title: Exposed Week 10, Sample 49

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

hyb_protocol: At each of the three time points, ambient air-exposed samples and HEPA-filtered samples were hybridized to Agilent microarrays (Agilent Technologies) at 65ºC overnight. Five arrays were removed from the study due to poor data quality.

scan_protocol: Arrays were scanned on an Agilent G2505B scanner. Data were acquired using the Agilent Feature Extraction software version 9.5.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities, were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: Universal Mouse Reference RNA

label_protocol: Total RNA (200 ng) from HEPA-filtered air or whole air-exposed mice, and Universal Mouse Reference RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine-labelled cRNA according to the manufacturer's instructions (Agilent Linear Amplification Kits, Agilent Technologies). Biological samples were labelled with Cy5 dye while the commercially available Stratagene mouse reference RNA was labelled with Cy3 dye.

extract_protocol: Total RNA isolated from 11 mouse cell lines is from Stratagene (Universal Mouse Reference RNA, Catalog #740100; La Jolla, CA, USA).

value: 11 mouse cell lines

source_name: C57BL/CBA male mouse lung tissue, exposed, week 10

growth_protocol: Mature male C57BL/6 x CBA F1 hybrid mice were exposed to either HEPA-filtered or ambient air in Hamilton, ON, Canada. Mice were housed in cages inside a vinyl utility shed, which had sections of shed walls cut out allowing for flow-through of ambient air. Mice breathing the HEPA-filtered air were housed in the same shed, but were kept inside a plexiglass unit that received only filtered air. Animals were exposed starting May 14, 2004 for 3 weeks (3wk), 10 weeks (10wk), or for 10 weeks followed by 6 weeks of recovery (during which time they were removed from the field and returned to the McMaster animal facility; 16wk). During the exposure period, the mice were closely monitored for any signs of stress. The temperatures both within the HEPA filtration units and within the ambient air units were monitored, with the average temperature in the HEPA units being 19.6ºC ± 4.9ºC (standard deviation) and the average temperature in the ambient air units being 19.8ºC ± 5.5ºC. Food and water were provided ad libitum. All animal procedures were carried out with the permission and in accordance with the guidelines of the Canadian Council on Animal Care and procedures approved by the McMaster University Animal Research Ethics Board.

extract_protocol: Total RNA was isolated from a random section of the whole lung using TRIzol reagent (Invitrogen, Burlington, ON, Canada) and purified using the RNeasy Mini Kit (Qiagen, Toronto, ON, Canada). RNA quality was confirmed by UV spectrophotometry and using an Agilent Bioanalyzer (Agilent Technologies Mississauga, ON, Canada).

treatment_protocol: Following exposure, animals were immediately sacrificed, and lung tissue was collected and flash frozen in liquid nitrogen.

tag: developmental stage

value: mature

value: lung

value: ambient air from polluted urban environment

tag: time point

value: week 10

tag: sampleID


title: JH_120319_Tweak_Cell_Lines_057

status: Public on Sep 30 2013

type: RNA

city: Watertown

first: Mary

last: Simcox

state: MA

address: 500 Arsenal St

country: USA

institute: Forma Therapeutics

description: Pancreas, carcinoma_pancreas_ADC, Unspecified sex, C57BL/6  cells grown orthotopically.

hyb_protocol: Hybridization followed manufacturer's recommendations

scan_protocol: GC_scanner3000 Affymetrix scanner was utilized with AGCC

data_processing: Statistical analysis was done by simple linear modeling using Partek Genomics Suite software.  A model containing fixed effects for treatment and time and their interaction was calculated, and contrasts were constructed for the overall TWEAK vs. vehicle treatment comparison and for each individual time point.  Relevant gene lists of interesting genes and patterns of genes were created.  Lists were generated for probesets where treatment induced changes had significance p values of <0.05 and which change at least 1.8-fold at 2 time points.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Pan02 cells, treated with 0ng_per_ml for 8hours

label_protocol: 5'IVT Express kit was followed according to manufacturer's recommendations

growth_protocol: Cells were seeded in appropriate media with 2% heat-inactivated FBS in humidified 95% air, 5% CO2 overnight in 6-well plates at 37oC.

extract_protocol: total RNA was extracted using Qiagen Rneasy Minikit.

treatment_protocol: 100 ng/ml TWEAK or media control was added on day 2 to subconfluent cells. For each time point and treatment, five replicates were generated.  One replicate from each treatment group was used for QC as assessed with immunoblotting for Fn14 expression. Samples were collected in all cell lines after 4 h, 8 h or 24 h of stimulation or control treatment with five replicates. For the U2OS and MDA-MB-436 arrays, 15 min and 1 h time points were also collected.

tag: strain

tag: cell line

tag: cell type

value: pancreatic carcinoma


title: ER1_cy5_s46b

city: Miami

first: Marjorie

middle: F.

last: Oleksiak

state: FL

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

institute: University of Miami

hyb_protocol: Labeled aRNA samples (2 pmol dye/µl) were hybridized to slides in 10 µl of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNase free poly(A) RNA (Sigma)] for 44 hours at 42° C.  Slides were prepared for hybridization by blocking in 5% ethanolamine, 100 mM Tris pH 7.8, and 0.1% SDS added just before use for 30 minutes at room temperature, washed for one hour in 4x SSC, 0.1% SDS at 50° C, and then boiled for 2 minutes in distilled water to denature the cDNAs.

scan_protocol: Arrays were scanned using  a ScanArray Express 4000 (Perkin Elmer).  Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: Log2 measures of loess normalized gene expression data were normalized using a linear mixed model in JMP Genomics 3.2 (SAS, Cary, NC, USA) to remove the effects of dye (fixed effect) and array (random effect) following a joint regional and spatial Lowess transformation in MAANOVA version 0.98.8 for R to account for both intensity and spatial bias.  The model was of the form yij = μ  + Ai + Dj + (AxD)ij + εij where, yij is the signal from the ith array with dye j, μ is the sample mean, Ai and Dj are the overall variation in arrays (arrays 1-80) and dyes (Cy3 and Cy5), (AxD)ij is the array x dye interaction and εij is the stochastic error.  Because we were not interested in differences due to developmental stage, we analyzed residuals from the above model separately by time (e.g., separately for times 5, 10 and 15 dpf).  Thus, residuals from this model were used for gene-by-gene analyses by time of population and treatment effects, using population, treatment and dye as fixed effects, and array as a random effect.  The model was rijn = μ  + Ai + Dj + Pn + Tk + PnxTk + εijn where Pn is the nth population and Tk is the kth treatment (DMSO or PCB-126).  For all mixed model analyses, we used a false discovery rate (FDR) p-value of < 0.01 to control for multiple testing

organism: Fundulus heteroclitus

source_name: ER1_1 ug/L BNF_cy5

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using Ambion’s Amino Allyl MessageAmp aRNA Kit to form copy template RNA by T7 amplification.  Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: Adult Fundulus were collected from both a reference site at King’s Creek, near the mouth of the York River in Gloucester County, Virginia (37°17’52.4”N, 76°25’31.4”W) and from a contaminated site on the Elizabeth River in Portsmouth, Virginia (36°48’27.48”N, 76°17’35.77”W).  Adult fish were depurated for 12 months in a recirculating system containing artificial seawater (ASW 25 ppt) prepared from Instant Ocean® (Mentor, OH).  Fish were kept at 23-25° C on a photoperiod of 14:10 L:D and fed a daily diet of Tetramin® Tropical Fish Food (Tetra Systems, Blacksburg VA, USA) and newly hatched brine shrimp (Artemia, Brine Shrimp Direct, Ogden, UT).  Killifish embryos were obtained from in vitro fertilization of pooled oocytes mixed with pooled milt from multiple males.  Embryos were examined 24 hours post fertilization (hpf) for viability and placed individually into 20 mL glass scintillation vials with 10 mL of treatment solution.

extract_protocol: Individual embryo RNA was extracted using a TRIzol buffer (Invitrogen, Carlsbad, CA, USA) followed by purification using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA).

treatment_protocol: Dimethyl sulfoxide (DMSO), ANF, BNF and ethoxyresorufin were purchased from Sigma-Aldrich (St. Louis, MO).  Killifish embryos were exposed to ANF (0, 50 or 100 µg/L) with or without 1 µg/L BNF.  Individual embryos of parents from both populations were exposed to the treatment solution or to the DMSO vehicle control from 24 to 120 hpf  (n = 20).  In all of the treatment groups, DMSO concentration was maintained at less than 0.03%.  At 120 hpf, embryos were removed from the dosing solution and placed into vials containing clean ASW.

tag: population

value: Elizabeth River, VA

tag: pollutant sensitivity

value: Resistant

tag: tissue

value: Whole embryo

tag: treatment

value: 1 ug/L BNF

tag: Stage


title: B6_2w_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Gene expression of leukocyte derived from B6 after 2 weeks CAWS administration

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.3.1.

label_protocol: RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 500ng of total RNA (pooled sample from 16 healthy control patients) with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA of leukocytes from whole blood of B6 and DBA/2mice was stabilized by RNAlater (Ambion), and then isolated using the LeukoLOCK, a total RNA Isolation System (Ambion, Austin, TX, USA), according to the manufacturer’s instructions.

treatment_protocol: At 2, 4, 8 or 9 weeks after CAWS injection, we sacrificed the survived mice for preparation of mRNA from PBMC.

value: leukocyte

tag: gender

value: male

tag: after administration

value: 2 weeks

tag: replicate

value: biological replicate 1


title: KC1_cy5_s16d

source_name: KC1_1 ug/L BNF_cy5

value: King's Creek, VA

value: Sensitive


title: JH_120319_Tweak_Cell_Lines_054

source_name: Pan02 cells, treated with 0ng_per_ml for 24hours


title: Control Week 10, Sample 38

country: Canada

source_name: C57BL/CBA male mouse lung tissue, control, week 10

value: HEPA-filtered air


title: Exposed Week 10, Sample 45

value: 11 mouse cell lines


title: Exposed Week 3, Sample 7

source_name: C57BL/CBA male mouse lung tissue, exposed, week 3

value: mature

value: week 3


title: JH_120319_Tweak_Cell_Lines_056

source_name: Pan02 cells, treated with 0ng_per_ml for 4hours


title: Exposed Week 10, Sample 53

value: lung

value: ambient air from polluted urban environment


title: KC1_cy3_s46b

source_name: KC1_1 ug/L BNF_cy3


title: Erc_cy3_s16d

value: vehicle control (DMSO)


title: B6_8w_rep1

description: Gene expression of leukocyte derived from B6 after 8 weeks CAWS administration

value: 8 weeks


title: Control Week 3, Sample 6

source_name: C57BL/CBA male mouse lung tissue, control, week 3


title: B6_0w_rep2_tech1

description: Gene expression of leukocyte derived from B6 after 0 week CAWS administration

value: 0 week

value: biological replicate 2


title: JH_120319_Tweak_Cell_Lines_050

source_name: Pan02 cells, treated with 100ng_per_ml for 4hours

value: pancreatic carcinoma


title: KCc_cy3_s2b

value: Whole embryo


title: Exposed Week 10, Sample 39

value: male

value: week 10


title: Control Week 16, Sample 50

source_name: C57BL/CBA male mouse lung tissue, control, week 16

value: week 16


title: JH_120319_Tweak_Cell_Lines_051


title: Control Week 16, Sample 46


title: JH_120319_Tweak_Cell_Lines_053


title: Exposed Week 3, Sample 1


title: Erc_cy5_s2b

value: Elizabeth River, VA

value: Resistant


title: JH_120319_Tweak_Cell_Lines_049


title: PC3Ato (gene expression)

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Homo sapiens

source_name: PC3 cells, treated with 10uM of Atorvastatin

label_protocol: First and second strand cDNA was prepared from the total RNA samples. Labeled cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Human prostate cancer cells (PC3 cells and LNCaP cells) were purchased from the American Type Culture Collection (Manassas, VA).  All prostate cancer cell lines were cultured in RPMI medium containing 10% FBS. PC3 and LNCaP cells were seeded in culture dishes so that cells reached ~30% confluence on Day 2.

extract_protocol: Total RNA to be used in both mRNA and miRNA assays was isolated and purified using the Ribopure RNA isolation kit (Invitrogen, Grand Island, NY).

treatment_protocol: On day 2, culture medium was replaced and cells were exposed to Atorvastatin (ATO) (10 µM) for 24 h.


title: Control Week 10, Sample 42

value: HEPA-filtered air


title: JH_120319_Tweak_Cell_Lines_044

source_name: Pan02 cells, treated with 100ng_per_ml for 24hours


title: Control Week 3, Sample 2

value: 11 mouse cell lines


title: JH_120319_Tweak_Cell_Lines_047

source_name: Pan02 cells, treated with 100ng_per_ml for 8hours


title: PC3Ctrl (gene expression)

source_name: PC3 cells, no treatment control


title: JH_120319_Tweak_Cell_Lines_060


title: JH_120319_Tweak_Cell_Lines_041


title: JH_120319_Tweak_Cell_Lines_046


title: JH_120319_Tweak_Cell_Lines_040


title: JH_120319_Tweak_Cell_Lines_045


title: LncapAto (gene expression)

source_name: Lncap cells, treated with 10uM of Atorvastatin

value: LNCaP


title: Control Week 10, Sample 40

source_name: Universal Mouse Reference RNA

value: mature


title: Exposed Week 10, Sample 57

source_name: C57BL/CBA male mouse lung tissue, exposed, week 10

value: lung


title: Control Week 3, Sample 10

value: week 3


title: esophageal SCC tissues_fresh_replicate5

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description: Gene expression in fresh esophageal SCC tissues

hyb_protocol: Fluorescence dye labeled cRNA was hybridized to Human Genome 4x44K v2 Microarray microarray according to the instructions of Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 8.0.0.0 was used for background subtraction and signal median normalization.

source_name: esophageal SCC tissues_fresh_replicate5

label_protocol: RNA was amplified and labeled using Agilent LowInput Quick Amp Labeling Kit.

extract_protocol: Total RNA was isolated using Trizol reagent (BioChain,Beijing, MD) according to the manufacture’s instructions. The quantity of RNA in each sample was assessed spectrophotometerically (NanoDrop Technologies, Wilmington, DE) and RNA integrity was assessed by formaldehyde agarose gel electrophoresis.

value: esophageal SCC tissues

value: female

tag: clinical stage

tag: tnm


title: Exposed Week 10, Sample 35

value: ambient air from polluted urban environment


title: Exposed Week 3, Sample 3


title: Control Week 16, Sample 54


title: LncapCtrl (gene expression)

source_name: Lncap cells, no treatment control


title: JH_120319_Tweak_Cell_Lines_038

source_name: Pan02 cells, treated with 0ng_per_ml for 24hours


title: Exposed Week 3, Sample 5


title: normal para-carcinoma tissues_fresh_replicate 4

description: Gene expression in fresh normal para-carcinoma tissues

value: normal para-carcinoma tissues


title: normal para-carcinoma tissues_fresh_replicate 5


title: esophageal SCC tissues_fresh_replicate3

source_name: esophageal SCC tissues_fresh_replicate3


title: normal para-carcinoma tissues_fresh_replicate 3


title: SAGE Aedes aegypti, susceptible, infected blood

type: SAGE

anchor: NlaIII

city: NOTRE DAME

first: David

last: Severson

state: IN

address: 138 GALVIN LIFE SCIENCE CENTER

department: Department of Biological Sciences

institute: University of Notre Dame

description: Recombinant SAGE plasmid-pZERO clones were purified by Eppendorf 96-well plasmid purification system and single pass sequencing was done on an ABI 3730xl DNA sequencer (Applied Biosystems, Foster city, CA)

data_processing: Individual SAGE ditags were extracted from the raw ABI sequences with software created for SAGE analysis: SAGE 2000 4.5 Software, Version E (Invitrogen). The software parses out individual tags, discards ambiguous sequences, cleaves redundant ditags and generates a table of the individual tags and their observed occurrences within the library

organism: Aedes aegypti

source_name: midgut tissues, 3hrs, 6hrs, 12hrs, 24hrs, 48hrs, 72hrs and 96hrs after dengue-2 infectious blood meal

extract_protocol: Samples of at least 15 midguts were dissected at 3, 6, 12, 24, 48, 72, and 96 hours post blood meal (infected or naïve) and sucrose meal. Total RNA was isolated using TRIZOL l® Reagent (Invitrogen, Carlsbad, CA)

treatment_protocol:
Virus serotype: Dengue-2, JAM1409 virus strain in vitro cultures were maintained in the Ae. albopictus C6/36 cell line.
Mosquito treatment: Cohorts of 30 starved Aedes aegypti aged 4-5 days were transferred to 500 ml paper cups were exposed to a dengue-2 infected or naïve blood meal, using standard artificial membrane feeders. Fully engorged females were provided a 5% sucrose solution ad libitum and maintained at 26oC and relative humidity. A cohort of 30 mosquitoes received a 5% sucrose meal (SM).

tag: Strains

value: Susceptible strain (SUS), Refractory strain (REF)

tag: Gender

tag: Age

value: 4-5 days

tag: Tissue

value: midgut

tag: Time

value: 3-96 hours after dengue-2 infectious blood meal


title: SAGE Aedes aegypti, refractory, infected blood


title: esophageal SCC tissues_fresh_replicate1

source_name: esophageal SCC tissues_fresh_replicate1


title: JH_120319_Tweak_Cell_Lines_042

tag: strain

tag: cell line

value: pancreatic carcinoma


title: normal para-carcinoma tissues_fresh_replicate1

value: male


title: SAGE Aedes aegypti, refractory, naive blood

source_name: midgut tissues, 3hrs, 6hrs, 12hrs, 24hrs, 48hrs, 72hrs and 96hrs after naive blood meal

extract_protocol: Samples of at least 15 midguts were dissected at 3, 6, 12, 24, 48, 72, and 96 hours post blood meal (infected or naïve) and sucrose meal. Total RNA was isolated using TRIZOL l® Reagent (Invitrogen, Carlsbad, CA).

value: 3-96 hours after naïve blood meal


title: Exposed Week 3, Sample 9

source_name: C57BL/CBA male mouse lung tissue, exposed, week 3

tag: developmental stage

tag: time point

tag: sampleID


title: normal para-carcinoma tissues_fresh_replicate 2

tag: tissue


title: SAGE Aedes aegypti, susceptible, naive blood


title: Exposed Week 16, Sample 61

source_name: C57BL/CBA male mouse lung tissue, exposed, week 16

tag: treatment

value: week 16


title: SAGE Aedes aegypti, susceptible and refractory, sucrose

data_processing: Individual SAGE ditags were extracted from the raw ABI sequences with a software created for SAGE analysis: SAGE 2000 4.5 Software, Version E (Invitrogen). The software parses out individual tags, discards ambiguous sequences, cleaves redundant ditags and generates a table of the individual tags and their observed occurrences within the library.

source_name: midgut tissues: 3hrs, 6hrs, 12hrs, 24hrs, 48hrs, 72hrs and 96hrs after sucrose meal

extract_protocol: Samples of at least 15 midguts were dissected at 3, 6, 12, 24, 48, 72, and 96 hours post blood meal (infected or naive) and sucrose meal. Total RNA was isolated using TRIZOL l® Reagent (Invitrogen, Carlsbad, CA).

value: 3-96 hours after sucrose meal


title: Control Week 10, Sample 34

value: 11 mouse cell lines

source_name: C57BL/CBA male mouse lung tissue, control, week 10

tag: gender

value: HEPA-filtered air

value: week 10


title: Control Week 16, Sample 58

source_name: C57BL/CBA male mouse lung tissue, control, week 16

value: mature

value: lung


title: Exposed Week 10, Sample 37


title: Control Week 3, Sample 4

source_name: C57BL/CBA male mouse lung tissue, control, week 3

value: week 3


title: esophageal SCC tissues_fresh_replicate2

source_name: esophageal SCC tissues_fresh_replicate2

value: esophageal SCC tissues


title: LNCaP cells treated with 24hr BP

status: Public on Sep 29 2013

city: Hualien

first: Sheng-Chun

last: Chiu

address: No. 707, Sec. 3, Chung Yang Rd

department: Department of Medical Research

country: Taiwan

institute: Buddhist TzuChi General Hospital

description:
9SGST003
Gene expression data from LNCaP cells treated with 24hr BP

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G, GCOS v1.4

data_processing: Raw intensity were background corrected and nomalized by Expression Console (RMA algorithsm). Gene level expression comparison were analyzed by R package.

source_name: LNCaP cells treated with 24hr BP

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

growth_protocol: LNCaP cells were growth in RPMI1640 medium with 10% FBS, 1% PS, at 37C/5 % CO2 incubator

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

treatment_protocol: Cells were seeding in 6-cm petri dish (density 8x10^5 cells). After cells attach for 24h, 70 ug/ml BP were added for 3 or 24 hr

value: LNCaP


title: P14 WT cl13 d7 rep2

city: La Jolla

middle: L

last: Doedens

state: CA

address: 9500 Gilman Drive, 0377

department: Division of Biology

institute: Univerisity of California, San Diego

hyb_protocol: Processed by Immgen consortium; Affy 1.0 ST Hyb Kit

scan_protocol: Processed by Immgen consortium; Affymetrix GeneChip Scanner

data_processing: Gene expression files were created and RMA normalized from the eight CEL files using the ExpressionFileCreator, version 11 in Genepattern software, with quantile normalization and background correct.

source_name: WT P14 CD8 T cells_LCMV-cl13_7 dpi

label_protocol: Processed by Immgen consortium; Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

growth_protocol: Isolate P14+ WT or VHL distal Lckcre+ cells from the spleens of donor mice, mix 1:1, and txfer ~10^4 iv to WT C57Bl6 recipients. Wait one day.

extract_protocol: Trizol, processed by Immgen consortium

treatment_protocol: Infect with LCMV-Armstrong 2x10^5 pfu ip or 2x10^6 pfu LCMV-cl13 iv.  Take spleens at day 6 (armstrong) or 7 (cl13) post-infection, sort on CD8α+CD4-KLRG1-Vα2+ and CD45 congenic marker on ice, then a second sort into trizol.

tag: host strain

tag: host strain genotype

value: wild type

tag: cd8+ t cell type

value: WT P14 CD8 T cells

tag: infected with

value: spleen

tag: cell type

value: FACS-isolated, responding  P14 donor cells

value: 7 dpi (day post-infection)


title: LNCaP cells treated with 3hr BP

description:
9SGST002
Gene expression data from LNCaP cells treated with 3hr BP

source_name: LNCaP cells treated with 3hr BP


title: LNCaP cells

description:
9SGST001
Gene expression data from LNCaP cells

source_name: LNCaP cells


title: esophageal SCC tissues_fresh_replicate4

source_name: esophageal SCC tissues_fresh_replicate4

value: male

tag: clinical stage

tag: tnm


title: P14 Vhl KO Arm d6 rep1

source_name: Vhl KO P14 CD8 T cells_LCMV-Arm_6 dpi

value: Vhl KO P14 CD8 T cells

value: LCMV-Armstrong

value: 6 dpi (day post-infection)


title: P14 Vhl KO cl13 d7 rep2

source_name: Vhl KO P14 CD8 T cells_LCMV-cl13_7 dpi


title: A. thaliana-A. halleri hybrid_1

city: Canberra

first: Ryo

last: Fujimoto

state: ACT

address: Cnr Clunies Ross St & Barry Dr

country: Australia

institute: CSIRO

description: Mature leaves, biological rep1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: GCOS/MAS5 standard processing

organism: Arabidopsis thaliana x Arabidopsis halleri subsp. gemmifera

source_name: Mature leaves

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: Controlled enviromental condition (22C) under fluorescent lights and a 16h/8h (day/light) photoperiod.

extract_protocol: Total RNA was isolated from mature leaves using SV Total RNA Isolation system (Promega)

tag: tissues

value: mature leaves before flowering


title: A. halleri_1

description: Mature leaves, biological rep1

organism: Arabidopsis halleri subsp. gemmifera


title: P14 Vhl KO cl13 d7 rep1


title: A. thaliana-A. lyrata hybrid_1

description: Mature leaves, biological rep1

organism: Arabidopsis thaliana x Arabidopsis lyrata


title: P14 WT cl13 d7 rep1


title: A. thaliana-A. halleri hybrid_2

description: Mature leaves, biological rep2


title: P14 WT Arm d6 rep1

source_name: WT P14 CD8 T cells_LCMV-Arm_6 dpi


title: A. lyrata_1

description: Mature leaves, biological rep1

organism: Arabidopsis lyrata subsp. lyrata


title: P14 WT Arm d6 rep2


title: A. halleri_2

description: Mature leaves, biological rep2


title: P14 Vhl KO Arm d6 rep2


title: A. thaliana_2

description: Mature leaves, biological rep2

organism: Arabidopsis thaliana


title: A. thaliana-A. lyrata hybrid_2

description: Mature leaves, biological rep2


title: A. lyrata_2

description: Mature leaves, biological rep2


title: A. thaliana_1

description: Mature leaves, biological rep1


title: slide2-array1

status: Public on Sep 28 2013

city: Edmonton

first: Stephen

last: Tsoi

address: 4-32G Agriculture/Forestry Centre

department: AFNS

institute: University of Alberta

description: Dye-swap replicate of biological replicate 1

hyb_protocol: Hybridization mixture was prepared together with Spike-In control according to Agilent Gene Expression Hybridization Kit 60-mer oligo microarray protocol version 4.0.

scan_protocol: Arrays were immediately scanned at 5 μm resolution after slides were washing and drying using an Axon 4200AL scanner (635 nm for Cy5 and at 532 nm for Cy3) using the autoscan feature from the default setting and images were analysed with Gene Pix Pro 6.0. software

data_processing: FlexArray software was used for data normalization following first with simple background subtraction, LOWESS normalization within and between arrays.

organism: Sus scrofa

source_name: Control

label_protocol: Antisense RNA (aRNA) was generated using RiboAmp HSPlus kit beforw labelling with Cy3 or Cy5 Fluorophore using ULS Fluorescent Labeling Kit from Kreatech. Labelling was done under ozone free environmental chamber.

growth_protocol: Sows were slaughtered 5 days after the bevahiour estrus and embryos were recovered.

extract_protocol: ArcturusW PicoPureW RNA Isolation Kit (Applied Biosystems, Carlsbad, CA, USA) was used for RNA extraction from EB with on column removal of DNA by DNase treatment using RNase-Free DNase kit according to the protocol from Qiagen

treatment_protocol: Three different type of experimental diets were given to gilts: 1) basal diet 0.2 mg/kg of natural Se  and 2.3 mg/kg of vitamin B6 (pyridoxine ) and top-dressed with 50 g of ground corn without supplemental Se or pyridoxine; 2) basal diet  plus0.3 mg/kg of feed of inorganic Se, as sodium selenite, and 10 mg/kg of feed of hydro-chloride pyridoxine; 3) similar condition as group 2 and replaced inorganic Se with 0.3 mg/kg of feed of organic Se as Se-enriched yeast.

value: Expanded blastocytes

tag: dietary supplement

value: No

source_name: Inorganic Se + B6

value: Inorganic Se + B6


title: slide4-array2

description: Biological replicate 3 of 4.

source_name: Organic Se + B6

value: Organic Se + B6

value: Yes


title: slide4-array3

description: Dye-swap replicate of technical replicate, pooled RNA extracted from EB of four sows

source_name: Control (techenical replicate)

source_name: Organic Se + B6 (techenical replicate)


title: slide3-array3

description: Biological replicate 2 of 4.


title: slide4-array1

description: Dye-swap replicate of biological replicate 3


title: slide3-array1

description: Biological replicate 1 of 4.


title: slide2-array2

description: Dye-swap replicate of biological replicate 2


title: slide3-array2


title: slide4-array4

description: Technical replicate, pooled RNA extracted from EB of four sows


title: slide1-array4

description: Biological replicate 4 of 4.


title: slide3-array4


title: slide2-array3


title: slide2-array4-2

description: Dye-swap replicate of biological replicate 4


title: slide1-array2

description: Biological replicate 2 of 4.


title: slide1-array1

description: Biological replicate 1 of 4.


title: slide1-array3

description: Biological replicate 3 of 4.


title: methane oxidation biocover top layer soil replicate 2

type: genomic

city: Seoul

first: Kyung-eun

last: Moon

address: 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha womans university

description:
bio4_chip1_0.1_B1_w595.txt
bio4_chip3_0.1_B1_w685.txt
bio4_chip1_0.1_B1_w595.tif
bio4_chip3_0.1_B1_w685.tif

hyb_protocol: Hybridization mixtures contained 15.8 L of diethylpyrocarbonate (DEPC)-treated water, 0.4 L of 10% sodium dodecyl sulfate (SDS), 0.8  l of 50×Denhardt’s reagent (Sigma, St. Louis, U.S.), 12  l of 20% saline-sodium citrate (SSC) and 11  l of Cy3- or Cy5-labelled RNA. Cover glasses were laid onto the microarray slides within the hybridization chambers, and the hybridization mixtures were applied between the slide and cover glasses. After hybridization, the microarray slides were immediately washed.

scan_protocol: Hybridized slides were scanned using an Axon GenePix 4100A laser scanner (Axon Inc., Sunnyvale, U.S.) or ArrayWoRx (Applied Precision, Issaquah, U.S.). Fluorescent images were captured and analyzed using GENEPIX PRO 5.1 software (Axon Inc.) or ImaGene image analysis software (BioDiscovery, El Segundo, U.S.).

data_processing: The data were analyzed with GENEPIX PRO 5.1 software (Axon Inc.) or ImaGene image analysis software (BioDiscovery, El Segundo, U.S.). The trimmed mean target(control probe) intensity of each array was arbitrarily set to 100.

molecule: genomic DNA

organism: unidentified methanotrophic bacterium

label_protocol: In vitro transcription was carried out using the MEGAscript T7 Kit with Cy-3 or Cy-5 UTP (Perkin Elmer Inc., Waltham, U.S.). RNA was purified using the MinElute Cleanup kit and eluted with 12 L of the elution buffer. Purified RNA was fragmented with RNA Fragmentation Reagents.

extract_protocol: genomic DNA extracted using FastDNA spin soil kit (MP Biomedicals Inc.) following manufacturer's instructions

tag: soil layer

value: top layer soil


title: methane oxidation biocover top layer soil replicate 1


title: methane oxidation biocover middle layer soil replicate 2

description:
bio4_chip2_0.1_B1_w595.txt
bio4_chip1_0.1_B1_w685.txt
bio4_chip2_0.1_B1_w595.tif
bio4_chip1_0.1_B1_w685.tif

value: middle layer soil


title: methane oxidation biocover middle layer soil replicate 3


title: methane oxidation biocover middle layer soil replicate 1


title: methane oxidation biocover bottom layer soil replicate 1

description:
bio4_chip3_0.1_B1_w595.txt
bio4_chip2_0.1_B2_w595.txt
bio4_chip3_0.1_B1_w595.tif
bio4_chip2_0.1_B2_w685.tif

value: bottom layer soil


title: methane oxidation biocover bottom layer soil replicate 3


title: methane oxidation biocover bottom layer soil replicate 2


title: methane oxidation biocover top layer soil replicate 3


title: JG.WT.1271 wt thymoc.JG.WT.1271.CEL

city: Orsay

first: Jacques

last: GHYSDAEL

address: Centre Universitaire, Bat 110

country: France

institute: Institut Curie

description:
normal thymus
cell suspension

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45oC, 60 rpm on Murine MG_U74Av2 GeneChips. The chips were then washed and stained in the GeneChip® Fluidics Station 400

scan_protocol: The chips were scanned with the Hewlett-Packard GeneArray Scanner G2500A. Raw data were extracted from the scanned images using the Affymetrix  Microarray Suite version 5.0 (MAS5).

data_processing: CEL files were processed with R to calculate probeset signal intensities using Robust Multi-array Average (RMA) algorithms

source_name: thymus

label_protocol: Biotinylated cRNA targets were prepared from 5.0 µg of total RNA following the one-cycle target labeling assay  in Affymetrix GeneChip® Expression Analysis Technical Manual (1999), P/N 701021 Rev. 5

growth_protocol: thymus collection on ice; mechanical thymus dissociation in PBS 0-4°C; cell centrifugation et lysis of pelleted cells

extract_protocol: Total RNA was isolated using the RNeasy kit from QIAGEN

tag: strain

tag: genotype/variation

value: wild type

tag: disease state

value: normal

value: thymus

value: thymocytes


title: JG.WT.Thy wt thymoc.

description:
normal thymus
cell suspension


title: JG.TJ.62 leukemia

description:
leukemic thymus
cell suspension

value: leukemia

value: leukemic cells


title: hippocampus_mutant_rep4

city: Krakow

first: Grzegorz

last: Kreiner

address: Smetna 12

department: Dept. Brain Biochemistry

country: Poland

institute: Institute of Pharmacology

hyb_protocol: Microarray experiments were carried out using MouseWG-6 v2 BeadChip arrays (Illumina Inc., San Diego, CA, USA) according to manufacturer's instructions.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Analysis of array data was performed using the Bed Array R package (Bioconductor suite). After background subtraction, the data were normalized using quantile normalization and then log2-transformed. Statistical analysis of differences in transcription was performed with limma from the Bioconductor suite. Ontology analyses were carried out using GSEA and identification of enriched putative transcription factor binding sites was performed using cREMaG.

source_name: mutant, 4wks after TAM

label_protocol: Labeling of the target RNAs (1-2μg total RNA).

extract_protocol: Extraction of total RNA was performed using QIAgen columns according to manufacturer's instructions. RNA quality was validated on Agilent Bioanalyser.

tag: genotype

value: TIFIACaMKCreERT2 mutant

value: hippocampus


title: JG.TJ.404 leukemia

description:
leukemic thymus
cell suspension

tag: tissue


title: JG.WT.1272 wt thymoc.JG.WT.1272.CEL

description:
normal thymus
cell suspension


title: JG.WT.1277 wt thymoc.JG.WT.1277.CEL

description:
normal thymus
cell suspension


title: hippocampus_mutant_rep6, technical replicate no2

source_name: mutant, 4wks after TAM technical replicate no2


title: JG.TJ.25 leukemia

description:
leukemic thymus
cell suspension


title: hippocampus_mutant_rep6, technical replicate no1

source_name: mutant, 4wks after TAM technical replicate no1


title: hippocampus_control_rep5

source_name: control, 4wks after TAM

value: wildtype


title: TJ2_1210 leukemia

description:
leukemic thymus
cell suspension

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45oC, 60 rpm on Mouse GeneChip® 430 2.0 arrays. The chips were then washed and stained in the GeneChip® Fluidics Station 450 using EukGE-WS2v5_450 script.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G at a resolution of 1.56 µm. Raw data were extracted from the scanned images using the Affymetrix GeneChip Operating Software (GCOS)

label_protocol: Biotinylated cRNA targets were prepared from 2.5 µg of total RNA following the one-cycle target labeling assay  in Affymetrix GeneChip® Expression Analysis Technical Manual (2005-2006), P/N 702232 Rev. 2

growth_protocol: thymus or bone marrow collection on ice; mechanical thymus and large bone crushing and tissue dissociation on grid in PBS 0-4°C; filtration; cell centrifugation et lysis of pelleted cells


title: hippocampus_mutant_rep3


title: hippocampus_control_rep4


title: JG.TJ.1241leukemia

description:
leukemic thymus
cell suspension


title: JG.TJ.1210 leukemia

description:
leukemic thymus
cell suspension


title: TJ2_1192 leukemia

description:
leukemic thymus
cell suspension


title: Grade I - 2

city: Padappai

first: Parvathi

last: MVS

address: near BDO office

department: Genetic toxicology

country: India

institute: International institute of biotechnology and toxicology

hyb_protocol: Agilent miRNA Hybridization kit (Cat # 5190-0408) was used for hybridization and done as per manufacturer protocol.

scan_protocol: • Scan Setting    Values for 8x15K Formats   • Scan region    Scan Area (61 x 21.6 mm)   • Scan resolution (μm)   5   • 5μm scanning mode   Single Pass   • eXtended Dynamic range  (selected)   • Dye channel    Green   • Green PMT    XDR Hi 100% , XDR Lo 5%

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Breast carcinoma, FFPE tissue sample, Grade I

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using Agilent miRNA labeling reagent and Hybridization Kit (Cat # 5190-0408)  according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.Ligation of one cyanine3 –pCp molecule to the 3’ end of RNA molecule with greater than 90% efficiency that generates fluorescent miRNA

extract_protocol: RNA extraction using Ambion's Tri-reagent method as per manufacturer protocol (part no.AM9738).  RNA concentration was estimated using Agilent Nanodrop Bioanalyser Spectrophotometer.

value: Female breast formalin fixed biopsy blocks

value: female

tag: age


title: Grade II - 2

source_name: Breast carcinoma, FFPE tissue sample, Grade II

tag: gender


title: JG.TJ.1209 leukemia

description:
leukemic thymus
cell suspension


title: Grade I - 1


title: JG.TJ.1192 leukemia

description:
leukemic thymus
cell suspension


title: Grade III - 2

source_name: Breast carcinoma, FFPE tissue sample, Grade III


title: TJ2_1261 leukemia

description:
leukemic thymus
cell suspension


title: hippocampus_mutant_rep5


title: ICN1_1840 leukemia

description:
leukemic bone marrow
cell suspension

source_name: bone marrow

value: bone marrow


title: Grade III - 1


title: hippocampus_mutant_rep2


title: JG.TJ.1.3 leukemia

description:
leukemic thymus
cell suspension


title: TJ2_1209 leukemia

description:
leukemic thymus
cell suspension


title: Grade II - 1


title: hippocampus_control_rep3


title: hippocampus_control_rep2


title: ICN1_24306 leukemia

description:
leukemic bone marrow
cell suspension


title: hippocampus_control_rep1


title: ICN1_1701 leukemia

description:
leukemic bone marrow
cell suspension


title: Complemented strain_LJ002_Fe+ replicate 2

status: Public on Sep 27 2013

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Micorbiology and Immunology

institute: OUHSC

hyb_protocol: Arrays were hybridized at 50C for 14 hours before electrochemical detection using an ElectraSense Reader (CombiMatrix).

scan_protocol: Arrays were scanned using ElectraSense Reader (CombiMatrix)

data_processing: Data files generated by the ElectraSense Reader software were imported into GeneSpringGX 12.5 for analysis after background subtraction of the “no oligo” control probes.

label: Biotin

organism: Neisseria gonorrhoeae

source_name: Iron replete growth conditions; cells harvested at 3 hrs

label_protocol: cDNA was generated from 10g of DNase-treated total RNA using an Applied Biosystems High-Capacity cDNA Archive Kit.  A. thaliana mRNA positive controls (SpotReport mRNA: Cab, RCA, and RBCL) were spiked into each reverse transcription reaction each at a final concentration of 1ng each (Stratagene).  Post-synthesis labeling of cDNA was accomplished using the Mirus Label IT Array Biotin Labeling Kit. The cDNA was purified after the removal of RNA template pre-labeling and after biotin-labeling of the cDNA, using a QIAquick PCR Purification Kit (Qiagen).  3g of biotin-labeled cDNA was hybridized to the custom 12K N. gonorrhoeae expression array, according to the CombiMatrix hybridization protocol.  Jackson LA, Dyer D (2012) Protocol for gene expression profiling using DNA microarrays in Neisseria gonorrhoeae. In: MacKenzie CR, editor. Diagnosis of Sexually Transmitted Diseases: Humana Press. pp. 343-357.

growth_protocol: All strains were routinely grown on GCB agar (Becton Dickinson) supplemented with 2% IsoVitale X (Becton Dickinson) from frozen stock cultures under 5% CO2 atmosphere at 37C. Cultures were grown in CDM-0 (Fe-deplete) to OD600 = 0.200 to Fe starve the cells.  Half of the culture was transferred into another 500 ml flask and 62.5 ml of CDM-0 added to each flask to reach 125 ml and Fe(NO3)3 added to the CDM-10 flask for a 10uM final concentration.  The cultures were then allowed to grow to stationary phase in a 37C shaking incubator (225rpm) with cells being collected at 3hr time point for RNA isolation.

extract_protocol: Total RNA was isolated as previously desribed, Jackson LA, Ducey TF, Day MW, Zaitshik JB, Orvis J, et al. (2010) Transcriptional and Functional Analysis of the Neisseria gonorrhoeae Fur Regulon. J Bacteriol 192: 77-85, with the following changes: Total RNA was DNA digested [1U RQ1 RNase-Free DNase per 1g RNA (Promega)] followed by RNA clean-up according to TriReagent protocol (Molecular Research Center, Inc.).  Quantitation was done using the NanoDrop ND-100 (NanoDrop Products) and RNA integrity assessed with Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer

treatment_protocol: Fe-deplete (CDM-0) and Fe-replete medium (CDM-10, supplemented with 10 Fe(NO3)3) were prepared as previously reported. Jackson LA, Ducey TF, Day MW, Zaitshik JB, Orvis J, et al. (2010) Transcriptional and Functional Analysis of the Neisseria gonorrhoeae Fur Regulon. J Bacteriol 192: 77-85


title: Complemented strain_LJ002_Fe+ replicate 3


title: Complemented strain_LJ002_Fe- replicate 3

source_name: Iron depleted growth conditions; cells harvested at 3 hrs


title: Complemented strain_LJ002_Fe- replicate 2


title: NrrF mutant strain_LJ001_Fe+ replicate 3


title: Complemented strain_LJ002_Fe- replicate 1


title: NrrF mutant strain_LJ001_Fe+ replicate 2


title: Complemented strain_LJ002_Fe+ replicate 1


title: NrrF mutant strain_LJ001_Fe- replicate 3


title: NrrF mutant strain_LJ001_Fe+ replicate 1


title: FA1090_Fe+ replicate 2


title: NrrF mutant strain_LJ001_Fe- replicate 2


title: NrrF mutant strain_LJ001_Fe- replicate 1


title: FA1090_Fe+ replicate 3


title: FA1090_Fe+ replicate 1


title: FA1090_Fe- replicate 3


title: FA1090_Fe- replicate 1


title: hippocampus_mutant_rep1


title: VIP3A_24h_rep1

city: Burjassot

first: Agata

middle: K

last: Jakubowska

state: Valencia

address: Dr. Moliner 50

department: Genetics

country: Spain

institute: University of Valencia

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua 24 hrs after treatment with VIP3A toxin
T1_R8_24

hyb_protocol: RNA labeling and hybridization, as well as array scanning and data extraction, were performed according to Agilent protocol, by the Microarray Analysis Service of the Principe Felipe Research Centre (CIPF), Valencia, Spain.

scan_protocol: S. exigua microarray chips were scanned using a G2505B Agilent scanner.

data_processing:
Data were extracted using Agilent Feature Extraction 9.5.1 software.
Arrays were normalized using spike-ins and quantile normalization methods in Babelomics 4.3 software. Normalized signal intensities are given.

organism: Spodoptera exigua

source_name: Spodoptera exigua midgut tissue, VIP3A-treated, 24hr

label_protocol: Agilent One-Color Spike-in Mix was added to the purified RNA and 600 ng of total RNA was used for complimentary RNA (cRNA) synthesis. Fluorescent labeling, fragmentation and hybridization were performed following the One-Color Microarray-Based Gene Expression Analysis (Quick-Amp labeling) protocol from Agilent.

growth_protocol: S. exigua larvae from the FRA colony kindly provided by M. López-Ferber (INRA, St. Christol les Alés, France) [33], were used in the experiments. The colony was reared at 25°C, with a relative humidity of 70%, and a photoperiod of 16 h:8 h (light: dark), on an artificial diet .

extract_protocol: The RNA from S. exigua midguts was purified using RNAzol reagent from Molecular Research Center, Inc. (Cincinnati, OH, USA), and purified using the RNAeasy Kit (Qiagen GmbH, Hilden, Germany) following the protocols provided by the manufacturers. The quality of RNA was assessed with an Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano protocol.

treatment_protocol: To synchronize the insects, late third instar S. exigua larvae (L3) were selected the day before the feeding experiments. The following day, approx. 16 h after the selection, the newly moulted L4 larvae were separated and exposed, individually, to a dose of Vip3Aa that produced a 99% growth inhibition (111 ng/cm2; value obtained from toxicity experiments performed in our laboratory, data not shown). As a control, the filtered supernatant obtained from the E. coli control culture and diluted to the same degree as was required to dilute the Vip3Aa-containing supernatant, was used to feed the larvae. Larvae were exposed to the supplemented food for 8 h and 24 h. After these times, only larvae that had fed (as determined by observing the food bites) were selected for midgut dissection. Midguts of the larvae from each treatment were pooled for further processing.

value: midgut

tag: larval stage

tag: treatment

tag: time


title: Control_rep1

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua
CN_R8

source_name: Spodoptera exigua midgut tissue, non-treated

value: non-treated

value: control


title: Control ONH 6

city: Iowa City

first: Dina

last: Ahram

state: Iowa

address: 375 Newton road

department: Genetics/Opthalmology

institute: UIOWA

description: AMD

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data obtained were subjected to an initial QC analysis through Partek® Genomics Suite™ 6.6 using default program settings. Background adjustment, quantile normalization and mean probe set summarization to genes were performed using the Robust Multichip Average (RMA) algorithm. Normalized data were log2-transformed and filtered to remove non-expressed genes from the data sets. Expressed genes are defined as those represented by probe sets that display log-expression values above 7.0 in at least two samples. Gene expression values are reported in our analysis as the ratios for OHT and glaucoma samples relative to control samples. Differentially expressed gene sets in POAG and OHT versus control samples are identified using an analysis of variance (Djaoued, Robichaud et al.) paired sample t-test with a fold change cut off value of 1.25 and P-value < 0.05.

source_name: Optic Nerve Head

label_protocol: RNA was extracted using Qiagen RNeasy minipreps. RNA was treated with RNase free DNase and its integrity was evaluated using a 2100 BioAnalyzer microfluidics-based platform (Agilent, Palo Alto, CA). 50-100ng total RNA amplified using a T7 RNA polymerase based approach, reverse transcribed, dye labeled and hybridized to Affymetrix Human Exon 1.0 ST array according to the manufacturer’s protocol.

extract_protocol: ONHs were isolated from eyes harvested within six hours post mortem. The anterior portion of the eye and the vitreous were removed from the posterior eyecup. The ONH was excised using a 4mm trephine punch. A 2-3mm long portion of the adjacent optic nerve was included in the isolated material. Visible traces of the RPE and neural retina were removed from the excised ONH to avoid tissue contamination. Collected ONHs were stored at -80°C until RNA extraction.

tag: group

value: Unaffected Control

value: 87 yrs old


title: Control ONH 5

description: Pseudophakia; AMD

value: 90 yrs old


title: VIP3A_24h_rep2

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua 24 hrs after treatment with VIP3A toxin
T1_R9_24


title: FA1090_Fe- replicate 2

value: wild type


title: Control_rep3

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua
CN_R10


title: Control ONH 1

description: Pseudophakia

value: 94 yrs old


title: Control_rep2

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua
CN_R9


title: Control ONH 3

description: Cataract; AMD

value: 83 yrs old


title: VIP3A_8h_rep3

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua 8 hrs after treatment with VIP3A toxin
T1_R10_8

source_name: Spodoptera exigua midgut tissue, VIP3A-treated, 8hr


title: OHT ONH 5

description: C/D ratio 0.25, Max IOP 22;  no meds; AMD

value: Ocular Hypertension

value: 93 yrs old


title: OHT ONH 6

description: C/D ratio 0.5, Max IOP 24; glaucoma suspect;  no meds

value: 91 yrs old


title: OHT ONH 2

description: C/D ratio 0.2, Max IOP 29;  no meds; AMD

value: 89 yrs old


title: POAG ONH 5

description: C/D ratio 0.8; thinning of neuroretinal rims, optic disc palor; Azopt user; AMD

value: Glaucoma Affected


title: OHT ONH 1

description: C/D ratio 0.3, Max IOP 25;  no meds; AMD

value: 86 yrs old


title: Control ONH 4

description: AMD

value: 88 yrs old


title: POAG ONH 6

description: C/D ratio 0.5; Betagan user; AMD

value: 95 yrs old


title: OHT ONH 4

description: C/D ratio 0.2, Max IOP 24;  no meds; AMD

value: 82 yrs old


title: POAG ONH 3

description: C/D ratio 0.8; peripapillary atrophy; Xalatan and betoptic user; AMD


title: POAG ONH 1

description: C/D ratio 0.7, Alphagan user


title: VIP3A_24h_rep3

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua 24 hrs after treatment with VIP3A toxin
T1_R10_24

value: midgut


title: POAG ONH 4

description: C/D ratio 0.85, Travoprost and brimonidine user; AMD


title: VIP3A_8h_rep2

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua 8 hrs after treatment with VIP3A toxin
T1_R9_8


title: OHT ONH 3

description: C/D ratio 0.2, Max IOP 22;  no meds; AMD

value: 84 yrs old


title: Control ONH 2

description: Pseudophakia; AMD

value: Unaffected Control


title: Huh7

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: SentrixID_SentrixPosition: 4835443035_L

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicate bead mesurements were averaged after removing outliers, and normalized DNA methylation level (beta-value) was computed by Genome Studio software (ver.3, Illumina).

label: Cy5 and Cy3

source_name: cell line

extract_protocol: Genomic DNA was extracted by using QIAcube nucleic acid isolation system (Qiagen) according to manufacturer's instruction.

tag: sample type

value: Huh7 cell line


title: VIP3A_8h_rep1

description:
Gene expression in the midgut of L4 larvae of Spodoptera exigua 8 hrs after treatment with VIP3A toxin
T1_R8_8


title: Hep3B

description: SentrixID_SentrixPosition: 4835443035_J

scan_protocol: Refer to the Illumina beadarray Assay System Manual

value: Hep3B cell line


title: HepG2

description: SentrixID_SentrixPosition: 4835443035_K

label_protocol: Refer to the Illumina beadarray Assay System Manual

value: HepG2 cell line


title: NY57

description: SentrixID_SentrixPosition: 4835443035_G

source_name: low-grade dysplastic nodule

value: low-grade dysplastic nodule


title: NY56

description: SentrixID_SentrixPosition: 4835443035_F


title: NY49

description: SentrixID_SentrixPosition: 4835443035_E


title: NY24

description: SentrixID_SentrixPosition: 4835443035_D


title: NY101

description: SentrixID_SentrixPosition: 4835443035_H

source_name: Healthy liver

value: Healthy liver


title: NY102

description: SentrixID_SentrixPosition: 4835443035_I


title: NY10

description: SentrixID_SentrixPosition: 4835443035_C


title: NY36

description: SentrixID_SentrixPosition: 4835443033_F

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: NY55

description: SentrixID_SentrixPosition: 4835443033_L

source_name: high-grade dysplastic nodule

value: high-grade dysplastic nodule


title: B92

description: SentrixID_SentrixPosition: 4835443033_J


title: NY331

description: SentrixID_SentrixPosition: 4835443033_D


title: NY17

description: SentrixID_SentrixPosition: 4835443033_G

source_name: Cirrhosis

value: Cirrhosis


title: NY323

description: SentrixID_SentrixPosition: 4835443033_C


title: NY58

description: SentrixID_SentrixPosition: 4835443035_A


title: NY34

description: SentrixID_SentrixPosition: 4835443033_E


title: NY321

description: SentrixID_SentrixPosition: 4835443033_B


title: NY29

description: SentrixID_SentrixPosition: 4835443033_K


title: NY37

description: SentrixID_SentrixPosition: 4835443033_H


title: NY319

description: SentrixID_SentrixPosition: 4835443033_A


title: NY309

description: SentrixID_SentrixPosition: 4835443036_J


title: NY232

description: SentrixID_SentrixPosition: 4835443036_H


title: NY313

description: SentrixID_SentrixPosition: 4835443036_K


title: NY61

description: SentrixID_SentrixPosition: 4835443035_B


title: NY228

description: SentrixID_SentrixPosition: 4835443036_G


title: NY307

description: SentrixID_SentrixPosition: 4835443036_I


title: NY218

description: SentrixID_SentrixPosition: 4835443036_D


title: NY226

description: SentrixID_SentrixPosition: 4835443036_F


title: NY222

description: SentrixID_SentrixPosition: 4835443036_E


title: NY208

description: SentrixID_SentrixPosition: 4835443036_C


title: NY204

description: SentrixID_SentrixPosition: 4835443036_A


title: NY206

description: SentrixID_SentrixPosition: 4835443036_B


title: NY18

description: SentrixID_SentrixPosition: 4835443032_K


title: Silkworm_Nb8d-3_vs_C8d

city: Chongqing

first: Tian

last: Li

address: Beibei District Tiansheng Road #2

department: State Key Laboratory of Silkworm Genome Biology

institute: Southwest University

description: Biological replicate 3 of 3 at 8dpi

hyb_protocol: Cy5-dCTP for test samples and Cy3-dCTP for reference samples labeled double-stranded cDNA dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.)

data_processing:
The raw data were extracted from imagines using LuxScan™ 3.0 software (CapitalBio Corp.)
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. The software from CapitalBio Crop was used.

organism: Bombyx mori

source_name: N. bombycis infected silkworm larvae at 8 days post infection

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: Silkworm larvae (p50 strain) maintained at the National Engineering Laboratory for Modern Silk (Soochow University, China) were reared on mulberry leaves at 25°C-26°C

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

treatment_protocol: Silkworm larvae were placed in a petri dish without food to maintain hunger before infection. N. bombycis spores were washed three times with distilled water. Approximately 600 μl of the spore solution and 6 grams of the artificial diet were thoroughly mixed in a plate. The mixture was then cut into fine grains and given to the hungry silkworms. Four duplicates were simultaneously performed. The larvae were raised at 25 ℃ with approximately 70% humidity and for approximately 5 hours before the larvae consumed the spore. After silkworm larvae were fed 5×104 spores per larva, samples from infected larvae (i.e., the treatment set) and uninfected larvae (i.e., the control set) were collected at 2, 4, 6, and 8 dpi.

tag: developmental stage

value: larval

value: whole body

value: Dazao (P50)

tag: infection

value: Nosema bombycis

source_name: Corresponding control silkworm

value: control


title: M98

description: SentrixID_SentrixPosition: 4835443032_J


title: Silkworm_Nb8d-2_vs_C8d

description: Biological replicate 2 of 3 at 8dpi


title: M94

description: SentrixID_SentrixPosition: 4835443032_H


title: Silkworm_Nb8d-1_vs_C8d

description: Biological replicate 1 of 3 at 8dpi


title: M96

description: SentrixID_SentrixPosition: 4835443032_I


title: M92

description: SentrixID_SentrixPosition: 4835443032_G


title: Silkworm_Nb4d-3_vs_C4d

description: Biological replicate 3 of 3 at 4dpi

source_name: N. bombycis infected silkworm larvae at 4 days post infection


title: Silkworm_Nb6d-2_vs_C6d

description: Biological replicate 2 of 3 at 6dpi

source_name: N. bombycis infected silkworm larvae at 6 days post infection


title: M81

description: SentrixID_SentrixPosition: 4835443032_D


title: M90

description: SentrixID_SentrixPosition: 4835443032_F


title: M53

description: SentrixID_SentrixPosition: 4835443032_C


title: Silkworm_Nb6d-1_vs_C6d

description: Biological replicate 1 of 3 at 6dpi


title: Silkworm_Nb2d-3_vs_C2d

description: Biological replicate 3 of 3 at 2dpi

source_name: N. bombycis infected silkworm larvae at 2 days post infection


title: M17

description: SentrixID_SentrixPosition: 4835443032_B


title: Silkworm_Nb4d-2_vs_C4d

description: Biological replicate 2 of 3 at 4dpi


title: Silkworm_Nb6d-3_vs_C6d

description: Biological replicate 3 of 3 at 6dpi


title: M88

description: SentrixID_SentrixPosition: 4835443032_E


title: M104

description: SentrixID_SentrixPosition: 4831231029_K


title: Silkworm_Nb2d-2_vs_C2d

description: Biological replicate 2 of 3 at 2dpi


title: B94

description: SentrixID_SentrixPosition: 4831231029_H


title: B96

description: SentrixID_SentrixPosition: 4831231029_I


title: M106

description: SentrixID_SentrixPosition: 4831231029_L


title: M15

description: SentrixID_SentrixPosition: 4835443032_A


title: B90

description: SentrixID_SentrixPosition: 4831231029_G


title: Silkworm_Nb4d-1_vs_C4d

description: Biological replicate 1 of 3 at 4dpi


title: B88

description: SentrixID_SentrixPosition: 4831231029_F


title: B84

description: SentrixID_SentrixPosition: 4831231029_D


title: B76

description: SentrixID_SentrixPosition: 4831231030_L


title: B82

description: SentrixID_SentrixPosition: 4831231029_C


title: B72

description: SentrixID_SentrixPosition: 4831231030_K


title: B86

description: SentrixID_SentrixPosition: 4831231029_E


title: B78

description: SentrixID_SentrixPosition: 4831231029_A


title: B29

description: SentrixID_SentrixPosition: 4831231030_E


title: Silkworm_Nb2d-1_vs_C2d

description: Biological replicate 1 of 3 at 2dpi


title: B35

description: SentrixID_SentrixPosition: 4831231030_H


title: B68

description: SentrixID_SentrixPosition: 4831231030_I


title: B33

description: SentrixID_SentrixPosition: 4831231030_G


title: B70

description: SentrixID_SentrixPosition: 4831231030_J


title: B13

description: SentrixID_SentrixPosition: 4831231030_A


title: NY317

description: SentrixID_SentrixPosition: 4835443036_L


title: B80

description: SentrixID_SentrixPosition: 4831231029_B


title: B19

description: SentrixID_SentrixPosition: 4831231030_C


title: B17

description: SentrixID_SentrixPosition: 4831231030_B


title: B25

description: SentrixID_SentrixPosition: 4831231030_D


title: B31

description: SentrixID_SentrixPosition: 4831231030_F


title: NY65

description: SentrixID_SentrixPosition: 4697036021_A


title: NY96

description: SentrixID_SentrixPosition: 4697036021_E


title: NY99

description: SentrixID_SentrixPosition: 4697036021_G


title: POAG ONH 2

description: C/D ratio 0.7, Alphagan user

value: Glaucoma Affected

value: 89 yrs old


title: NY82

description: SentrixID_SentrixPosition: 4697036021_C


title: Blood_Control_16_time-point T3

city: Kingston

first: Colin

middle: D.

last: Funk

state: Ontario

address: 18 Stuart Street

department: Biomedical and Molecular Sciences

institute: Queen's University

description: Gene expression in blood of Control 16 24 hrs after exercise

hyb_protocol: Labeled RNA was hybridized to Agilent whole genome expression array (4x44K) at 65°C for 17h in rotisserie in a hybridization oven. Disassembled arrays were washed in GE wash buffer 1&2 for 1 minutes each.

scan_protocol: Images were scanned with Agilent scanner at 5µm resolution.

data_processing: Raw data obtained from the microarrays were imported into Nexus Expression 3.0 (BioDiscovery Inc, Hawthorne, CA, USA) and processed according to the default settings of the software, which included a local background correction, removal of flagged spots and performing quantile normalization.

source_name: Whole blood, Control 16, 24 hrs after exericse

label_protocol: Total RNA (200 ng) from each sample was spiked with One-Color RNA Spike-In Kit reagents (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.Subsequent amplification and labeling of the samples to generate fluorescent cRNA (complimentary RNA) were carried out using the One-Color Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.Labeled cRNA was purified using an RNeasy Mini kit (Qiagen). Only cRNA samples with a yield >1.65 µg, and a specific activity >9 pmol Cy3/µg cRNA were used for subsequent hybridization onto microarray slides.

extract_protocol: RNA was isolated from blood sample aliquots (2.5 ml) using a PAXgene blood RNA kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol. Residual DNA was removed with DNase I treatment, according to the manufacturer’s instructions (Qiagen GmbH, Hombrechtikon, Germany). The quality of the isolated RNA was checked with Agilent RNA 6000 Nano Assay kit reagents using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with a RNA Integrity Number (RIN) of 7.0 or higher were used for further analysis. The RNA samples were quantified using a standard Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA).

treatment_protocol: Whole blood samples for each participant were stored in PAXgene blood RNA tubes (Qiagen GmbH, Germany) at -80 °C from all three time-points until further analysis.

value: Whole blood

value: Male

tag: subject

tag: time point

value: 24 hrs after exercise


title: Blood_Control_17_time-point T3

description: Gene expression in blood of Control 17 24 hrs after exercise

source_name: Whole blood, Control 17, 24 hrs after exericse


title: NY329

description: SentrixID_SentrixPosition: 4697036020_J


title: NY327

description: SentrixID_SentrixPosition: 4697036020_H


title: Blood_Control_11_time-point T3

description: Gene expression in blood of Control 11 24 hrs after exercise

source_name: Whole blood, Control 11, 24 hrs after exericse


title: Blood_Control_14_time-point T2

description: Gene expression in blood of Control 14 immediately after exercise

source_name: Whole blood, Control 14, immediately after exericse

value: immediately after exercise


title: Blood_Control_11_time-point T2

description: Gene expression in blood of Control 11 immediately after exercise

source_name: Whole blood, Control 11, immediately after exericse


title: NY39

description: SentrixID_SentrixPosition: 4697036020_L


title: NY311

description: SentrixID_SentrixPosition: 4697036020_D


title: Blood_Control_18_time-point T2

description: Gene expression in blood of Control 18 immediately after exercise

source_name: Whole blood, Control 18, immediately after exericse


title: NY310

description: SentrixID_SentrixPosition: 4697036010_K


title: NY223

description: SentrixID_SentrixPosition: 4697036010_I


title: NY326

description: SentrixID_SentrixPosition: 4697036010_B


title: Blood_Control_12_time-point T2

description: Gene expression in blood of Control 12 immediately after exercise

source_name: Whole blood, Control 12, immediately after exericse


title: Blood_Control_17_time-point T1

description: Gene expression in blood of Control 17 before exercise

source_name: Whole blood, Control 17, before exericse

value: before exercise


title: Blood_Control_16_time-point T2

description: Gene expression in blood of Control 16 immediately after exercise

source_name: Whole blood, Control 16, immediately after exericse


title: Blood_Control_17_time-point T2

description: Gene expression in blood of Control 17 immediately after exercise

source_name: Whole blood, Control 17, immediately after exericse


title: NY107

description: SentrixID_SentrixPosition: 4697036021_J

source_name: Healthy liver


title: NY108

description: SentrixID_SentrixPosition: 4697036021_L


title: 25mg/kg Sample 9

city: Ottawa

first: Sarah

last: Labib

address: 204b-50 Colombine

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations.  Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Male MutaTMMouse, aged 24-26 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine forestomachs were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 6.6.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of BaP dissolved in olive oil were selected to dose the animals: 25 mg/kg BW, 50 mg/kg BW, and 75 mg/kg BW.  Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: MutaTMMouse

value: Forestomach

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: Blood_Athlete_4_time-point T3

description: Gene expression in blood of Athlete 4 24 hrs after exercise

source_name: Whole blood, Athlete 4, 24 hrs after exericse

value: athlete


title: Blood_Control_18_time-point T3

description: Gene expression in blood of Control 18 24 hrs after exercise

source_name: Whole blood, Control 18, 24 hrs after exericse


title: NY325

description: SentrixID_SentrixPosition: 4697036020_F

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: Blood_Control_13_time-point T2

description: Gene expression in blood of Control 13 immediately after exercise

source_name: Whole blood, Control 13, immediately after exericse


title: Blood_Control_18_time-point T1

description: Gene expression in blood of Control 18 before exercise

source_name: Whole blood, Control 18, before exericse


title: Blood_Control_16_time-point T1

description: Gene expression in blood of Control 16 before exercise

source_name: Whole blood, Control 16, before exericse


title: Blood_Control_11_time-point T1

description: Gene expression in blood of Control 11 before exercise

source_name: Whole blood, Control 11, before exericse


title: NY328

description: SentrixID_SentrixPosition: 4697036010_D

source_name: Cirrhosis

value: Cirrhosis


title: 75 mg/kg Sample 20

source_name: 75 mg/kg


title: Blood_Athlete_1_time-point T3

description: Gene expression in blood of Athlete 1 24 hrs after exercise

source_name: Whole blood, Athlete 1, 24 hrs after exericse


title: NY104

description: SentrixID_SentrixPosition: 4697036021_F

value: Healthy liver


title: Blood_Athlete_7_time-point T2

description: Gene expression in blood of Athlete 7 immediately after exercise

source_name: Whole blood, Athlete 7, immediately after exericse


title: Blood_Athlete_9_time-point T2

description: Gene expression in blood of Athlete 9 immediately after exercise

source_name: Whole blood, Athlete 9, immediately after exericse


title: Blood_Athlete_2_time-point T3

description: Gene expression in blood of Athlete 2 24 hrs after exercise

source_name: Whole blood, Athlete 2, 24 hrs after exericse


title: NY224

description: SentrixID_SentrixPosition: 4697036020_B


title: Blood_Athlete_6_time-point T2

description: Gene expression in blood of Athlete 6 immediately after exercise

source_name: Whole blood, Athlete 6, immediately after exericse


title: M80

description: SentrixID_SentrixPosition: 4697036010_G


title: Blood_Athlete_5_time-point T2

description: Gene expression in blood of Athlete 5 immediately after exercise

source_name: Whole blood, Athlete 5, immediately after exericse


title: NY103

description: SentrixID_SentrixPosition: 4697036021_D

source_name: Healthy liver


title: NY106

description: SentrixID_SentrixPosition: 4697036021_H


title: M79

description: SentrixID_SentrixPosition: 4697036020_I


title: Blood_Athlete_3_time-point T2

description: Gene expression in blood of Athlete 3 immediately after exercise

source_name: Whole blood, Athlete 3, immediately after exericse


title: Control Sample 5

source_name: vehicle control

source_name: Universal Mouse Reference RNA


title: M67

description: SentrixID_SentrixPosition: 4697036020_E

source_name: hepatocellular carcinoma


title: M69

description: SentrixID_SentrixPosition: 4697036020_G


title: 50mg/kg Sample 15


title: Blood_Athlete_1_time-point T2

description: Gene expression in blood of Athlete 1 immediately after exercise

source_name: Whole blood, Athlete 1, immediately after exericse


title: Blood_Athlete_2_time-point T2

description: Gene expression in blood of Athlete 2 immediately after exercise

source_name: Whole blood, Athlete 2, immediately after exericse


title: Blood_Athlete_4_time-point T2

description: Gene expression in blood of Athlete 4 immediately after exercise

source_name: Whole blood, Athlete 4, immediately after exericse


title: Blood_Athlete_4_time-point T1

description: Gene expression in blood of Athlete 4 before exercise

source_name: Whole blood, Athlete 4, before exericse


title: Control Sample 4


title: 75 mg/kg Sample 19


title: Blood_Athlete_3_time-point T3

description: Gene expression in blood of Athlete 3 24 hrs after exercise

source_name: Whole blood, Athlete 3, 24 hrs after exericse


title: 50mg/kg Sample 14


title: 50mg/kg Sample 13


title: Blood_Athlete_3_time-point T1

description: Gene expression in blood of Athlete 3 before exercise

source_name: Whole blood, Athlete 3, before exericse


title: M12

description: SentrixID_SentrixPosition: 4697036010_E

source_name: Cirrhosis


title: Blood_Athlete_1_time-point T1

description: Gene expression in blood of Athlete 1 before exercise

source_name: Whole blood, Athlete 1, before exericse


title: B98

description: SentrixID_SentrixPosition: 4697036010_J


title: Blood_Athlete_2_time-point T1_rep2

description: Gene expression in blood of Athlete 2 before exercise, replicate 2

source_name: Whole blood, Athlete 2, before exericse, replicate 2


title: M35

description: SentrixID_SentrixPosition: 4697036020_C


title: 25mg/kg Sample 7


title: 75 mg/kg Sample 18

source_name: 75 mg/kg


title: M11

description: SentrixID_SentrixPosition: 4697036020_A


title: Blood_Athlete_2_time-point T1_rep1

description: Gene expression in blood of Athlete 2 before exercise, replicate 1

source_name: Whole blood, Athlete 2, before exericse, replicate 1


title: 25mg/kg Sample 6


title: 50mg/kg Sample 12


title: Control Sample 3


title: Control Sample 2


title: B97

description: SentrixID_SentrixPosition: 4697036010_C


title: 25mg/kg Sample 8


title: 75 mg/kg Sample 17


title: Control Sample 1


title: B74

description: SentrixID_SentrixPosition: 4697036010_H


title: B45

description: SentrixID_SentrixPosition: 4697036021_I


title: CPE-human-6

city: Amsterdam

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

country: Netherlands

institute: Netherlands Institute for Neuroscience

description:
reference ch2: tissue: RPE/chodoid, Cy3
CPE replicate 6 of 7 of healthy human choroid plexus

hyb_protocol: Labeled human CPE RNA and labeled human common reference sample were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner, protocol GE2-v5_95_Fec07

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files.
Further data processing was done in R (version 2.14.0 for Windows, R Development Core Team, 2009), with package Limma. We read in the raw data (RG <-read.maimage). Next, we normalized within arrays (method 'loess', resulating in MA) and between arrays (method aquantile). In the matrix table, we listed these normalized red channels of each human CPE sample (log2).

source_name: healthy human choroid plexus

label_protocol: aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier.

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Qiagen Benelux, Venlo, The Netherlands). Subsequently, the mRNA component was amplified with Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion Applied Biosystems Europe B.V.).

treatment_protocol: With laser dissection microscopy, the CPE cells were specifically cut out from cryosections of the choroid plexus (10um) mounted on PEN-membrane slides

value: choroid plexus epithelium

tag: cell sampling

value: laser dissection microscopy


title: B66

description: SentrixID_SentrixPosition: 4697036010_F


title: B73

description: SentrixID_SentrixPosition: 4697036010_A


title: genomic DNA from adult normal liver A [X104052_NORMAL.A]

city: Stony Brook

first: Jinyu

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

description: normal liver

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
matrix signal intensities value definition: Unmethylated and methylated signal intensities

source_name: genomic DNA from adult normal liver A

label_protocol: Standard Illumina Protocol

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

value: unknown

value: adult normal liver

tag: tissue source

value: UCLA


title: CPE-human-5

description:
reference ch2: tissue: RPE/chodoid, Cy3
CPE replicate 5 of 7 of healthy human choroid plexus


title: CPE-human-7

description:
reference ch2: tissue: RPE/chodoid, Cy3
CPE replicate 7 of 7 of healthy human choroid plexus


title: M102

description: SentrixID_SentrixPosition: 4697036010_L


title: genomic DNA from adult normal liver D [X104055_NORMAL.D]

description: normal liver

source_name: genomic DNA from adult normal liver D


title: genomic DNA from adult normal liver G [X104058_NORMAL.G]

description: normal liver

source_name: genomic DNA from adult normal liver G


title: CPE-human-3

description:
reference ch2: tissue: RPE/chodoid, Cy3
CPE replicate 3 of 7 of healthy human choroid plexus


title: CPE-human-2

description:
reference ch2: tissue: RPE/chodoid, Cy3
CPE replicate 2 of 7 of healthy human choroid plexus


title: genomic DNA from adult normal liver C [X104054_NORMAL.C]

description: normal liver

source_name: genomic DNA from adult normal liver C


title: siAgo1 repeat

city: San Francisco

first: Vera

last: Huang

address: 1450 Third Street, Helen Diller Cancer Research Building, Room 302

department: Urology

institute: UCSF

description: Ago1 siRNA transfection

hyb_protocol: Hybridization, washes, and scanning were performed by following the GeneChip Expression Analysis Technical Manual 702232 Rev. 3

scan_protocol: GeneChip scanner GCS3000

data_processing: Affymetrix GeneChip Command Console.  Version 3.2.2. RMA

source_name: PC-3 cells

label_protocol: Ovation Pico WTA V2 & Encore Biotin Module (NuGen) were used to prepare probes for hybridization to Affymetrix GeneChip Human Gene 1.0 ST Arrays

growth_protocol: PC-3 cells cultured at exponential phase

extract_protocol: Total cellular RNA was isolated using RNeasy kit. The resulting total RNA concentration and quality were assessed by the Agilent™ Bioanalyzer

treatment_protocol: PC-3 cells were mock transfected or transfected with a pool of control siRNAs (siControl) or Ago1 siRNAs (siAgo1) at 10 nM total concentration for 48 hrs

tag: cell line


title: genomic DNA from adult normal liver B [X104053_NORMAL.B]

description: normal liver

source_name: genomic DNA from adult normal liver B

tag: disease state


title: genomic DNA adjacent tissue [0846-03D_N12]

description: diseased liver

source_name: genomic DNA adjacent tissue

value: adjacent liver

value: CHTN


title: Mock

description: Mock transfection

value: Mock


title: genomic DNA adjacent tissue [0846-03H_N14]

description: diseased liver

value: Male


title: siControl

description: Control siRNA transfection

value: siControl


title: Mock repeat

description: Mock transfection


title: genomic DNA HCC tissue [0846-03C_T12]

description: diseased liver

source_name: genomic DNA HCC tissue

value: HCC


title: siControl repeat

description: Control siRNA transfection


title: genomic DNA from adult normal liver H [X104059_NORMAL.H]

description: normal liver

source_name: genomic DNA from adult normal liver H


title: 221MDAI2_MyoDwtSmoA2

city: Seattle

first: James

middle: M

last: Olson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: brain tumor, MyoD +/+;SmoA2, end-stage

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities were quantile normalized using the Bioconductor package “lumi”

source_name: medulloblastoma

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

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

value: medulloblastoma

tag: genotype

value: MyoD +/+;SmoA2


title: genomic DNA HCC tissue [0846-03G_T14]

description: diseased liver


title: genomic DNA adjacent tissue [0846-03B_N11]

description: diseased liver


title: 221MDP7_MyoDHetSmoA2

description: brain tumor, MyoD +/-;SmoA2, end-stage

tag: tissue

value: MyoD +/-;SmoA2


title: genomic DNA adjacent tissue [0846-02H_N10]

description: diseased liver

value: Female


title: 221MDV7_MyoDwtSmoA2

description: brain tumor, MyoD +/+;SmoA2, end-stage


title: 221MDV3_MyoDHetSmoA2

description: brain tumor, MyoD +/-;SmoA2, end-stage


title: genomic DNA adjacent tissue [0846-03F_N13]

description: diseased liver


title: CPE-human-1

description:
reference ch2: tissue: RPE/chodoid, Cy3
CPE replicate 1 of 7 of healthy human choroid plexus


title: genomic DNA from adult normal liver F [X104057_NORMAL.F]

description: normal liver

source_name: genomic DNA from adult normal liver F


title: genomic DNA HCC tissue [0884-01D_T13]

description: diseased liver


title: 221MDP5_MyoDwtSmoA2

description: brain tumor, MyoD +/+;SmoA2, end-stage


title: CPE-human-4

description:
reference ch2: tissue: RPE/chodoid, Cy3
CPE replicate 4 of 7 of healthy human choroid plexus


title: genomic DNA HCC tissue [0846-03A_T11]

description: diseased liver


title: genomic DNA HCC tissue [0846-02G_T10]

description: diseased liver


title: genomic DNA adjacent tissue [0846-02F_N9]

description: diseased liver


title: CPE-mouse-1

description:
reference ch2: tissue: RPE/chodoid
reference ch2: strain: C57BL/6, Cy3
CPE replicate 1 of 3 of healthy mouse choroid plexus

hyb_protocol: Labeled mouse CPE RNA and labeled mouse common reference sample were applied to microarrays slides enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner, protocol GE2-v4_95_Feb07 for mouse data

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files.
Further data processing was done in R (version 2.14.0 for Windows, R Development Core Team, 2009), with package Limma. We read in the raw data (RG <-read.maimage). Next, we normalized the data within arrays (method 'loess', resulating in MA) and between arrays (method aquantile). In the matrix table, we listed these normalized red channels of each mouse CPE sample (log2).

source_name: healthy mouse choroid plexus

growth_protocol: not applicable

treatment_protocol: With laser dissection microscopy, the CPE cells were specifically cut out from cryosections of the whole brain (20 um) mounted on PEN-membrane slides

tag: strain


title: CPE-mouse-3

description:
reference ch2: tissue: RPE/chodoid
reference ch2: strain: C57BL/6, Cy3
CPE replicate 3 of 3 of healthy mouse choroid plexus


title: ESC shDnmt3L2 rep2

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

hyb_protocol: Direct Hybridization of RNA library was performed using Standard Operating Procedures in Whole-Genome Gene Expression Direct Hybridization Assay Guide (Illumina)

scan_protocol: Chips were scanned using Illumina HiScan software

data_processing: Data were normalized using quantile normalization and background subtraction by default parameters in Illumina Genome Studio (V.2011.1) Module Gene Expression (V.1.9.0).

label_protocol: RNA library were performed using Illumina Total Prep RNA Amplification Kit following the manufacturing protocol

growth_protocol: Embryonic stem cells were cultured in DMEM high glucose medium (Invitrogen) supplemented with 15% FBS (Millipore), 0.1mM nonessential amino acids (Invitrogen), 1mM sodium pyruvate (Invitrogen), 0.1mM 2-mercaptoethanol, 1500U/ml LIF (Millipore), 25 U of penicillin/ml, and 25 µg of streptomycin/ml.

extract_protocol: RNA was extracted using TRIzol reagent from Invitrogen.

treatment_protocol: Cells were transfected with shRNAs and selected with Puromicin for 3 days before RNA extraction

tag: cell type

value: E14 embryonic stem cells

tag: transfected with


title: ESC shDnmt3L3 rep1


title: genomic DNA HCC tissue [0846-02E_T9]

description: diseased liver

tag: gender


title: ESC shDnmt3L3 rep2


title: CPE-mouse-2

description:
reference ch2: tissue: RPE/chodoid
reference ch2: strain: C57BL/6, Cy3
CPE replicate 2 of 3 of healthy mouse choroid plexus


title: genomic DNA adjacent tissue [0846-02B_N7]

description: diseased liver


title: ESC shDnmt3L1 rep2


title: siAgo1

description: Ago1 siRNA transfection

tag: treatment


title: Chop-/- PBS #3

first: David

middle: Thomas

last: Rutkowski

state: IA

address: 51 Newton Rd.

department: Anatomy and Cell Biology

institute: University of Iowa Carver College of Medicine

hyb_protocol: 750ng of this product were mixed with Illumina hybridization buffer, placed onto Illumina mouseRef8 v2 BeadChips (Part No. BD-202-0202), and incubated at 58º C for 17h, with rocking, in an Illumina Hybridization Oven.  Following hybridization, the arrays were washed, blocked, then stained with streptavidin-Cy3 (Amersham/GE Healthcare, Piscataway, NJ) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.

scan_protocol: Beadchips were scanned with the Illumina iScan System (ID #N054)

data_processing: Data were collected using the GenomeStudio software v2011.1. Default parameters within GenomeStudio were used.

source_name: whole liver RNA 9 months old

label_protocol: 100 nanograms total RNA was converted to amplified Biotin-aRNA  using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924) according to the manufacturer’s recommended protocol. The amplified Biotin-aRNA  product was purified through a QIAGEN RNeasy MinElute  Cleanup column (QIAGEN Cat #74204) according to modifications from Epicentre.

extract_protocol: Resected livers or liver tumors were flash frozen in liquid nitrogen. Total RNA was extracted from frozen material using Trizol.

value: male

value: Chop-/-

value: whole liver

value: PBS


title: ESC shGFP rep2

value: shGFP


title: Chop-/- DEN #5

value: 25 mg/kg DEN


title: wild-type DEN #6

value: wild-type


title: Chop-/- DEN #6


title: ESC shDnmt3L2 rep1


title: Chop-/- DEN tumor #2

source_name: liver tumor RNA 9 months old

value: liver tumor


title: ESC shDnmt3L1 rep1


title: ESC shGFP rep1


title: genomic DNA HCC tissue [0846-02C_T8]

description: diseased liver

value: CHTN


title: genomic DNA adjacent tissue [0884-01C_N8]

description: diseased liver

value: adjacent liver


title: mouse embryo-E5_cultured in Wide_rep3

city: Izumi

first: Isao

last: Matsuo

address: 840 Murodo-cho

department: Department of Molecular Embryology

institute: Osaka Medical Center and Research Institute for Maternal and Child Health

description: Gene expression data from E5 mouse embryos cultured in the wide cavity for 8 hours

hyb_protocol: Performed according to the manufacturer's (Affymetrix) recommendations

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

data_processing: Raw intensities from the CEL files were analyzed using Agilent GeneSpring GX Version 11.5.1

source_name: mouse embryo, E5, cultured in wide cavity, 8hours

label_protocol: Samples were labeled with biotin using GeneChip WT Terminal Labeling Kit

growth_protocol: Animals were housed under spf conditions.

extract_protocol: Total RNA was isolated using Rneasy Plus Micro Kit (Qiagen, Valencia, CA). RNA concentrations were measured using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA). RNA quality was analyzed with RNA 6000 Pico Kit and Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA).

treatment_protocol: Embryos were collected at E5.0 and cultured in the narrow and wide cavity for 8 hours under 37C and 5% CO2. After culture, 30 embryos per 1 sample were collected and dissolved in Buffer RLT Plus (Rneasy Plus Micro Kit, Qiagen)

value: cultured in wide cavity

value: whole embryo


title: genomic DNA adjacent tissue [0846-01H_N6]

description: diseased liver

value: Male


title: genomic DNA HCC tissue [0846-02A_T7]

description: diseased liver

value: HCC


title: Chop-/- DEN #7


title: genomic DNA adjacent tissue [0846-01F_N5]

description: diseased liver


title: genomic DNA HCC tissue [0884-01B_T6]

description: diseased liver


title: DeltaBcLTF1_Light_r3

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, subjected to a light stimulation. It is the third of four deltaBcLTF1_light (Delta_L) biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization on microarrays were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche)  and the reagents from Invitrogen (Life technologies, France).

scan_protocol: Scanning was performed by PartnerChip (http://www.partnerchip.fr/) using NimbleScan.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS website (http://anais.versailles.inra.fr/).

organism: Botrytis cinerea

source_name: Botrytis cinerea B0510_deltaBcLTF1

label_protocol: Synthesis of double-stranded cDNA and Cy3-labeling were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)

growth_protocol: Wild type B05.10 and the deltaBcLTF1 mutant were grown for 3 days on solid CM before non-sporulating mycelia were transferred to solid CM covered with cellophane overlays. Cultures were incubated for 52 h in darkness, and then half of the cultures were transferred to white light. After 60 min all four cultures (WT-D; WT-L; deltaBcLTF1-D; deltaBcLTF1-L) were harvested.

extract_protocol: Total RNA was extracted using the Trizol procedure. Total RNA was treated with the DNA-free kit to remove any trace of DNA (Ambion - Applied Biosystems, France).

value: Mutant deltaBcLTF1

tag: light treatment

value: Light


title: DeltaBcLTF1_Light_r4

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, subjected to a light stimulation. It is the fourth of four deltaBcLTF1_light (Delta_L) biological replicates used in this experiment, each from separate cultures.


title: mouse embryo-E5_cultured in Wide_rep2


title: DeltaBcLTF1_Light_r2

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, subjected to a light stimulation. It is the second of four deltaBcLTF1_light (Delta_L) biological replicates used in this experiment, each from separate cultures.


title: Chop-/- DEN tumor #1


title: DeltaBcLTF1_Light_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, subjected to a light stimulation. It is the first of four deltaBcLTF1_light (Delta_L) biological replicates used in this experiment, each from separate cultures.


title: wild-type DEN #5


title: wild-type PBS #3


title: mouse embryo-E5_cultured in Narrow_rep3

description: Gene expression data from E5 mouse embryos cultured in the narrow cavity for 8 hours

source_name: mouse embryo, E5, cultured in narrow cavity, 8hours

value: cultured in narrow cavity


title: genomic DNA adjacent tissue [0884-01A_N3]

description: diseased liver


title: genomic DNA from adult normal liver E [X104056_NORMAL.E]

description: normal liver

source_name: genomic DNA from adult normal liver E

value: unknown

value: adult normal liver

value: UCLA


title: genomic DNA HCC tissue [0846-01C_T3]

description: diseased liver


title: DeltaBcLTF1_Dark_r2

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, cultured in darkness. It is the second of four deltaBcLTF1_dark (Delta_D) biological replicates used in this experiment, each from separate cultures.

value: Dark


title: DeltaBcLTF1_Dark_r4

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, cultured in darkness. It is the fourth of four deltaBcLTF1_dark (Delta_D) biological replicates used in this experiment, each from separate cultures.


title: genomic DNA HCC tissue [0846-01A_T2]

description: diseased liver

value: Female


title: genomic DNA adjacent tissue [0846-01B_N2]

description: diseased liver


title: mouse embryo-E5_cultured in Wide_rep1


title: DeltaBcLTF1_Dark_r3

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF1, cultured in darkness. It is the third of four deltaBcLTF1_dark (Delta_D) biological replicates used in this experiment, each from separate cultures.


title: Chop-/- PBS #2

value: male

value: Chop-/-

value: whole liver

value: PBS


title: mouse embryo-E5_cultured in Narrow_rep1


title: mouse embryo-E5_cultured in Narrow_rep2