:
Sample name: NaB_Rep3_48h
Gene expression data HeLa cells treated with sodium butyrate for 48h

value: sodium butyrate


title: HeLa control for 48h, biological rep3

description:
Sample name: Control_Rep3_48h
Gene expression data Untreated HeLa cells, control 48h


title: HeLa control for 48h, biological rep1

description:
Sample name: Control_Rep1_48h
Gene expression data Untreated HeLa cells, control 48h


title: Sample_63: 2G12

description: IgG


title: HeLa treated with sodium butyrate for 48h, biological rep2

description:
Sample name: NaB_Rep2_48h
Gene expression data HeLa cells treated with sodium butyrate for 48h


title: Sample_64: 2G12

description: IgG


title: mocki chromatin profile_3


title: Sample_61: 2G12

description: IgG


title: Washi chromatin profile_3


title: Sample_60: 2G12

description: IgG


title: Washi chromatin profile_1


title: Sample_59: 2G12

description: IgG


title: mocki chromatin profile_2


title: Sample_65: 5F3

description: IgG


title: HeLa treated with sodium butyrate for 48h, biological rep1

description:
Sample name: NaB_Rep1_48h
Gene expression data HeLa cells treated with sodium butyrate for 48h


title: Sample_58: 2G12

description: IgG


title: Leaf_6:00_28DPS_Nipponbare Cy3

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

hyb_protocol: 825ng of labelled cRNA were hybridized using Gene Expression Hybridization Kit following manufacturer's instructions at NIAS RGRC Open Laboratory.

scan_protocol: Scanned with Agilent G2505C.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

organism: Oryza sativa

source_name: rice, leaf

label_protocol: 200 ng of total RNA were reverse-transcribed and labelled using Low Input Quick Amp Labeling Kit following manufacturer's instructions. Labelled cRNA were purified with Qiagen RNeasy mini kit.

growth_protocol: Light / Dark conditions: 8:00-22:30, 450 μmol m-2 s-1 photosynthetic photon flux density (PPFD), 28 oC ambient temperature / 22:30-8:00, 0 μmol m-2 s-1, 24 oC.

extract_protocol: Total RNA was extracted using Promega Maxwell 16 Instrument following manufacturer's instructions.

treatment_protocol: The youngest fully expanded leaf from 3 plants were sampled and immediately frozen using liquid N.

tag: variety

value: Nipponbare

tag: developmental stage(days past sown)

tag: sampling time (h)


title: HeLa treated with trichostatin A for 48h, biological rep3

description:
Sample name: TSA_Rep3_48h
Gene expression data HeLa cells treated with trichostatin A for 48h

value: trichostatin A


title: Leaf_14:00_28DPS_Kasalath Cy5

value: Kasalath


title: Leaf_10:00_Koshihikari_49DPS 2 Cy5

description: Leaf_10:00_Koshihikari_49DPS 2

value: Koshihikari


title: HeLa treated with trichostatin A for 48h, biological rep2

description:
Sample name: TSA_Rep2_48h
Gene expression data HeLa cells treated with trichostatin A for 48h


title: Leaf_22:00_28DPS_Kasalath Cy5


title: Leaf_14:00_28DPS_Nipponbare Cy3


title: Leaf_10:00_Koshihikari_28DPS 2 Cy3

description: Leaf_10:00_Koshihikari_28DPS 2


title: Leaf_8:00_Koshihikari_28DPS Cy5


title: HeLa treated with trichostatin A for 48h, biological rep1

description:
Sample name: TSA_Rep1_48h
Gene expression data HeLa cells treated with trichostatin A for 48h


title: HeLa control for 12h, biological rep3

description:
Sample name: Control_Rep3_12h
Gene expression data Untreated HeLa cells, control 12h


title: Sample_57: 2G12

description: IgG

tag: specificity


title: HeLa control for 12h, biological rep2

description:
Sample name: Control_Rep2_12h
Gene expression data Untreated HeLa cells, control 12h


title: Leaf_8:00_Koshihikari_49DPS Cy3


title: HeLa treated with sodium butyrate for 12h, biological rep3

description:
Sample name: NaB_Rep3_12h
Gene expression data HeLa cells treated with sodium butyrate for 12h


title: HeLa control for 12h, biological rep1

description:
Sample name: Control_Rep1_12h
Gene expression data Untreated HeLa cells, control 12h


title: Sample_56: VRC03

description: IgG

tag: epitope


title: Sample_55: VRC03

description: IgG

tag: concentration (ug/ml)


title: Leaf_6:00_Koshihikari_49DPS Cy5


title: HeLa treated with sodium butyrate for 12h, biological rep2

description:
Sample name: NaB_Rep2_12h
Gene expression data HeLa cells treated with sodium butyrate for 12h


title: LM8_24_3

description: Mouse osteosarcoma cell line


title: Leaf_2:00_Koshihikari_49DPS Cy5


title: Sample_53: VRC03

description: IgG


title: Sample_52: VRC03

description: IgG


title: Leaf_4:00_Koshihikari_49DPS Cy3


title: HeLa treated with sodium butyrate for 12h, biological rep1

description:
Sample name: NaB_Rep1_12h
Gene expression data HeLa cells treated with sodium butyrate for 12h


title: Leaf_6:00_Koshihikari_28DPS Cy3


title: Leaf_4:00_Koshihikari_28DPS Cy5


title: Leaf_20:00_Koshihikari_49DPS Cy3


title: Leaf_0:00_Koshihikari_49DPS Cy3


title: Leaf_20:00_Koshihikari_28DPS Cy5


title: Leaf_0:00_Koshihikari_28DPS Cy5


title: Leaf_22:00_Koshihikari_28DPS Cy3


title: Sample_54: VRC03

description: IgG


title: Leaf_22:00_Koshihikari_49DPS Cy5


title: Leaf_2:00_Koshihikari_28DPS Cy3


title: Leaf_18:00_Koshihikari_49DPS Cy5


title: HeLa treated with trichostatin A for 12h, biological rep1

description:
Sample name: TSA_Rep1_12h
Gene expression data HeLa cells treated with trichostatin A for 12h


title: CTL_YFP_IFNG_unstimulated

description: Gene expression data from YFP+ (IFNg+) cells on d7 of culture

hyb_protocol: Hybridisation cocktails were prepared using 5.5ug cDNA as described in the Eukaryotic Array manual from Affymetrix, using the Hybridisation, Wash and Stain (HWS) kit (Affymetrix)

scan_protocol: Arrays were scanned using the GCS3000 7G scanner (affymetrix) following manufacturer's protocols.

data_processing: CEL files were imported into Partek Genomics Suite and processed using the RMA algorithm

source_name: primary CD4+ T cells from spleen

label_protocol: 500ng total RNA was labelled using the Ambion WT kit and WT Terminal Labelling kit from Affymetrix to make cDNA

growth_protocol: Control and dnRara expressing naïve CD4+CD25negCD44loCD62Lhi T cells were isolated by flow cytometry. Cells were cultured with T-cell depleted irradiated splenocytes with anti CD3 (5ug/ml), IL-2 (100U/ml), IL-12  (10ng/ml) and anti IL-4 (10ug/ml) for 3 days followed by IL-2 (50U/ml) for 4 days.

extract_protocol: Total RNA was extracted from FACS sorted cells using TRIzol LS, following manufacturers instructions.

treatment_protocol: Cells were harvested directly from culture without prior restimulation

value: Wild Type


title: HeLa treated with trichostatin A for 12h, biological rep2

description:
Sample name: TSA_Rep2_12h
Gene expression data HeLa cells treated with trichostatin A for 12h


title: Leaf_18:00_Koshihikari_28DPS Cy3


title: Sample_51: VRC03

description: IgG


title: DNRAR_YFP_IFNG_unstimulated

value: dnRara


title: Leaf_16:00_Koshihikari_28DPS Cy5


title: Sample_50: VRC03

description: IgG


title: Sample_49: VRC03

description: IgG


title: Leaf_6:00_28DPS_Kasalath Cy5


title: Sample_48: VRC01

description: IgG


title: Leaf_16:00_Koshihikari_49DPS Cy3


title: CTL_YFP_IFNG_biological rep3

treatment_protocol: Cells were restimulated with 100 ng/ml phorbol 12-myristate 13-acetate (PMA) and 500 ng/ml ionomycin for 4 h prior to FACS sorting for isolation of YFP+ (IFN-g+) CD4+ T-cells


title: Sample_47: VRC01

description: IgG


title: Leaf_14:00_Koshihikari_49DPS Cy5


title: Sample_46: VRC01

description: IgG


title: Leaf_12:00_Koshihikari_49DPS Cy3


title: Sample_45: VRC01

description: IgG


title: CTL_YFP_IFNG_biological rep1


title: Leaf_14:00_Koshihikari_28DPS Cy3


title: Leaf_10:00_Koshihikari_49DPS Cy5


title: Sample_44: VRC01

description: IgG


title: CTL_YFP_IFNG_biological rep2


title: Leaf_10:00_Koshihikari_28DPS Cy3


title: Leaf_22:00_28DPS_Nipponbare Cy3


title: DNRAR_YFP_IFNG_biological rep3


title: DNRAR_YFP_IFNG_biological rep1


title: Sample_43: VRC01

description: IgG


title: Sample_42: VRC01

description: IgG


title: SAOS_35_3

description:
human osteosarcoma cell line
SAMPLE 21

hyb_protocol: Human SurePrint G3 8x60K microarrays were incubated for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then  immediately air dried prior scanning.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the low input quick amplification labeling kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 143B, HOS, LM5 and SaOS-2 cells were cultured at same conditions and at 75% confulence the RNAs were isolated

treatment_protocol: 143B, HOS, LM5 and SaOS-2 cells were cultured in in Dulbecco’s Modified Eagle Medium (DMEM containing 4.5 g/l glucose)/Ham F12 (Invitrogen, Carlsbad, CA, USA) (1:1) supplemented with 10% fetal calf serum (FCS), 1 unit/ml penicillin G, and 1 μg/ml streptomycin. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2

value: Osteoblastic

tag: passage number

value: Passage number 35


title: SAOS_73_2_17

description:
human osteosarcoma cell line
SAMPLE 23

value: Passage number 73


title: DNRAR_YFP_IFNG_biological rep2

tag: strain


title: SAOS_73_1

description:
human osteosarcoma cell line
SAMPLE 22


title: SAOS_73_3

description:
human osteosarcoma cell line
SAMPLE 24


title: Sample_41: VRC01

description: IgG


title: SAOS_35_2_14

description:
human osteosarcoma cell line
SAMPLE 20


title: Sample_39: b12

description: IgG


title: Sample_38: b12

description: IgG


title: Sample_37: b12

description: IgG


title: LM5_40_3

description:
human osteosarcoma cell line
SAMPLE 18

value: Passage number 40


title: SAOS_35_1

description:
human osteosarcoma cell line
SAMPLE 19


title: Sample_36: b12

description: IgG


title: Sample_40: b12

description: IgG


title: LM5_40_1

description:
human osteosarcoma cell line
SAMPLE 16


title: Sample_62: 2G12

description: IgG


title: LM5_04_3

description:
human osteosarcoma cell line
SAMPLE 15

value: Passage number 04


title: Sample_33: b12

description: IgG

value: HIV-1 specific


title: Sample_32: F425 B4e8

description: IgG


title: Sample_29: F425 B4e8

description: IgG


title: Sample_30: F425 B4e8

description: IgG


title: Sample_34: b12

description: IgG


title: Sample_28: F425 B4e8

description: IgG


title: Sample_31: F425 B4e8

description: IgG


title: Sample_27: F425 B4e8

description: IgG


title: Sample_35: b12

description: IgG


title: Sample_23: 447-52D

description: IgG


title: Sample_24: 447-52D

description: IgG


title: Sample_26: F425 B4e8

description: IgG


title: Sample_25: F425 B4e8

description: IgG


title: Sample_22: 447-52D

description: IgG


title: Sample_21: 447-52D

description: IgG


title: Sample_20: 447-52D

description: IgG


title: HOS_74_1

description:
human osteosarcoma cell line
SAMPLE 10

value: HOS

value: Passage number 74


title: LM5_40_2

description:
human osteosarcoma cell line
SAMPLE 17


title: Sample_18: 447-52D

description: IgG


title: Sample_17: 447-52D

description: IgG


title: Sample_19: 447-52D

description: IgG


title: HeLa treated with trichostatin A for 12h, biological rep3

description:
Sample name: TSA_Rep3_12h
Gene expression data HeLa cells treated with trichostatin A for 12h

value: cervical cancer (HeLa) cells


title: LM5_04_1

description:
human osteosarcoma cell line
SAMPLE 13


title: HOS_74_3

description:
human osteosarcoma cell line
SAMPLE 12


title: HOS_33_3

description:
human osteosarcoma cell line
SAMPLE 9

value: Passage number 33


title: 143B_43_2_10

description:
human osteosarcoma cell line
SAMPLE 5

value: Osteolytic

value: Passage number 43


title: LM5_04_2

description:
human osteosarcoma cell line
SAMPLE 14


title: 143B_43_1

description:
human osteosarcoma cell line
SAMPLE 4


title: HOS_33_2

description:
human osteosarcoma cell line
SAMPLE 8


title: HOS_33_1

description:
human osteosarcoma cell line
SAMPLE 7


title: wt. vs. Gcn2 glyphosate-treated seedlings, replicate 1

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

hyb_protocol: Before hybridization, slides were pre-hybridized at 42ºC for 45 m in 5xSSC, 0.1%SDS and 0.1 mg/mL BSA. Microarray hybridizations and washings were done in manual chambers at 42ºC, according to Forment et al., 2005

scan_protocol: Scanning and Image Analysis was performed using GenePix Pro 6.0 software (Molecular Devices).

data_processing: Global media normalized, background subtracted data obtained from log2 of processed Cy5 signal/processed Cy3 signal.

organism: Arabidopsis

source_name: seedling

label_protocol: 1.5 µg of total RNA was labeled using MessageAmp II amplification kit from Life Technologies, following manufacturer instructions. Labeling was done using Cy3 and Cy5 dyes from GE (RPN5661).

growth_protocol: Arabidopsis thaliana accession Landsberg erecta (Ler-0) and Genetrap GT8359 were used. After stratification at 4°C in the dark for 5 days, seeds were sowed on 1% agar-containing MS Salts, 1% sucrose, pH 5.5, and grown at 23°C with a 16-h-light/8-h-dark cycle.

extract_protocol: Total RNA of glyphosate-treated 16-days-old seedlings was extracted using RNeasy kit (Qiagen).

treatment_protocol: Plantlets were submerged in 200 µM glyphosate (SIGMA)  for 1 minute, and incubated for further grow on liquid MS medium, 1% sucrose, pH 5.5, under the same conditions. Samples for microarray experiments were collected 6 hours after treatment

tag: genotype/variation

value: wt

value: glyphosate-treated


title: Sample_15: 1D9

description: IgG

value: tat


title: wt. vs. Gcn2  seedlings, replicate 3

extract_protocol: Total RNA of  16-days-old seedlings was extracted using RNeasy kit (Qiagen).


title: wt. vs. Gcn2 glyphosate-treated seedlings, replicate 2


title: wt. vs. Gcn2  seedlings, replicate 1


title: Leaf_12:00_Koshihikari_28DPS Cy5

value: Koshihikari


title: 143B_06_1

description:
human osteosarcoma cell line
SAMPLE 1

tag: cell line

value: Passage number 06


title: 143B_43_3

description:
human osteosarcoma cell line
SAMPLE 6

tag: properties


title: wt. vs. Gcn2 glyphosate-treated seedlings, replicate 3


title: Sample_16: Den3

description: IgG

value: Dengue specific

value: Dengue


title: HOS_74_2

description:
human osteosarcoma cell line
SAMPLE 11

value: Osteoblastic


title: Sample_14: 1G7

description: IgG

value: rev


title: Sample_13: 91-5

description: IgG

value: gag p24


title: Blood_wt_rep2

city: Hohhot

first: Xinfeng

last: Liu

address: 24 Zhaojun Road

institute: Inner Mongolia University

description: Gene expression in wild type cattle blood

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Bos taurus

source_name: Jugular vein Blood, wild type, replicate 2

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed  to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) and purified using an RNeasy® Mini Kit (QIAGEN, Germany) following the manufacturer's instructions.Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: tissue

value: whole blood

tag: gender

value: female

tag: age

value: 3 years


title: 143B_06_2_8

description:
human osteosarcoma cell line
SAMPLE 2


title: Blood_fat-1_rep3

description: Gene expression in fat-1 trasgenic cattle blood

source_name: Jugular vein Blood, fat-1, replicate 3


title: Blood_wt_rep3

source_name: Jugular vein Blood, wild type, replicate 3


title: wt. vs. Gcn2  seedlings, replicate 2


title: Sample_12: #564

description: IgG

value: HIV-1 specific

value: vif


title: Sample_11: 4E10_

description: IgG


title: Sample_10: 2F5

description: IgG


title: Sample_9: 240-D

description: IgG


title: Blood_wt_rep1

source_name: Jugular vein Blood, wild type, replicate 1


title: total_RNA_genotypeC_pair3

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing:
Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
probe group file: GPL13185_mjay.pgf
Data were analyzed with Omniviewer software: http://exon.ucsc.edu/omniviewer/. The Omniviewer output is available on the series record. The "A" set represents the Nxf1-CAST mutants and the "B" set represents the Nxf1-B6 mutants.

source_name: Brain

label_protocol: WT Terminal Labeling Kit, Affymetrix

extract_protocol: Each brain was homogenized in Trizol reagent on a Polytron PT2100. RNA was extracted from Trizol (LifeTechnologies) according to the manufacturer’s instructions, then further purified using an RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Same-sex pairs of mice, homozygous with respect to alternative alleles at Nxf1 (B6 or CAST).

value: brain

value: B6.CAST congenic line

tag: generation

value: C

tag: Sex

value: F


title: KURC3 vehicle

city: Kyoto

first: Shibasaki

last: Noboru

address: 54 Shogoinkawahara-cho Sakyo-ku

department: Urology

institute: Kyoto University

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

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

data_processing: The data were analyzed with GeneChip® Command Console® Software（AGCC） and global scaling as normalization method.

label: Biotin Allonamide Triphosphate

source_name: renal cancer xenograft tumor of KURC3 treated with vehicle only

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol of GeneChip® WT Terminal Labeling Kit. (GeneChip® WT Terminal Labeling and Hybridization User Manual 2009, Affymetrix).

growth_protocol: human renal cancer tissues were transplanted into severe combined immunodefficiency mice and passaged stably. We named them as KURC (Kyoto University Renal Cancer) 1, 2, and 3.

extract_protocol: Total RNA was isolated and purified using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: We administered 40 mg/day of sunitinib into KURC1, 2, and 3 orally, and evaluated the effect of sunitinib treatment.

value: xenograft tumor of renal cell carcinoma

tag: treatment

value: vehicle

tag: xenograft mode


title: KURC2 sunitinib-sensitive

source_name: renal cancer xenograft tumor of KURC2 treated with sunitinib and resected at sunitinib-sensitive status

value: 40 mg/day of sunitinib


title: Blood_fat-1_rep1

source_name: Jugular vein Blood, fat-1, replicate 1

value: 3.5 years


title: KURC3 sunitinib-resistance

source_name: renal cancer xenograft tumor of KURC3 treated with sunitinib and resected at sunitinib-resistant status


title: Sample_7: 2G12

description: IgG

source_name: monoclonal antibody


title: Blood_fat-1_rep2

source_name: Jugular vein Blood, fat-1, replicate 2


title: KURC2 vehicle

source_name: renal cancer xenograft tumor of KURC2 treated with vehicle only


title: Sample_6: F105

description: IgG


title: Sample_5: VRC03

description: IgG


title: KURC1 vehicle#2

source_name: renal cancer xenograft tumor of KURC1 treated with vehicle only


title: KURC1 sunitinib-resistance#1

source_name: renal cancer xenograft tumor of KURC1 treated with sunitinib and resected at sunitinib-resistant status


title: KURC1 sunitinib-sensitive#1

source_name: renal cancer xenograft tumor of KURC1 treated with sunitinib and resected at sunitinib-sensitive status


title: KURC1 vehicle#1


title: total_RNA_genotypeB_pair2

value: B

value: M


title: Sample_8: 5F3

description: IgG


title: total_RNA_genotypeC_pair2


title: Sample_4: VRC01

description: IgG


title: total_RNA_genotypeC_pair1


title: total_RNA_genotypeB_pair3


title: Aug_12_2008_at_12:42_and_12:43

hyb_protocol: 825ng of labeled cRNA were used for hybridization according to manufacturer's protocol. Open-lab in rgrc in NIAS was used.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1). LOWESS normalization.

source_name: rice,leaf,in the field

label_protocol: 400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using NTP and 400 µM Cy5 (or Cy3) CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.

growth_protocol: Rice plants were grown in a paddy field in Tsukuba, Japan in 2008 using a typical cultivation method. Transplanted date was June 6.

extract_protocol: Total RNA extracted using QIAGEN RNeasy Plant Mini Kit following manufacturer's instructions

treatment_protocol: Rice leaves were sampled at the paddy field. Cut leaves were frozen using liquid N imeditately after sampling.

tag: cultivar

tag: sampling time


title: total_RNA_genotypeB_pair1


title: Aug_12_2008_at_12:48_and_12:49


title: Aug_12_2008_at_12:46_and_12:47


title: Aug_12_2008_at_12:40_and_12:41


title: Sample_2: F425 B4e8

description: IgG

tag: specificity


title: Aug_12_2008_at_12:44_and_12:45


title: Sample_3: b12

description: IgG

tag: epitope


title: KURC1 sunitinib-resistance#2


title: Sample_134: HIVIG

description: Total IgG

source_name: purified polyclonal IgG

tag: concentration (ug/ml)

value: 1/100 dilution

tag: hiv status

value: positive


title: Sample_132: IVIG

description: Total IgG

value: negative


title: Sample_133: HIVIG

description: Total IgG


title: Aug_12_2008_at_12:33_and_12:34


title: Sample_131: IVIG

description: Total IgG


title: 143B_06_3

description:
human osteosarcoma cell line
SAMPLE 3

source_name: Osteosarcoma commercial human cell lines

value: Osteolytic

tag: passage number

value: Passage number 06


title: Aug_12_2008_at_12:38_and_12:39


title: Aug_12_2008_at_12:31_and_12:32


title: Sample_129: Subject 27

description: Total IgG

source_name: serum

value: HIV-1 specific

value: ART treated


title: Sample_1: 447-52D

description: IgG


title: CA16_PBMC_14-2nd-DPI

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

description:
Sample name: 10
Gene expression after 14 day at second post infection in rhesus neonates PBMC

hyb_protocol: Each slide was hybridized with 1.65 μl of Cy3-labeled cRNA using the Gene Expression Hybridization Kit (Agilent) in a Hybridization Oven (Agilent). After 17 hours of hybridization, slides were washed in staining dishes (Thermo, MA, USA) with the Gene Expression Wash Buffer Kit (Agilent). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed  with the Gene Expression Wash Buffer Kit (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Macaca mulatta

source_name: PBMC, 14-2nd dpi

label_protocol: mRNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA using the manufacturer’s Low Input Quick Amp Labeling protocol (Agilent). Labeled cRNA was purified using the RNeasy Mini Kit (QIAGEN, GmBH, Germany). Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA from the PBMCs using TRIzol Reagent (Invitrogen, CA, USA) and purified using RNeasy Mini Kit (QIAGEN, GmBH, Germany). The RNA Integrity Number (RIN) was also evaluated to inspect RNA integrity using an Agilent Bioanalyzer 2100 (Agilent, CA, USA).

treatment_protocol: Freshly peripheral blood from experiment or control monkeys was sampled, then was isolated the PBMCs.

tag: developmental stage

value: neonatal

tag: infection

value: Coxsackievirus A16

tag: time

value: 14 day at second post infection

tag: cell type

value: PBMC


title: CA16_PBMC_7-1st-DPI

description:
Sample name: 2
Gene expression after 7 day at first post infection in rhesus neonates PBMC

source_name: PBMC, 7-1st dpi

value: 7 day at first post infection


title: Aug_12_2008_at_12:29_and_12:30


title: Aug_12_2008_at_12:27_and_12:28


title: Aug_12_2008_at_12:23_and_12:24


title: Aug_12_2008_at_12:17_and_12:18


title: Sample_130: Subject 28

description: Total IgG


title: Sample_128: Subject 26

description: Total IgG


title: Sample_125: Subject 23

description: Total IgG


title: Sample_126: Subject 24

description: Total IgG


title: Aug_12_2008_at_12:25_and_12:26


title: Aug_12_2008_at_12:19_and_12:20


title: CA16_PBMC_7-2nd-DPI

description:
Sample name: 8
Gene expression after 7 day at second post infection in rhesus neonates PBMC

source_name: PBMC, 7-2nd dpi

value: 7 day at second post infection


title: Sample_124: Subject 22

description: Total IgG


title: Aug_12_2008_at_12:21_and_12:22


title: Sample_123: Subject 21

description: Total IgG


title: Sample_122: Subject 20

description: Total IgG


title: Aug_12_2008_at_12:13_and_12:14


title: CA16_PBMC_3-2nd-DPI

description:
Sample name: 6
Gene expression after 3 day at second post infection in rhesus neonates PBMC

source_name: PBMC, 3-2nd dpi

value: 3 day at second post infection


title: Sample_127: Subject 25

description: Total IgG


title: Sample_121: Subject 19

description: Total IgG


title: Aug_12_2008_at_12:07_and_12:08


title: Sample_119: Subject 17

description: Total IgG


title: Sample_120: Subject 18

description: Total IgG


title: Sample_118: Subject 16

description: Total IgG


title: Sample_117: Subject 15

description: Total IgG


title: Aug_12_2008_at_12:03_and_12:04


title: Sample_116: Subject 14

description: Total IgG


title: CA16_PBMC_0DPI

description:
Sample name: 1
Gene expression after 0 day in rhesus neonates PBMC

source_name: PBMC, 0 dpi

value: control

value: 0 day in rhesus neonates PBMC


title: Aug_12_2008_at_12:11_and_12:12


title: Aug_12_2008_at_12:05_and_12:06


title: Sample_114: Subject 12

description: Total IgG


title: Aug_12_2008_at_12:15_and_12:16


title: Aug_12_2008_at_12:01_and_12:02


title: Sample_113: Subject 11

description: Total IgG


title: placenta E7.5-Grhl2knockout-rep1

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

institute: Hannover Medical School

hyb_protocol: Hybridization was done according to standard Illumina's whole-genome gene expression direct hybridization assay protocols.

scan_protocol: Standard Illumina® scanning protocols were used.

data_processing:
The data table contains all quantile normalized probes.
After quantile normalization of the data, we filtered out only probes for genes with a valid RefSeq ID (referring to the annotation file provided by Illumina; http://www.switchtoi.com/annotationfiles.ilmn) and with a P-value of the respective log2-transformed expression values less than 0.05 using Student's t test. For our analyses, only the most differentially expressed probes (one for each gene) were used.

source_name: mouse placenta

label_protocol: Amplified and biotinylated cRNA for hybridization with Illumina® Sentrix® Mouse WG6 v2.0 Gene Expression Bead Chip Arrays (San Diego, CA, USA) were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies, Darmstadt, Germany). Quality control was performed with Agilent Bioanalyzer.

extract_protocol: The extraembryonic trophectoderm-derived tissues (chorion, ectoplacental cone and giant cell layer) at E7.5 and the visually identified placenta at E9.5 were separated from embryonic tissue and maternal uterus tissue. Then, total RNA from E7.5 trophectoderm-derived tissues and E9.5 placentas was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions including RNase-free DNase I treatment (Qiagen, Hilden, Germany).

tag: strain

tag: tissue

value: placenta

value: embryonic day 7.5 (E7.5)

tag: genotype/variation


title: Sample_111: Subject 9

description: Total IgG

value: 1/100 dilution

value: positive


title: placenta E7.5-Grhl2knockout-rep3

tag: age


title: Aug_12_2008_at_12:09_and_12:10


title: Sample_115: Subject 13

description: Total IgG

tag: treatment


title: placenta E7.5-wild-type-rep2

value: wild-type


title: Aug_12_2008_at_12:36_and_12:37


title: Human reset cell_L2i+PKCi_2wks

city: Minato-ku

first: Hideki

last: Masaki

state: Tokyo

address: 4-6-1 Shirokanedai

department: Institute of Medical Science

institute: University of Tokyo

description: Gene expression of reset cells 2 weeks after switching medium from L2i+Dox to L2i+PKCi

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Reset cells converted from PB004-hiPSC line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Not provided

tag: gender

value: female


title: placenta E9.5-Grhl2knockout-rep1

value: embryonic day 9.5 (E9.5)


title: placenta E7.5-wild-type-rep1


title: placenta E9.5-Grhl2knockout-rep3


title: placenta E9.5-Grhl2knockout-rep2


title: placenta E9.5-wild-type-rep2


title: Human iPSC_bFGF

description: Gene expression of conventional human iPSC cultured with bFGF

source_name: Female PB004-hiPSC line induced from peripheral blood


title: placenta E7.5-wild-type-rep3


title: Human reset cell_L2i+Dox

description: Gene expression of reset cells under L2i+Dox condition


title: placenta E7.5-Grhl2knockout-rep2


title: placenta E9.5-wild-type-rep3


title: Sample_112: Subject 10

description: Total IgG

value: HIV-1 specific

value: ART treated


title: Bovine raw milk whey supernatant after ultracentrifugation

status: Public on Mar 09 2015

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

institute: Morinaga Milk Industry Co., Ltd.

hyb_protocol: Cy3 labelled RNA samples were hybridized to Bovine miRNA microarrays (Release 17.0) (Agilent Technologies) at 55 ºC for 20 hr. After hybridyzation, the microarray slides were washed and dried according to the manufacture's instruction.

scan_protocol: The microarray slides were scanned on an Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: Fluorescent signal intensities were extracted from the images with the Feature Extraction Software (v.10.7.3.1) (Agilent Technologies). The raw signal values were normalized to Percentile Shift 75th when importing the Feature Extraction files into GeneSpring GX 11.5.1.

label_protocol: Total purified RNA from 3 samples were mixed equally. And cyanine-3 (Cy3) labeled cRNA was prepared from 40 ng RNA using the miRNA Complete Labeling Reagent and Hyb kit (Agilent) according to the manufacture's instruction, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified using an miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany). Briefly, exosome and supernatant samples were diluted with five volumes of QIAzol Lysis Reagent, mixed thoroughly by vortexing and incubated for 5 min. Then chloroform (equal volume to sample) was added to homogenate, mixed thoroughly by vortexingand incubated for 3 min. The homogenate were centrifuged (12,000 x g, 4 ºC, 15 min). The resulting aqueous phase was mixed thoroughly with 1.5 volumes of 100 % ethanol and passed through an miRNeasy column. The column was washed according to the manufacture's protocol, and RNA was eluted in nuclease free water. The quanity and integrity of the RNA were assessed using RNA 6000 Pico Kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Whey samples from raw milk were ultracentrifuged (10,000 g, 4 °C, 90 min). Resulted supernatant was carefully collected avoiding contamination of pelleted exosome. Pelleted exosome was resuspended in PBS and ultracentrifuged (10,000 g, 4 °C, 90 min) to wash. This wash step was done totally twice.

tag: breed

value: Holstein


title: Bovine raw milk whey-derived exosome

source_name: Bovine raw milk whey-derived exosome


title: 6 dpi, Δsee1 infected seedling Rep 2 (Cy3)

city: Marburg

first: Gunther

last: Doehlemann

state: Hessen

address: Karl von Frisch Strasse 10

department: Department of Organismic Interactions

institute: Max Planck Institute for Terrestrial Microbiology

description: Gene expression in 6 dpi infected see1 mutant infected seedling-Rep2

hyb_protocol: 750 ng of each labeled target cRNA was hybridized for 17 hrs at 60C

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual. Images were processed with the Agilent feature extraction software (version 9.5.1.1)

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction was normalized again to the median array intensity. Avergae intensities were then calculated for probes with atleast 3 or 4 good intensities.

organism: Zea mays

label_protocol: Total RNA (200 ng) was amplified and labelled with Cy3 and Cy5 using Agilent Low RNA Input Fluorescent Linear Amplification kit.

growth_protocol: Plants were grown in multiple plantings in a greenhouse equipped with lights providing 50% of summer noon solar fluence (16-h light/8-h dark) at Max Planck Institute, Marburg, Germany; infected and dissected greenhouse; tissues were collected and frozen in liquid nitrogen immediately

extract_protocol: Total RNA was extracted from the 50 mg of collected frozen tissue with Qiagen Rneasy Mini kit, Digested with Dnase I, and cleaned up with the Rneasy colums

treatment_protocol: Needle infections of 8 days seedlings were performed by injecting approximaly 1 ml of the grown U. maydis culture cell suspension into the base of the seedling. The mock samples were injected with equal amount of water instead of the cell suspension.

value: Seedling leaves

value: see1 mutant


title: 6 dpi, Mock injected seedling, Rep 2 (Cy 3)

description: Gene expression in 6 dpi infected mock maize seedling -Rep2

value: Mock


title: placenta E9.5-wild-type-rep1


title: 6 dpi, Δsee1 infected seedling Rep 3 (Cy3)

description: Gene expression in 6 dpi infected see1 mutant infected seedling-Rep3


title: 6 dpi, Mock injected seedling, Rep 1 (Cy 3)

description: Gene expression in 6 dpi infected mock maize seedling -Rep1


title: 6 dpi, SG200 infected seedling Rep1 (Cy3)

description: Gene expression in 6 dpi infected SG200 wildtype infected seedling-Rep1

value: SG200 wildtype


title: 6 dpi, SG200 infected seedling Rep 3 (Cy3)

description: Gene expression in 6 dpi infected SG200 wildtype infected seedling-Rep3


title: 6 dpi, Δsee1 infected seedling Rep1 (Cy3)

description: Gene expression in 6 dpi infected see1 mutant infected seedling-Rep1


title: 6 dpi, Mock injected seedling, Rep 3 (Cy 3)

description: Gene expression in 6 dpi infected mock maize seedling -Rep3


title: 5446 - E9.5 ALK23 KO- LP1

city: Saint Louis

first: David

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

description:
4051964039_F
BMPR KO #1

hyb_protocol: Performed using standard Illumina protocol on Illumina Mouse6 v1.1 bead arrays by the Genome Technology Access Center (GTAC) at Washington University

scan_protocol: Standard Illumina protocol for bead arrays.

data_processing:
Background subtraction and cubic spline normalization and differential expression in the wild type and knockout prospective lens and retina were performed using Illumina Genome Studio software
Value is the mean hybridization intensity for all beads (~25-50 ) contining the indicated oligonucleotide probe.

source_name: BMPR KO

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

growth_protocol: Pregnant mice euthanized and embryos removed at E9.5

extract_protocol: Total RNA was extracted and purified from the prospective lens or retina tissue using a Qiagen RNeasy Microkit (Qiagen# 74004). 15 ng of total RNA was amplified to produce 3–5 μg of cDNA using a Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc, #3300-12).

treatment_protocol: Embryos frozen in OCT and sectioned at 10 microns. Laser microdissection of the lens ectoderm on a Leica LMD-6000 system after slides were dipped in 70% ethanol at 4 °C for 1 min, washed in RNAase-free water twice for 30 s, rinsed in 95% ethanol, and stained in Eosin Y. Stained samples were washed in 95% ethanol and dehydrated in 100% ethanol and xylene..

tag: strain background

value: mixed background (C57BL6, FVB)

value: BMPR KO

value: prospective lens or retina tissue


title: 5444 - E9.5 ALK23 WT- LP2

description:
4051964039_E
BMPR WT #2

source_name: BMPR WT

value: wild type


title: 5447 - E9.5 ALK23 KO- LP2

description:
4051964039_C
BMPR KO #2


title: 5443 - E9.5 ALK23 WT- LP1

description:
4051964039_B
BMPR WT #1


title: 5448 - E9.5 ALK23 KO- LP3

description:
4051964039_A
BMPR KO #3


title: 5445 - E9.5 ALK23 WT- LP3

description:
4051964039_D
BMPR WT #3


title: VC-063

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 7.5ug of Cy5-labeled sample was combined with 7.5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v7.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924)

scan_protocol: Scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C

data_processing:
Quantified signal intensities and pre-processed data with Agilent Feature Extraction 11.0.1.1
FE files loaded into Nexus Copy Number Software v.7.5.1  (Biodiscovery Inc.) for analysis.

source_name: plasma cell-free DNA

label_protocol: 50ng gDNA (or as much as possible if yield was less) was whole genome amplified with Sigma WGA2 kit.  2.5ug WGA product was labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 2 min 95C heat step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with QIAamp Circulating Nucleic Acid Kit (Cat No 55114)

tag: disease state

value: Castrate resistant prostate cancer

tag: sample type

value: plasma

source_name: male reference DNA (Promega Corp)

value: male reference DNA (Promega Corp)


title: VC-068


title: VC-064


title: VC-062


title: blood_lun_028

first: Ottmar

last: Distl

address: Buenteweg 17 p

department: Institute for Animal Breeding and Genetics

institute: University of Veterinary Medicine Hannover

description: Sample name: TIHO-Lundehund_028

hyb_protocol: Standard Illumina protocol for Infinium HD Beadchip

scan_protocol: Illumina iScan with Dual-Scanner Autoloader

data_processing: Illumina GenomeStudio Version 2011.1 with Genotyping Module 1.9.4

organism: Canis lupus familiaris

source_name: blood

extract_protocol: Genomic DNA was extracted from the blood samples through a standard ethanol fractionation with concentrated sodiumchloride (6 M NaCl) and sodium dodecyl sulphate (10% SDS).

value: Lundehund

value: blood


title: blood_lun_017

description: Sample name: TIHO-Lundehund_017

label_protocol: Standard Illumina protocol for Infinium HD Beadchip

value: female


title: blood_lun_027

description: Sample name: TIHO-Lundehund_027

value: male


title: VC-057


title: blood_lun_022

description: Sample name: TIHO-Lundehund_022


title: 6 dpi, SG200 infected seedling Rep 2 (Cy3)

description: Gene expression in 6 dpi infected SG200 wildtype infected seedling-Rep2


title: blood_lun_019

description: Sample name: TIHO-Lundehund_019


title: blood_lun_024

description: Sample name: TIHO-Lundehund_024


title: VC-058


title: VC-056


title: blood_lun_025

description: Sample name: TIHO-Lundehund_025


title: blood_lun_014

description: Sample name: TIHO-Lundehund_014


title: blood_lun_020

description: Sample name: TIHO-Lundehund_020


title: blood_lun_018

description: Sample name: TIHO-Lundehund_018


title: blood_lun_026

description: Sample name: TIHO-Lundehund_026


title: blood_lun_021

description: Sample name: TIHO-Lundehund_021


title: blood_lun_023

description: Sample name: TIHO-Lundehund_023


title: VC-055


title: VC-054


title: blood_lun_013

description: Sample name: TIHO-Lundehund_013