title: F4/80lowPMO_co-infected_day14/5_rep1


title: F4/80lowPMO_SL3261_day5_rep3

status: Public on Feb 14 2017

type: RNA

city: Manchester

first: Dominik

middle: Andreas

last: Rückerl

address: Oxford Road

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: The University of Manchester

description: Gene expression data from bacterial infection induced, recruited, blood monocyte derived macrophages

hyb_protocol: 5.5 ug of fragmented and labeled sscDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 with the following options: probesets were quantile normalised and RMA background correction applied. Probesets were summarised to genes by calculating the means (log 2).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: F4/80 low peritoneal macrophages from Salmonella Typhimurium (SL3261) infected C57BL/6 females 5 d.p.i.

label_protocol: Total RNA (10 ng) were converted to cDNA, fragmented and biotinylated using the GeneChip WT Pico Reagent kit (Affymetrix)  following the manufacturer's instruction.

growth_protocol: C57BL/6 female mice, aged approx 7-10 weeks at the start of the experiment housed in IVC cages under SPF conditions.

extract_protocol: Total RNA were extracted using the RNeasy Mini Kit (Qiagen) as described by the manufacturer.

treatment_protocol: Animals were infected with 200 L3 H.polygyrus and 9 days post infection co-infected with 3x10^4 cfu Salmonella Typhimurium (SL3261) and peritoneal macrophages analysed 5 days later (Day 14 p. H.polygyrus infection). As control uninfected (naïve) or single H.polygyrus / Salmonella Typhimurium infected animals were used. Whole peritoneal cells were isolated by peritoneal lavage and F4/80 high / low macrophages sorted by flow cytometry (CD19-TCRb-, SiglecF-, Ly6G-, CD11b+, CD115+, F4/80 high / low)

tag: tissue

value: peritoneal cavity

tag: strain

tag: Sex

value: female

tag: cells

value: F4/80 low macrophages

tag: infection


title: F4/80highPMO_co-infected_day14/5_rep4

description: Gene expression data from helminth expanded tissue resident macrophages remaining in the cavity after co-infection

source_name: F4/80 high peritoneal macrophages from Heligmosomoides polygyrus / Salmonella Typhimurium (SL3261) consecutively co-infected C57BL/6 females 14 / 5 d.p.i.

value: F4/80 high macrophages

value: co-infected


title: 48h infected replicate2

city: Pretoria

first: Bianca

last: Reeksting

address: 117 Lunnon Road

department: Department of Genetics

country: South Africa

institute: University of Pretoria

description: Biological replicate 2 of 3:48h infected

hyb_protocol: Hybridization was carried out according to the two-colour microarray-based gene expression analysis protocol (Agilent)

scan_protocol: Microarray slides were scanned using the Axon GenePix 400B scanner (Molecular devices)

data_processing: Axon GenePix6.0 software was used for image analysis. Normalization and statistical analysis was carried out in the R environment

organism: Persea americana

source_name: Root_48h infected

label_protocol: 4-6ug of RNA was transcribed into single stranded cDNA priming with random nonamer and oligo(dt) primers, using the Superscript III Reverse transcriptase. Samples labelled with Cy5 and References with Cy3 (CyDye Post-Labelling Reactive Dye Pack, GE Healthcare Life Sciences)

growth_protocol: Plants were grown under greenhouse conditions in 2l containers in soil-perlite mix (1:1)

extract_protocol: Total RNA extracted using phenol chloroform extraction

treatment_protocol: Split into one of four groups: control, flooded, infected, combination treatment

value: root

tag: rootstock

value: Dusa

tag: time-point

value: 48 hours

source_name: pooled reference

tag: reference type

value: Reference pool (0h, 8h, 22h, 48h, 96h, 7d)


title: 48h control replicate3

description: Biological replicate 3 of 3:48h control

source_name: Root_48h control


title: F4/80highPMO_co-infected_day14/5_rep3


title: 48h control replicate2

description: Biological replicate 2 of 3:48h control


title: 48h flooded replicate3

description: Biological replicate 3 of 3:48h flooded

source_name: Root_48h flooded


title: 48h flooded and infected replicate2

description: Biological replicate 2 of 3:48h flooded and infected

source_name: Root_48h flooded and infected


title: 48h flooded replicate2

description: Biological replicate 2 of 3:48h flooded


title: F4/80highPMO_co-infected_day14/5_rep1


title: F4/80highPMO_co-infected_day14/5_rep2


title: Sting-/- MEF with K289R ISD 4h rep2

city: Miami

first: Glen

last: Barber

state: FL

address: 1550 NW 10th Ave, Room 511

department: Cell Biology

country: USA

institute: University of Miami

description:
K289R-ISD_2
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using cubic spline with background subtraction.

source_name: Sting-/- MEFs, hSTING-K289R

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

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit following the prescribed protocol provided with the kit. Quality control was performed with Thermo NanoDrop.

treatment_protocol: Sting-/- MEFs were reconstituted with wild type hSTING, hSTING-K224R or hSTING-K289R, or mock transfected.

tag: strain/background

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)

tag: age

value: 2 weeks

tag: genotype/variation

value: Sting-/-

tag: transfection

tag: time


title: 22h flooded and infected replicate3

description: Biological replicate 3 of 3:22h flooded and infected

source_name: Root_22h flooded and infected

value: 22 hours


title: Sting-/- MEF with K289R Mock rep2

description:
K289R-M_2
Replicate 2

source_name: Sting-/- MEFs, mock

value: Mock


title: Sting-/- MEF with K289R ISD 4h rep1

description:
K289R-ISD_1
Replicate 1


title: 22h infected replicate3

description: Biological replicate 3 of 3:22h infected

source_name: Root_22h infected


title: 22h control replicate3

description: Biological replicate 3 of 3:22h control

source_name: Root_22h control


title: F4/80highPMO_H.poly infected_day14_rep2

description: Gene expression data from helminth expanded tissue resident macrophages

source_name: F4/80 high peritoneal macrophages from Heligmosomoides polygyrus infected C57BL/6 females 14 d.p.i.


title: 22h flooded replicate3

description: Biological replicate 3 of 3:22h flooded

source_name: Root_22h flooded


title: Sting-/- MEF with K224R Mock rep1

description:
K224R-M_1
Replicate 1


title: F4/80highPMO_H.poly infected_day14_rep3


title: Sting-/- MEF with K224R ISD 4h rep1

description:
K224R-ISD_1
Replicate 1

source_name: Sting-/- MEFs, hSTING-K224R


title: F4/80highPMO_naive_rep3

description: Gene expression data from tissue resident macrophages

source_name: F4/80 high peritoneal macrophages from naïve C57BL/6 females

value: naïve


title: Sting-/- MEF with K224R Mock rep2

description:
K224R-M_2
Replicate 2


title: F4/80highPMO_naive_rep4


title: F4/80highPMO_H.poly infected_day14_rep1


title: 48h flooded and infected replicate1

description: Biological replicate 1 of 3:48h flooded and infected


title: Sting-/- MEF with K289R Mock rep1

description:
K289R-M_1
Replicate 1


title: Sting-/- MEF with K224R ISD 4h rep2

description:
K224R-ISD_2
Replicate 2


title: F4/80highPMO_H.poly infected_day14_rep4


title: 48h control replicate1

description: Biological replicate 1 of 3:48h control


title: F4/80highPMO_naive_rep1


title: 22h flooded and infected replicate2

description: Biological replicate 2 of 3:22h flooded and infected


title: Sting-/- MEF with hSTING ISD 4h rep1

description:
STING-ISD_1
Replicate 1

source_name: Sting-/- MEFs, WT hSTING

value: WT hSTING


title: F4/80highPMO_naive_rep2


title: Sting-/- MEF with hSTING ISD 4h rep2

description:
STING-ISD_2
Replicate 2


title: Sting-/- MEF with hSTING Mock rep2

description:
STING-M_2
Replicate 2


title: Sting-/- MEF with hSTING Mock rep1

description:
STING-M_1
Replicate 1


title: 48h infected replicate1

description: Biological replicate 1 of 3:48h infected


title: 22h flooded and infected replicate1

description: Biological replicate 1 of 3:22h flooded and infected


title: 22h infected replicate2

description: Biological replicate 2 of 3:22h infected


title: Buccal_MGOS_laser_rep1

city: Rio de Janeiro

first: Fabio

last: Passetti

address: Av. Brasil, 4365

department: Pav. Leonidas Deane

country: Brazil

institute: FIOCRUZ

hyb_protocol: 5.5 ug of sscDNA were fragmented, washed and labeled before hybridization. Fragmented and labeled DNA were hybridized in Affymetrix GeneChip® Human.  Gene 1.0 ST arrays and scanned according to the protocol described in WT  Sense Target Labeling Assay Manual (Version 4; FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

organism: Homo sapiens

source_name: Buccal swab, patient MGOS, laser treated, day 10

label_protocol: 200ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: Total RNA was isolated from ejectable buccal swabs using the RNeasy Mini Kit (QIAGEN).

value: buccal sample

tag: disease state

value: head and neck squamous cell carcinoma


title: 48h flooded replicate1

description: Biological replicate 1 of 3:48h flooded


title: Buccal_RJS_laser_rep1

source_name: Buccal swab, patient RJS, laser treated, day 10


title: 22h infected replicate1

description: Biological replicate 1 of 3:22h infected


title: 22h control replicate1

description: Biological replicate 1 of 3:22h control


title: Buccal_RJS_laser_rep2


title: Buccal_NVL_laser_rep2

source_name: Buccal swab, patient NVL, laser treated, day 10


title: 22h flooded replicate2

description: Biological replicate 2 of 3:22h flooded

source_name: pooled reference


title: 22h control replicate2

description: Biological replicate 2 of 3:22h control


title: 22h flooded replicate1

description: Biological replicate 1 of 3:22h flooded


title: Buccal_PPR_placebo_rep1

source_name: Buccal swab, patient PPR, placebo, day 10


title: Buccal_LPS_placebo_rep2

source_name: Buccal swab, patient LPS, placebo, day 10


title: Buccal_MGOS_laser_rep2


title: Buccal_FPNF_placebo_rep1

source_name: Buccal swab, patient FPNF, placebo, day 10


title: Buccal_NVL_laser_rep1


title: Buccal_FPNF_placebo_rep2


title: Buccal_PPR_placebo_rep2


title: Buccal_EFM_placebo_rep1

source_name: Buccal swab, patient EFM, placebo, day 10


title: Buccal_EFM_placebo_rep2


title: Day 0 replicate 2

status: Public on Feb 13 2017

city: Frederick

first: Janice

last: Duy

state: MD

address: 1425 Porter St.

department: Diagnostics Systems Division

institute: U.S. Army Medical Research Institute of Infectious Diseases

description:
Control
Day0_2

data_processing:
Cq values were calculated using the second derivative method of the integrated Roche LightCycler 480 software version 1.5.1.
Cq values were imported into GenEx 6 Academic Enterprise software for further analysis.
MiRNA expression levels were calculated using the ΔΔCq method with global normalization. Briefly, interplate and spike-in calibrations were performed, followed by removal of samples with Cq > 39.4 and miRNAs that were not detected in 5/6 replicates. Global normalization of Cq values was performed by using the mean of all samples with Cq < 36 (per day). Relative quantities of each miRNA were calculated with respect to the average expression level on day 0, then data were log2 transformed and compared using a paired t-test.
Matrix normalized sheet reports values after interplate calibration and global normalization.
Fold change sheet reports log2 transformed test/control (day 7/day 0) values. Non-normalized values, Normalized values and and fold-change data are available on the series record.

label: SYBR Green

organism: Macaca mulatta

source_name: Archived plasma_day 0_post-exposure to aerosolized Ebola virus

label_protocol: RT-PCR assays were performed using the Exiqon microRNA Ready-to-Use PCR Human panel I+II V3.R (catalog number 203612). cDNA synthesis was performed using the cDNA Synthesis Kit II using 8 μL RNA for each 40 μL sample reaction.

extract_protocol: After TRIzol phase separation, the aqueous phase was used as input to the miRNeasy Mini Kit for total RNA extraction. 5 μg of molecular biology-grade glycogen was added as an RNA co-precipitant.

treatment_protocol: Plasma was mixed with 3 volumes of TRIzol LS after separation from whole blood.

value: plasma

tag: day post-exposure


title: Day 7 replicate 1

description:
Time of death
Day7_1

source_name: Archived plasma_day 7_post-exposure to aerosolized Ebola virus


title: Buccal_LPS_placebo_rep1


title: Day 0 replicate 1

description:
Control
Day0_1


title: Day 0 replicate 3

description:
Control
Day0_3


title: pDC.CLN_3

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

country: France

institute: CIML

description: Untreated

hyb_protocol: Following fragmentation and end-labeling, 2.07 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package.

source_name: Plasmacytoid dendritic cells_cutaneous lymph node

label_protocol: 1 to 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

extract_protocol: Plasmacytoid dendritic cells were purified by flow cytometry and total RNA was extracted with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.

value: cutaneous lymph nodes

tag: cell markers

value: plasmacytoid dendritic cells


title: siGALNT2 rep3

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

description: Gene expression after siRNA knockdown of GALNT2 in AGS cells

hyb_protocol: Agilent Gene Expression Hybridization Kits was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agenr and 20 ul of Agilent 2xGExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (US9230696) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: AGS cell siGALNT2 48hr, replicate 3

label_protocol: cDNA prepared from 10μg of total RNA were labeled with aa-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA).  Alexa/CyDye was incorporated to aa-cDNA followed by column purification with Alexa/CyDye-cDNA cRNA purification (Qiagen).

growth_protocol: In 10% FBS/RPMI

extract_protocol: RNA was prepared using the Genejet RNA Purification kit (Thermo Scientific) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: siControl(C) or siGALNT2 (G) for 48 hours

value: GALNT2 specific siRNA

value: AGS


title: Day 7 replicate 2

description:
Time of death
Day7_2

tag: tissue


title: Day 7 replicate 3

description:
Time of death
Day7_3


title: siGALNT2 rep2

source_name: AGS cell siGALNT2 48hr, replicate 2


title: gingival fibromatosis gingiva

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: gingival fibromatosis

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: GF tissue was also obtained during conventional gingivectomy from a 5-year-old female patient who presented with GF. The patient had no significant family or medical history of disease transmission, which made it difficult to identify the exact cause of the gingival enlargement.

extract_protocol: GF tissue was homogenized using a homogenizer. The Rneasy Fibrous Mini kit (Qiagen) was then used to extract total RNA from GF tissue, according to the manufacturer's instructions.

treatment_protocol: GF tissue was also obtained during conventional gingivectomy. GF tissue was immediately frozen and stored in liquid nitrogen.

value: gingiva

tag: disease status

value: gingival fibromatosis


title: pDC.CLN_2

description: Untreated

tag: strain


title: siGALNT2 rep1

source_name: AGS cell siGALNT2 48hr, replicate 1


title: siC rep2

source_name: AGS cell siC 48hr, replicate2

value: non-targeting siRNA


title: siC rep1

source_name: AGS cell siC 48hr, replicate 1


title: Ca9-22_RUNX2

first: Wei-Min

last: Chang

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

institute: Academia Sinica

description: Gene expression data from Ca9-22 cells expressing RUNX2 vector

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with blasticidin for two weeks.  Stably transduced cells were use for this experiment.

tag: cell line

value: gingival carcinoma


title: siC rep3

source_name: AGS cell siC 48hr, replicate3


title: CD4+ T cells of yin

city: Beijing

first: Jianping

last: Guo

address: NO.11,Xizhimen South Street,Xicheng District

department: Rheumatology & Immunology

country: China

institute: Peking University, People's Hospital

description: Gene expression data from CD4+ T cells of healthy controls

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The gene expression array data were digitalized using GeneChip Operating Software (GCOS) (v.1.4, Affymetrix), and normalized by eliminating the highest and lowest 2% of the data using MAS5 algorithm (Affymetrix).

source_name: CD4+ T cells  from PBMC of healthy control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: A total of 12 ml whole blood samples were drawn and stored at 4℃ less than 4h. Samples were layered onto Ficoll-Paque Plus and PBMCs were separated by density gradient centrifugation. An automated magnetic beadbased positive selection protocol was used to isolate CD4 cells (Stemcell Technologies, Vancouver, Canada).Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: healthy control

value: CD4+ T cells from PBMC


title: CD4+ T cells of yang chunying T


title: CD4+ T cells of ye


title: CD4+ T cells of zou meijuan


title: CD4+ T cells of mei xiang T

source_name: CD4+ T cells from PBMC of healthy control


title: CD4+ T cells of liang hongting T


title: CD4+ T cells of chen meiwen T


title: CD4+ T cells of cai min


title: CD4+ T cells of ZhangLingLing_1

description: Gene expression data from CD4+ T cells of RA patients

source_name: CD4+ T cells  from PBMC of active RA patients

value: rheumatoid arthritis


title: CD4+ T cells of LiuWeiHong_1


title: CD4+ T cells of TangWenPing_1

source_name: CD4+ T cells from PBMC of active RA patients


title: CD4+ T cells of YangGuangWen_1


title: CD4+ T cells of YiYuZhi_1


title: CD4+ T cells of li jianping


title: CD4+ T cells of XueQingLian_1


title: CD4+ T cells of FengMingXia_1


title: EHUH003_deltaVP30_72h_3_RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Huh cells, deltaVP-30-inoculated, 72h, bioreplicate 3

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

growth_protocol: Cells and virus were grown on 10% FBS DMEM supplemented with L-glut, Pen/Strep, nonessential amino acids and sodium pyruvate.

extract_protocol: RNA was extracted with 1mL of Trizol.

treatment_protocol: Cells were infected with a multiplicity of infection of 10.

tag: infection


title: EHUH003_deltaVP30_72h_5_RNA

source_name: Huh cells, deltaVP-30-inoculated, 72h, bioreplicate 5


title: CD4+ T cells of SongXianTang_1


title: CD4+ T cells of CongBo_1


title: EHUH003_deltaVP30_72h_4_RNA

source_name: Huh cells, deltaVP-30-inoculated, 72h, bioreplicate 4


title: CD4+ T cells of LiuJianPing_1


title: CD4+ T cells of GuanShuFeng_1


title: CD4+ T cells of MaYanChun_1


title: CD4+ T cells of GongHuiLing_1


title: EHUH003_Mock_72h_5_RNA

source_name: Huh cells, mock-inoculated, 72h, bioreplicate 5

value: mock


title: FaDu-Control

first: Kai-Chun

last: Li

address: No. 1, Sec. 4, Roosevelt Road

description: gene expression data from FaDu cells with Luc knockdown

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

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

source_name: FaDu cells

growth_protocol: FaDu cells were kept in RPMI containing medium with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin at 37oC in a humidified atmosphere with 5% CO2.

extract_protocol: Trizol and phenochloroform were used to extract RNA of FaDu shLuc or shG9a cells.

treatment_protocol: Cells were infected with lentivirus containing shLuc or shG9a plasmid for 72 hours. Briefly, mRNA were transcripted into Biotin-labeled cRNA in vitro, and then fragmented and hybridized to Human U133 2.0 plus array

tag: lentivirus

value: shLuc

value: human pharyngeal squamous cell cancer


title: EHUH003_deltaVP30_72h_2_RNA

source_name: Huh cells, deltaVP-30-inoculated, 72h, bioreplicate 2


title: EHUH003_deltaVP30_72h_1_RNA

source_name: Huh cells, deltaVP-30-inoculated, 72h, bioreplicate 1


title: EHUH003_Mock_72h_3_RNA

source_name: Huh cells, mock-inoculated, 72h, bioreplicate 3


title: EHUH003_Mock_72h_4_RNA

source_name: Huh cells, mock-inoculated, 72h, bioreplicate 4


title: FaDu-shG9a-67

description: gene expression data from FaDu cells with G9a knockdown


title: EHUH003_Mock_72h_1_RNA

source_name: Huh cells, mock-inoculated, 72h, bioreplicate 1


title: EHUH003_deltaVP30_48h_5_RNA

source_name: Huh cells, deltaVP30-inoculated, 48h, bioreplicate 5


title: EHUH003_Mock_48h_1_RNA

source_name: Huh cells, mock-inoculated, 48h, bioreplicate 1


title: EHUH003_Mock_72h_2_RNA

source_name: Huh cells, mock-inoculated, 72h, bioreplicate 2


title: EHUH003_deltaVP30_24h_4_RNA

source_name: Huh cells, deltaVP30-inoculated, 24h, bioreplicate 4


title: EHUH003_Mock_48h_4_RNA

source_name: Huh cells, mock-inoculated, 48h, bioreplicate 4


title: EHUH003_deltaVP30_48h_4_RNA

source_name: Huh cells, deltaVP30-inoculated, 48h, bioreplicate 4


title: EHUH003_deltaVP30_48h_3_RNA

source_name: Huh cells, deltaVP30-inoculated, 48h, bioreplicate 3


title: EHUH003_deltaVP30_48h_1_RNA

source_name: Huh cells, deltaVP30-inoculated, 48h, bioreplicate 1


title: EHUH003_deltaVP30_24h_2_RNA

source_name: Huh cells, deltaVP30-inoculated, 24h, bioreplicate 2


title: EHUH003_Mock_48h_3_RNA

source_name: Huh cells, mock-inoculated, 48h, bioreplicate 3


title: EHUH003_deltaVP30_24h_5_RNA

source_name: Huh cells, deltaVP30-inoculated, 24h, bioreplicate 5


title: EHUH003_deltaVP30_24h_1_RNA

source_name: Huh cells, deltaVP30-inoculated, 24h, bioreplicate 1


title: EHUH003_Mock_48h_5_RNA

source_name: Huh cells, mock-inoculated, 48h, bioreplicate 5


title: EHUH003_deltaVP30_24h_3_RNA

source_name: Huh cells, deltaVP30-inoculated, 24h, bioreplicate 3


title: EHUH003_deltaVP30_48h_2_RNA

source_name: Huh cells, deltaVP30-inoculated, 48h, bioreplicate 2


title: EHUH003_Mock_24h_4_RNA

source_name: Huh cells, mock-inoculated, 24h, bioreplicate 4


title: EHUH003_Mock_24h_5_RNA

source_name: Huh cells, mock-inoculated, 24h, bioreplicate 5


title: EHUH003_Mock_24h_1_RNA

source_name: Huh cells, mock-inoculated, 24h, bioreplicate 1


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast subline C6 (DMEM with 25mM glucose)

type: genomic

city: Los Angeles

first: Thomas

middle: G.

last: Graeber

state: CA

address: 570 Westwood Plaza, Bldg 114, Room 4341 CNSI

department: Mol & Med Pharmacology

institute: UCLA

description: Sample name: p53ko_ctrl_C6_P27

hyb_protocol: 55 μl 2X Hi-RPM hybridization buffer, 11 μl 10X aCGH blocking agent, 5 μl Cot-1 DNA (1.0 mg/ml) were added to the test and reference gDNA mix and ran 3 mins at 95°C, 30 mins at 37°C to promote binding of the gDNA targets to the probes and to prevent nonspecific binding. The mix was then allowed to hybridize to the microarray slide at 65°C for 24 hrs. After hybridization, slides were washed sequentially using Agilent Oligo aCGH/ChIP-on-Chip Washer Buffers.

scan_protocol: Microarrays were scanned using an Agilent Technologies Scanner G2505C. The raw data was extracted using Agilent Feature Extraction 11.5.1.1.

data_processing:
Bioconductor analysis tools were used for data processing: background correction and print-tip loess normalization were performed in snapCGH package; circular binary segmentation was performed on log2(test/reference)-transformed copy-number profiles using DNAcopy package.
File processed_data_seg.mean.seg.txt is linked to the Series record. "seg.mean" indicates the metric that is used for the copy number information.  ".seg" allows the file to be dragged and dropped into the Integrative Genome Viewer (IGV).

molecule: genomic DNA

source_name: p53fl/fl mouse embryonic fibroblasts

label_protocol: The Agilent SureTag DNA Labeling Kit was used to fragment, amplify, label, purify, and prepare the gDNA for hybridization.  Only samples with greater than 1.6 260/280 ratio and with validated DNA integrity (by running a 1% agarose gel for 30 mins at 85V) were used. Restriction digestion using Alu I (10 μg/μl) and RSA I (10 μg/μl) and stabilizing acetylated BSA (10 μg/μl) was run on samples for 2 hrs at 37°C, 20 mins at 65°C to fragment isolated gDNA. 5 μl Random Primers were added to the 24 μl of the restriction digest and sample mix for 3 mins at 95°C, 10 mins on ice to anneal to the ssDNA fragments. To amplify the gDNA while generating labeled targets for array hybridization 1 μl of Exo-Klenow fragment of DNA polymerase, 5 μl 10XdNTPs, and 3 μl Cy5-dUTP (Cy3-dUTP) were added to the restriction digest and test (reference) sample mix and ran for 2 hrs at 37°C, 10 mins at 65°C. Unreacted dye and unincorporated nucleotides were removed from the labeled gDNA using Amicon 30 kDa column purification.  The degree of labeling and concentration was then determined, and the test and reference gDNA mixed at a 1:1 ratio.

growth_protocol: CD1 mouse embryonic fibroblasts, E14.5, were purchased from Stem Cell Technologies. p53fl/fl MEFs were obtained at day E14.5 from p53fl/fl (FVB.129P2-Trp53tm1Brn/Nci) crossed with C57BL/6-129/SV mice. MEF cells were maintained in Dulbecco’s Modified Eagle’s Medium without pyruvate and supplemented with 10% FBS and 1% SPF. Cells were lifted and re-plated at a density of 9 x 105 viable cells / 60 mm dish every 3-4 days (ie, 3T9 protocol).

extract_protocol: Genomic DNA was harvested using the DNeasy kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Overexpression of HK1, HK2, kinase-dead HK2 (HK2 KD, D209A / D657A) or ENO2 glycolysis enzymes and the MYC oncogene or the control protein RFP in CD1 MEFs was accomplished by transduction of non-immortalized cells with pDS-FB-neo retrovirus, followed by selection in 600 μg/ml G418. Deletion of p53 in p53fl/fl MEFs was induced by infection of non-immortalized cells with either retroviral Cre-GFP or Cre-ERT2 plus treatment with 1 μM 4-OHT. To protect cells from reactive oxygen species (ROS), cells were cultured either at physiological oxygen concentrations (3% O2), with 2,500 U/ ml catalase from bovine liver (Sigma-Aldrich), or with both 3% O2 and catalase.

tag: passage

tag: type

value: control

source_name: C57BL/6J mouse tissue

value: reference


title: EHUH003_deltaVP30_8h_5_RNA

source_name: Huh cells, deltaVP30-inoculated, 8h, bioreplicate 5


title: EHUH003_deltaVP30_8h_4_RNA

source_name: Huh cells, deltaVP30-inoculated, 8h, bioreplicate 4


title: EHUH003_Mock_24h_3_RNA

source_name: Huh cells, mock-inoculated, 24h, bioreplicate 3


title: EHUH003_Mock_24h_2_RNA

source_name: Huh cells, mock-inoculated, 24h, bioreplicate 2


title: EHUH003_Mock_48h_2_RNA

source_name: Huh cells, mock-inoculated, 48h, bioreplicate 2


title: EHUH003_deltaVP30_8h_3_RNA

source_name: Huh cells, deltaVP30-inoculated, 8h, bioreplicate 3


title: EHUH003_Mock_8h_4_RNA

source_name: Huh cells, mock-inoculated, 8h, bioreplicate 4


title: EHUH003_Mock_8h_5_RNA

source_name: Huh cells, mock-inoculated, 8h, bioreplicate 5


title: EHUH003_Mock_8h_3_RNA

source_name: Huh cells, mock-inoculated, 8h, bioreplicate 3


title: pMIG-Cre p53fl/fl mouse embryonic fibroblast single cell clone from subline A2 rep.2 (DMEM with 25mM glucose)

description: Sample name: p53ko_scc_A2.3_P107

value: p53fl/fl (FVB.129P2-Trp53tm1Brn/Nci) crossed with C57BL/6-129/SV

value: single cell clone


title: EHUH003_Mock_8h_1_RNA

source_name: Huh cells, mock-inoculated, 8h, bioreplicate 1


title: EHUH003_deltaVP30_0h_2_RNA

source_name: Huh cells, deltaVP30-inoculated, 0h, bioreplicate 2


title: EHUH003_deltaVP30_0h_5_RNA

source_name: Huh cells, deltaVP30-inoculated, 0h, bioreplicate 5


title: EHUH003_deltaVP30_0h_4_RNA

source_name: Huh cells, deltaVP30-inoculated, 0h, bioreplicate 4


title: EHUH003_Mock_0h_2_RNA

source_name: Huh cells, mock-inoculated, 0h, bioreplicate 2


title: EHUH003_deltaVP30_0h_3_RNA

source_name: Huh cells, deltaVP30-inoculated, 0h, bioreplicate 3


title: EHUH003_Mock_0h_3_RNA

source_name: Huh cells, mock-inoculated, 0h, bioreplicate 3


title: Treatment 1

city: Taoyuan

first: Ailun

last: Tseng

address: 300 Jhong Da Rd.

institute: National Central University

description: mice treated with 500 mg/kg Astragalus membranaceus

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. 200μl of hybridize solution were subjected to each array. Hybridize 16 hours at 45° at 60 rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChip 3000 7G (Affymetrix)

data_processing: Data were processed using Expression console software. The gene expression intensity was RMA normalized.

source_name: subcutanous tumor from HCT116 mouse xenograft

label_protocol: The cDNA synthesis and labeling were carried out according to Affymetrix GeneChip® WT PLUS Reagent protocol (Affymetrix).

growth_protocol: Mice were treated for 28 days.

extract_protocol: The mice tumors total RNA was extracted using PureLink® RNA Mini Kit (Ambion, Carlsbad, CA, USA).

treatment_protocol: The animals were gauge fed with 500 mg/kg Astragalus membranaceus or only distilled water every day.

value: HCT116 mouse xenograft

tag: host

value: mouse


title: EHUH003_deltaVP30_0h_1_RNA

source_name: Huh cells, deltaVP30-inoculated, 0h, bioreplicate 1


title: EHUH003_Mock_0h_5_RNA

source_name: Huh cells, mock-inoculated, 0h, bioreplicate 5


title: EHUH003_Mock_0h_4_RNA

source_name: Huh cells, mock-inoculated, 0h, bioreplicate 4


title: Treatment 5


title: EHUH003_Mock_0h_1_RNA

source_name: Huh cells, mock-inoculated, 0h, bioreplicate 1


title: Treatment 3


title: Control 7

description: mice treated with water


title: Treatment 8


title: Treatment 4


title: EHUH003_Mock_8h_2_RNA

source_name: Huh cells, mock-inoculated, 8h, bioreplicate 2


title: Control 6

description: mice treated with water


title: Control 5

description: mice treated with water


title: pDC.CLN_1

description: Untreated

source_name: Plasmacytoid dendritic cells_cutaneous lymph node

value: cutaneous lymph nodes

tag: cell type

value: plasmacytoid dendritic cells


title: Treatment 7


title: Ca9-22_Empty vector

description: Gene expression data from Ca9-22 cells expressing control vector

source_name: Ca9-22_Empty vector


title: Control 8

description: mice treated with water


title: Control 4

description: mice treated with water


title: Treatment 2


title: Control 3

description: mice treated with water


title: Treatment 6


title: Control 2

description: mice treated with water


title: Control 1

description: mice treated with water


title: non rep1

city: Okayama

first: Kazunori

last: Watanabe

address: 3-1-1 tsushimanaka

country: Japan

institute: Okayama University

description: non-treated

hyb_protocol: The hybridization used Hybridization, Wash, and Stain Kit (Affymetrix, Inc) according to the manufacturer's instructions.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an GeneChip Scanner 3000 7G (Affymetrix, Inc).

data_processing: Data acquisition and normalization (RMA) were used AffymetrixR Expression Console Software.

label: Biotin

source_name: non-treat rep1

label_protocol: 100 µg total RNA was labeled using the FlashTag Biotin HSR RNA Labeling kit (Affymetrix, Inc) according to the manufacturer's instructions.

growth_protocol: SH-SY5Y cells were  maintained Dulbecco’s modified Eagle medium (DMEM)-F12 (1:1) medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin at 37˚C in an atmosphere of 5% CO2.

extract_protocol: Total RNA containing miRNA was extracted from cells using the miRNeasy Plus Mini Kit

treatment_protocol: SH-SY5Y cells were seeded onto collagen-coated dishes were treated with 30 µM retinoic acid in DMEM-F12 medium for 2 and 14 days.

tag: agent

value: non-treated


title: day 2 rep3

description: retinoic acid-treated for 2 day

source_name: day 2 rep3

value: retinoic acid-treated

tag: time point

value: 2 day


title: day 14 rep1

description: retinoic acid-treated for 14 day

source_name: day 14 rep1

value: 14 day


title: non rep3

description: non-treated

source_name: non-treat rep3


title: day 14 rep2

description: retinoic acid-treated for 14 day

source_name: day 14 rep2


title: non rep2

description: non-treated

source_name: non-treat rep2


title: 36_L19_J

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

country: Singapore

institute: Temasek Life Sciences Laboratory

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is ninth of the ten biological replicates.

hyb_protocol: Hybridization was performed for 16 to 20 hours using MAUI hybridization system (BioMicro Systems) according to Roche NimbleGen expression array protocol.

scan_protocol: Prior to scanning the microarray chip was washed with NimbleGen Wash Buffer Kit (Roche NimbleGen) according to manufacturer's protocol. Then the chip was scanned at 5 um resolution with Axon GenePix 4000B Microarray Scanner (Molecular Devices) according to Roche NimbleGen expression array protocol.

data_processing: The raw data(.pair file) was subjected to RMA (Robust-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 NimbleScan version 2.6 software package.

organism: Danio rerio

source_name: trunk, juvenile, high temperature

label_protocol: Amplified double stranded cDNA was labeled using NimbleGen One-Color DNA Labelling Kit (Roche NimbleGen) according to manufacturer's protocol.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) according to manufacturer's protocol. To obtain sufficient amount for labelling, whole transcriptome amplification was performed using Ovation RNA Amplificiation System V2 (NuGen).

treatment_protocol: Zebrafish were exposed to either high (36 oC) or control (28 oC) temperature from 18 to 32 dpf. After treatment the fish were reared at 28 oC until sampling at 37 or 90 dpf.

value: trunk

tag: temperature (oc)

tag: age (dpf)


title: day 14 rep3

description: retinoic acid-treated for 14 day

source_name: day 14 rep3


title: 28_L04_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is fourth of the eight biological replicates.

source_name: trunk, juvenile, control temperature


title: 28_L01_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is first of the eight biological replicates.


title: 36_L11_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is first of the ten biological replicates.


title: 36_L17_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is seventh of the ten biological replicates.


title: 36_L16_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is sixth of the ten biological replicates.


title: day 2 rep2

description: retinoic acid-treated for 2 day

source_name: day 2 rep2


title: 36_L14_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is fourth of the ten biological replicates.


title: 36_L15_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is fifth of the ten biological replicates.


title: 28_L02_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is second of the eight biological replicates.


title: 28_L09_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is eighth of the eight biological replicates.


title: 36_L18_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is eighth of the ten biological replicates.


title: 36_L13_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is third of the ten biological replicates.


title: 36_L12_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is second of the ten biological replicates.


title: 36_G23_Fe

description: This sample is an adult ovary exposed to high temperature (36 oC). It is third of the four adult female biological replicates.

source_name: gonad, adult, high temperature

value: ovary


title: 28_L06_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is sixth of the eight biological replicates.


title: day 2 rep1

description: retinoic acid-treated for 2 day

source_name: day 2 rep1


title: 36_L20_J

description: This sample is a juvenile trunk exposed to high temperature (36 oC). It is tenth of the ten biological replicates.


title: 28_L07_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is seventh of the eight biological replicates.


title: 36_G22_Fe

description: This sample is an adult ovary exposed to high temperature (36 oC). It is second of the four adult female biological replicates.


title: 28_L05_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is fifth of the eight biological replicates.


title: 36_G24_Fe

description: This sample is an adult ovary exposed to high temperature (36 oC). It is fourth of the four adult female biological replicates.


title: 36_G02_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is second of the ten adult male biological replicates.

value: testis


title: 36_G08_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is eighth of the ten adult male biological replicates.


title: 28_G17_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is seventh of the ten adult male biological replicates.

source_name: gonad, adult, control temperature


title: 28_L03_J

description: This sample is a juvenile trunk exposed to control temperature (28 oC). It is third of the eight biological replicates.


title: 28_G14_Fe

description: This sample is an adult ovary exposed to control temperature (28 oC). It is fourth of the four adult female biological replicates.


title: 36_G05_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is fifth of the ten adult male biological replicates.


title: 28_G20_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is tenth of the ten adult male biological replicates.


title: 36_G09_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is ninth of the ten adult male biological replicates.


title: 28_G03_Fe

description: This sample is an adult ovary exposed to control temperature (28 oC). It is second of the four adult female biological replicates.


title: 28_G12_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is sixth of the ten adult male biological replicates.


title: 36_G07_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is seventh of the ten adult male biological replicates.


title: 36_G03_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is third of the ten adult male biological replicates.


title: 28_G01_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is first of the ten adult male biological replicates.


title: 36_G01_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is first of the ten adult male biological replicates.


title: 36_G10_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is tenth of the ten adult male biological replicates.


title: 28_G19_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is ninth of the ten adult male biological replicates.


title: 36_G06_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is sixth of the ten adult male biological replicates.


title: 28_G18_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is eighth of the ten adult male biological replicates.


title: 36_G04_M

description: This sample is an adult testis exposed to high temperature (36 oC). It is fourth of the ten adult male biological replicates.


title: 28_G08_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is fourth of the ten adult male biological replicates.


title: 36_G21_Fe

description: This sample is an adult ovary exposed to high temperature (36 oC). It is first of the four adult female biological replicates.


title: 28_G07_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is third of the ten adult male biological replicates.


title: 28_G06_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is second of the ten adult male biological replicates.


title: 28_G02_Fe

description: This sample is an adult ovary exposed to control temperature (28 oC). It is first of the four adult female biological replicates.


title: 28_G04_Fe

description: This sample is an adult ovary exposed to control temperature (28 oC). It is third of the four adult female biological replicates.


title: 28_G09_M

description: This sample is an adult testis exposed to control temperature (28 oC). It is fifth of the ten adult male biological replicates.


title: Low birth weight male rat kidney 3

city: SuZhou

first: Yanhong

address: Jingde road 303

department: Department of nephrology, Institute of pediatric research

institute: Children’s Hospital affiliated to Soochow University

description:
LBW-3
LncRNA expression in the kidneys of low birth weight male rats at postnatal day 10.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-062716 Rat lncRNA Array 8*60 K (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring 12.0 (Agilent). Probes that have flags in Detected in at least 100.0 percent of samples in any 1 condition out of 2 conditions were maintained.

organism: Rattus norvegicus

source_name: Kidney form low birth weight rats at postnatal day 10

label_protocol: 0.1ug total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP (Cy3) using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, then followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Male rats with low birth weight born from dams fed a low-protein diet throughout gestation and the first 10 days of lactation period, and control male rats with normal birth weight born from normal protein diet dams.

extract_protocol: RNA derived from rat kidneys was extracted using mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's recommendations. RNA quality and quantity were evaluated using a NanoDrop ND-2000 Spectrophotometer (Thermo Scientific) and RNA integrity was assessed by Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: strain/background

value: Sprague Dawley

tag: birth weight

value: low

value: kidney

tag: gender

value: male

tag: age

value: postnatal day 10


title: Control male rat kidney 3

description:
Control-3
LncRNA expression in the kidneys of normal control male rats at postnatal day 10.

source_name: Kidney from normal rats at postnatal day 10

value: normal

tag: tissue


title: 02_KPS-T2

city: Houston

first: Giannicola

last: Genovese

state: TX

address: 1901 East Road

department: Genomic Medicine

institute: UTMDACC

hyb_protocol: according to manufacturer specifications

data_processing:
Samples were processed on Affymetrix Mouse 430_2 microarray platform. Resulting CEL files were imported into Gene Pattern software from the Broad Institute, and converted to normalized GCT format using default parameters in module, ExpressionFileCreator. Normalized GCT table format was used for Gene Set Enrichment Analysis (GSEA) using GSEA software provided by the Broad Institute, Cambridge MA.
GCT file for GSEA input was created using ExpressionFileCreator module in GenePattern software using default parameters for Affymetrix Mouse 430_2 chip: RMA quantile normalization with background correction and median scaling.

source_name: vehicle treated Smarcb1 depleted mouse pancreatic tumor

growth_protocol: Smarcb1 deficient pancreatic tumors were treated with tamoxifen to induce restoration to the physiological level of Smarcb1 expression. Vehicle treated tumors were used as controls.

extract_protocol: Trizol

treatment_protocol: vehicle vs tamoxifen

tag: strain background

value: Smarcb1 deficient pancreatic tumor

tag: treated with

value: vehicle (control)

value: depleted


title: Low birth weight male rat kidney 1

description:
LBW-1
LncRNA expression in the kidneys of low birth weight male rats at postnatal day 10.


title: Control male rat kidney 1

description:
Control-1
LncRNA expression in the kidneys of normal control male rats at postnatal day 10.


title: 10_KPS+T5

scan_protocol: according to manufacturer specifications

source_name: tamoxifen treated Smarcb1 restored mouse pancreatic tumor

value: tamoxifen

value: restored


title: GG MS 2

description: GG MS 2 (Mouse430_2)

source_name: Kras mutant pancreatic epithelial cells_mesenchymal morphology

label_protocol: according to manufacturer specifications

growth_protocol: Kras mutant pancreatic epithelial cells were cultured under oncogenic stress. Spontaeneous senescence escapers were isolated, expanded and functionally characterized.

treatment_protocol: not applicable

value: Kras mutant mouse pancreatic epithelial cells

tag: histopathology

value: mesenchymal morphology


title: Low birth weight male rat kidney 2

description:
LBW-2
LncRNA expression in the kidneys of low birth weight male rats at postnatal day 10.


title: 09_KPS+T4


title: 08_KPS+T3


title: 06_KPS+T1


title: 05_KPS-T5


title: GG EPI 3

description: GG EPI 3 (Mouse430_2)

source_name: Kras mutant pancreatic epithelial cells_epithelial morphology

value: epithelial morphology


title: 03_KPS-T3


title: GG MS 4

description: GG MS 4 (Mouse430_2)


title: 04_KPS-T4


title: Control male rat kidney 2

description:
Control-2
LncRNA expression in the kidneys of normal control male rats at postnatal day 10.


title: GG EPI 1

description: GG EPI 1 (Mouse430_2)


title: GG MS 3

description: GG MS 3 (Mouse430_2)


title: GG EPI 4

description: GG EPI 4 (Mouse430_2)


title: 01_KPS-T1


title: Sox9_XY_TS34_rep1

city: Krakow

first: Dagmara

last: Podkowa

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

description: Gene expression data from gonads after the sexual differentiation.

hyb_protocol: Microarrays were hybridized overnight with 5 ug biotin-labelled ss-DNA, and washed in fluidics station wash protocol: FS450_0001.

scan_protocol: GeneChip scanner 3000 7G was used.

data_processing: RMA signal intensity calculation

source_name: Supporting cells isolated from gonad of XY mouse fetus at TS34

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual.

extract_protocol: Total RNA from was isolated using Trizol as described above and further purified with RNeasy Mini kit per manufacturer’s instructions (Qiagen, Valencia, CA). 200 ng total RNA was then used for GeneChip analysis. Preparation of terminal-labeled cDNA, hybridization to genome-wide murine Gene Level 1.0 ST GeneChips (Affymetrix, Santa Clara, CA, USA) and scanning of the arrays were carried out according to manufacturer’s protocols (https://www.affymetrix.com).

treatment_protocol: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 10 minutes. The trypsin was replaced by PBS. The samples were stained with DAPI and FACS sorted.

tag: strain

value: Tg(Sox9-cre/ERT2)1Msan/J, progeny of C57BL/6

tag: Sex

tag: developmental stage

value: Supporting cells

tag: gene reported


title: Sox9_XY_TS34_rep2

tag: cell type


title: Sry_XX_TS34_rep1

source_name: Supporting cells isolated from gonad of XX mouse fetus at TS34

value: Tg(Sry-EGFP)92Ei, progeny of CD-1

value: female

value: Sry


title: Sry_XX_TS34_rep3


title: Oct4_XY_TS34_rep3

source_name: Germ cells isolated from gonad of XY mouse fetus at TS34

value: progeny of C57BL/6NJ on mixed background

value: Germ cells


title: Sry_XX_TS34_rep2


title: GG EPI 2

description: GG EPI 2 (Mouse430_2)


title: Sox9_XY_TS34_rep3

value: male


title: Oct4_XY_TS34_rep2


title: GG MS 1

description: GG MS 1(Mouse430_2)


title: Oct4_XX_TS34_rep3

source_name: Germ cells isolated from gonad of XX mouse fetus at TS34


title: Oct4_XX_TS34_rep1


title: Oct4_XY_TS34_rep1


title: Oct4_XX_TS34_rep2


title: Mafb_XY_TS34_rep3

source_name: Interstitial cells isolated from gonad of XY mouse fetus at TS34

value: progeny of 129S6/SvEvTac on mixed background

value: Interstitial cells

value: Mafb


title: Mafb_XY_TS34_rep2


title: Mafb_XY_TS34_rep1


title: Mafb_XX_TS34_rep2

source_name: Stromal cells isolated from gonad of XX mouse fetus at TS34

value: Stromal cells


title: Sox9_XY_TS24_rep3

description: Gene expression data from gonads during the sexual differentiation.

source_name: Supporting cells isolated from gonad of XY mouse fetus at TS24


title: Mafb_XX_TS34_rep3


title: Mafb_XX_TS34_rep1


title: Sry_XX_TS24_rep2

source_name: Supporting cells isolated from gonad of XX mouse fetus at TS24


title: 07_KPS+T2

value: Smarcb1 deficient pancreatic tumor

value: tamoxifen


title: Sox9_XY_TS24_rep2


title: Sry_XX_TS24_rep1


title: genomic DNA from PBMC 44

city: Iowa City

first: Robert

middle: A

last: Philibert

state: Iowa

address: MEB, 500 Newton Road, Room 2-126D

department: Psychiatry

institute: University of Iowa

description: non-smoker PBMC sample

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: Genome Studios V2011.1

label: Cy5 and Cy3

source_name: PBMC 44

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using QIAamp DNA Blood Mini Kit according to standard instructions

value: Male

value: peripheral blood mononuclear cells

tag: group

value: Control


title: genomic DNA from PBMC 46

description: non-smoker PBMC sample

source_name: PBMC 46


title: genomic DNA from PBMC 45

description: non-smoker PBMC sample

source_name: PBMC 45


title: Oct4_XY_TS24_rep2

source_name: Germ cells isolated from gonad of XY mouse fetus at TS24


title: genomic DNA from PBMC 49

description: non-smoker PBMC sample

source_name: PBMC 49


title: Sox9_XY_TS24_rep1

value: Tg(Sox9-cre/ERT2)1Msan/J, progeny of C57BL/6


title: genomic DNA from PBMC 47

description: non-smoker PBMC sample

source_name: PBMC 47


title: Sry_XX_TS24_rep3

value: Supporting cells


title: Oct4_XX_TS24_rep3

source_name: Germ cells isolated from gonad of XX mouse fetus at TS24


title: Oct4_XY_TS24_rep1


title: Oct4_XY_TS24_rep3


title: genomic DNA from PBMC 51

description: non-smoker PBMC sample

source_name: PBMC 51


title: genomic DNA from PBMC 50

description: non-smoker PBMC sample

source_name: PBMC 50


title: genomic DNA from PBMC 41

description: non-smoker PBMC sample

source_name: PBMC 41


title: genomic DNA from PBMC 38

description: non-smoker PBMC sample

source_name: PBMC 38


title: genomic DNA from PBMC 52

description: non-smoker PBMC sample

source_name: PBMC 52


title: genomic DNA from PBMC 43

description: non-smoker PBMC sample

source_name: PBMC 43


title: genomic DNA from PBMC 42

description: non-smoker PBMC sample

source_name: PBMC 42


title: genomic DNA from PBMC 48

description: non-smoker PBMC sample

source_name: PBMC 48


title: Oct4_XX_TS24_rep2


title: genomic DNA from PBMC 40

description: non-smoker PBMC sample

source_name: PBMC 40


title: Mafb_XY_TS24_rep3

source_name: Interstitial cells isolated from gonad of XY mouse fetus at TS24


title: genomic DNA from PBMC 35

description: non-smoker PBMC sample

source_name: PBMC 35


title: genomic DNA from PBMC 36

description: non-smoker PBMC sample

source_name: PBMC 36


title: genomic DNA from PBMC 37

description: non-smoker PBMC sample

source_name: PBMC 37


title: genomic DNA from PBMC 39

description: non-smoker PBMC sample

source_name: PBMC 39


title: Mafb_XY_TS24_rep2


title: Mafb_XY_TS24_rep1


title: Mafb_XX_TS24_rep1

source_name: Stromal cells isolated from gonad of XX mouse fetus at TS24


title: Mafb_XX_TS24_rep2


title: genomic DNA from PBMC 32

description: non-smoker PBMC sample

source_name: PBMC 32


title: genomic DNA from PBMC 33

description: non-smoker PBMC sample

source_name: PBMC 33


title: genomic DNA from PBMC 34

description: non-smoker PBMC sample

source_name: PBMC 34


title: Sry_XY_TS13_rep3

description: Gene expression data from gonads before the onset of sexual differentiation.

source_name: Supporting cells isolated from gonad of XY mouse fetus at TS13

value: Tg(Sry-EGFP)92Ei, progeny of CD-1


title: genomic DNA from PBMC 30

description: non-smoker PBMC sample

source_name: PBMC 30


title: Oct4_XX_TS24_rep1

source_name: Germ cells isolated from gonad of XX mouse fetus at TS24

value: female


title: Sry_XY_TS13_rep1

value: Sry


title: Sry_XY_TS13_rep2


title: Sry_XX_TS13_rep2

source_name: Supporting cells isolated from gonad of XX mouse fetus at TS13


title: genomic DNA from PBMC 31

description: non-smoker PBMC sample

source_name: PBMC 31


title: Mafb_XX_TS24_rep3


title: genomic DNA from PBMC 29

description: non-smoker PBMC sample

source_name: PBMC 29


title: Sry_XX_TS13_rep1


title: genomic DNA from PBMC 27

description: non-smoker PBMC sample

source_name: PBMC 27


title: Oct4_XY_TS13_rep3

source_name: Germ cells isolated from gonad of XY mouse fetus at TS13

value: progeny of C57BL/6NJ on mixed background


title: genomic DNA from PBMC 28

description: non-smoker PBMC sample

source_name: PBMC 28


title: Oct4_XY_TS13_rep2

value: Germ cells


title: genomic DNA from PBMC 24

description: smoker PBMC sample

source_name: PBMC 24

value: Smoker


title: genomic DNA from PBMC 25

description: non-smoker PBMC sample

source_name: PBMC 25


title: Oct4_XX_TS13_rep3

source_name: Germ cells isolated from gonad of XX mouse fetus at TS13


title: Oct4_XY_TS13_rep1

value: male


title: Mafb_XY_TS13_rep3

source_name: Interstitial cells isolated from gonad of XY mouse fetus at TS13

value: progeny of 129S6/SvEvTac on mixed background

value: Interstitial cells


title: Mafb_XY_TS13_rep2

value: Mafb


title: Sry_XX_TS13_rep3


title: genomic DNA from PBMC 23

description: smoker PBMC sample

source_name: PBMC 23


title: Oct4_XX_TS13_rep2


title: genomic DNA from PBMC 20

description: smoker PBMC sample

source_name: PBMC 20


title: genomic DNA from PBMC 22

description: smoker PBMC sample

source_name: PBMC 22


title: genomic DNA from PBMC 21

description: smoker PBMC sample

source_name: PBMC 21


title: genomic DNA from PBMC 19

description: smoker PBMC sample

source_name: PBMC 19


title: Mafb_XX_TS13_rep3

source_name: Stromal cells isolated from gonad of XX mouse fetus at TS13

value: Stromal cells


title: Mafb_XX_TS13_rep2


title: genomic DNA from PBMC 16

description: smoker PBMC sample

source_name: PBMC 16


title: N87-TR4

city: Verona

first: Carmine

last: Carbone

state: Select a State or Province

address: p.zza L.A. Scuro 10

country: Italy

institute: Policlinico Universitario GB Rossi

description:
9407205085_K
SAMPLE 5
Human cancer cells

hyb_protocol: Hybridization of cRNAs (750 ng) was carried out using Illumina Human 48k gene chips (Human HT-12 V4 BeadChip). Array washing was performed using Illumina High Temp Wash Buffer for 10’ at 55°C, followed by staining using streptavidin-Cy3 dyes (Amersham Biosciences).

scan_protocol: Standard Illumina scanning protocol. Probe intensity data were obtained using the Illumina GenomeStudio software (Genome Studio V2011.1).

data_processing: Data were normalized using cubic spline by the Illumina GenomeStudio.

source_name: N87-TR4, trastuzumab resistant

label_protocol: Synthesis of biotinylated cRNA was performed using the IlluminaTotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol using 500ng of total RNA.

growth_protocol: All cell lines were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% heat-inactivated FBS, 20 mmol/L HEPES (pH 7.4), penicillin (100 UI/mL), streptomycin (100 mg/mL), and 4 mmol/L glutamine (ICN Biomedicals Ltd.) in a humidified atmosphere of 95% air and 5% CO2 at 37°C.

extract_protocol: Total RNA was obtained from subconfluent cells using Trizol reagent (Ambion, Warrington, UK) and following the procedures outlined by the supplier. The quality of RNA was determined by electrophoresis on agarose gel and staining with ethidium bromide, the 18S and 28S bands were visualized by ultraviolet light. Total RNA was quantified by absorbance at 260 nm.

tag: cell line

value: gastric cancer cell line

tag: trastuzumab sensitivity

value: resistant


title: genomic DNA from PBMC 14

description: smoker PBMC sample

source_name: PBMC 14

value: Male

value: peripheral blood mononuclear cells


title: genomic DNA from PBMC 26

description: non-smoker PBMC sample

source_name: PBMC 26

value: Control


title: Mafb_XY_TS13_rep1


title: genomic DNA from PBMC 18

description: smoker PBMC sample

source_name: PBMC 18


title: N87-TR3

description:
9407205085_J
SAMPLE 4
Human cancer cells

source_name: N87-TR3, trastuzumab resistant


title: genomic DNA from PBMC 17

description: smoker PBMC sample

source_name: PBMC 17


title: Mafb_XX_TS13_rep1


title: Oct4_XX_TS13_rep1


title: N87-TR2

description:
9407205085_I
SAMPLE 3
Human cancer cells

source_name: N87-TR2, trastuzumab resistant


title: N87-TR1

description:
9407205085_H
SAMPLE 2
Human cancer cells

source_name: N87-TR1, trastuzumab resistant


title: genomic DNA from PBMC 10

description: smoker PBMC sample

source_name: PBMC 10


title: NCI-N87

description:
9407205085_G
SAMPLE 1
Human cancer cells

source_name: NCI-N8, trastuzumab sensitive

value: sensitive


title: genomic DNA from PBMC 11

description: smoker PBMC sample

source_name: PBMC 11


title: genomic DNA from PBMC 15

description: smoker PBMC sample

source_name: PBMC 15


title: Mock transfection to MCF-7 cells

city: Pusan

first: Ho Sung

last: Kang

address: 30, Jangjeon-dong

department: Departmemt of Molecular Biology

institute: Pusan National University

description: Gene expression data from mock transfected cells

hyb_protocol: The Cy3-labeled aRNAs were resuspended in 50ul of hybridization solution (Agilent technologies, CA). After labeled aRNAs were placed on Agilent SurePrint G3 Human GE 8x60K array (Agilent technologies, CA) and covered by a Gasket 8-plex slide (Agilent technologies, CA). The slides were hybridized for 17hr at 65 ℃ oven. The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: The arrays were analyzed using an Agilent scanner with associated software. Gene expression levels were calculated with Feature Extraction v10.7.3.1 (Agilent technologies, CA). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm.

data_processing: The data were processed based on quantile normalization method using the GeneSpring GX 11.5.1 (Agilent technologies, CA). This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 11.5.1 (Agilent technologies, CA).

source_name: control samples (Mock 48hr)

label_protocol: Each total RNA sample (200ng) was labeled and amplified using Low Input Quick Amp labeling kit (Agilent  technologies, CA)

growth_protocol: Human breast adenocarcinoma cell line MCF-7 were obtained from ATCC and grown in normal growth medium (EMEM media supplemented with 10% (v/v) heat-inactivated fetal bovine serum and 1% penicillin/streptomycin in a 37ºC humidified incubator with 5% CO2.

extract_protocol: Total RNA extraction was performed 48h after transfection according to the manufacturer's instructions (TRIzol reagent, Invitrogen, Paisley, UK).

treatment_protocol: MCF-7 cells were transiently transfected with mock or pCAGGS/Dlx-2 with JetPEI (Polyplus, Illkirch, France) according to the manufacturers protocol.

value: breast adenocarcinoma cell line

tag: transfection

value: pCAGGS (mock)


title: Dlx-2 transfection to MCF-7 cells

description: Gene expression data from Dlx-2 transfected cells

source_name: experimental samples (Dlx-2 48hr)


title: genomic DNA from PBMC 9

description: smoker PBMC sample

source_name: PBMC 9


title: genomic DNA from PBMC 13

description: smoker PBMC sample

source_name: PBMC 13


title: genomic DNA from PBMC 12

description: smoker PBMC sample

source_name: PBMC 12


title: CLAfl015.t5.r2

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

department: Plant Industry

country: Australia

institute: CSIRO

description: Gene expression data obtained from total RNA extracted from berry flesh with seeds.

hyb_protocol: Affymetrix Fluidics Station 450, Biotin/Streptavidin detection

scan_protocol: The GeneChips were scanned using theGeneChip Scanner 3000

data_processing: Data normalized using the GCRMA R package from Bioconductor

organism: Vitis vinifera

source_name: Grape berry flesh with seeds, 4 weeks post flowering

label_protocol: Affymetrix One Cycle cDNA synthesis kit, Affymetrix GeneChip Sample Cleanup kit, Affymetrix IVT labeling kit

growth_protocol: Berries were collected from bunches on field grown plants

extract_protocol: The modified RNAeasy RNA extraction method (Qiagen)

treatment_protocol: Vines were spur pruned

tag: Cabernet Sauvignon


title: CLAsk015.t5.r2

description: Gene expression data obtained from total RNA extracted from berry skin.

source_name: Grape berry skin, 4 weeks post flowering


title: CLAfl041.t14.r1

description: Gene expression data obtained from total RNA extracted from berry deseeded flesh.

source_name: Grape berry deseeded flesh, 13 weeks post flowering


title: CLAsk041.t14.r1

source_name: Grape berry skin, 13 weeks post flowering


title: CLAfl014.t5.r1


title: CLAsk014.t5.r1


title: WILsp049_04.t18.rep1

description: Gene expression data from deseeded berries pooled from several bunches

data_processing: Data normalised using the GCRMA R package from Bioconductor

source_name: Grape berry 17 weeks post flowering

label_protocol: Affymetrix One Cycle cDNA synthesis kit, Affymetrix GeneChip Sample Cleanup kit, Affymetrix IVT labelling kit


title: genomic DNA from PBMC 2

description: smoker PBMC sample

source_name: PBMC 2


title: genomic DNA from PBMC 5

description: smoker PBMC sample

source_name: PBMC 5


title: WILsp047_04.t17.rep2

source_name: Grape berry 16 weeks post flowering


title: genomic DNA from PBMC 8

description: smoker PBMC sample

source_name: PBMC 8


title: WILsp052_04.t19.rep1

source_name: Grape berry 18 weeks post flowering


title: WILsp046_04.t17.rep1


title: genomic DNA from PBMC 6

description: smoker PBMC sample

source_name: PBMC 6


title: WILsp050_04.t18.rep2


title: genomic DNA from PBMC 7

description: smoker PBMC sample

source_name: PBMC 7


title: WILsp044_04.t16.rep1

source_name: Grape berry 15 weeks post flowering


title: CLAfl042.t14.r2


title: genomic DNA from PBMC 3

description: smoker PBMC sample

source_name: PBMC 3


title: WILsp045_04.t16.rep2


title: WILsp039_04.t14.rep1

source_name: Grape berry 13 weeks post flowering


title: WILsp042_04.t15.rep2

source_name: Grape berry 14 weeks post flowering


title: WILsp038_04.t13.rep2

source_name: Grape berry 12 weeks post flowering


title: WILsp041_04.t15.rep1


title: WILsp040_04.t14.rep2


title: WILsp037_04.t13.rep1


title: genomic DNA from PBMC 4

description: smoker PBMC sample

source_name: PBMC 4


title: ngo0406::cm cells replicate 3

city: Warsaw

first: Monika

middle: Julita

last: Adamczyk-Poplawska

address: Miecznikowa 1

institute: University of Warsaw

description: total RNA from not pooled samples

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled cRNAs were hybridized onto the microarray for 17 h at 65°C and hybridized microarrays were washed according to the Agilent protocol. Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit were used respectively to hybridize and wash the hybridized microarray.

scan_protocol: Microarray slides were scanned using the Agilent G2565CA Microarray Scanner System.

data_processing:
GeneSpring version 12.5 (Agilent Technologies) was used for data analysis. Normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering (Student’s t-test against zero, asymptotic P value computation and Benjamini Hochberg FDR multiple testing correction).
Arbitrary fold change (FC) cut-offs of >1.5 or >2 tested/reference

organism: Neisseria gonorrhoeae

source_name: wild type (control)

label_protocol: The Low Input Quick Amp Labeling WT (LIQA WT) Kit (Agilent Technologies) was used to amplify and label whole transcripts. Additionally, the RNA Spike In Kit for Two color v4.0 (Agilent Technologies) was used according to manufacturer`s instructions. (i) cDNA synthesis using total RNA (50 ng) as template; (ii) cRNA synthesis and labeling using cDNA as template, T7 RNA polymerase, NTPs and fluorescent dye. Simultaneously two mixtures were prepared, one reaction with Cy3 as fluorescent dye, the second one with Cy5; (iii) purification of labeled cRNA and measurement of the efficiency of incorporation of the Cy5 or Cy3 dye. The Cy3 dye was used to label the cRNA wt strain, and the Cy5 dye to label the cRNA N. gonorrhoeae mutant strain.

growth_protocol: Cells were grown overnight on GCB agar plate with hemoglobin and Kellog supplement at 37C and 5 % CO2

extract_protocol: Cells were then harvested from one plate and total RNA was isolated using the High Pure RNA Isolation Kit (Roche), according to the manufacturer’s recommendations.

tag: genotype

value: wt

source_name: ngo0406::cm mutant

value: KO of NgoAV (ngo406::cm)

tag: interrupted gene

value: hsdSAV


title: ngo0406::cm cells replicate 2

description: total RNA from not pooled samples


title: WILsp032_04.t11.rep1

source_name: Grape berry 10 weeks post flowering


title: ngo0406::cm cells replicate 1

description: total RNA from not pooled samples


title: ngo0406::cm cells replicate 4

description: total RNA from not pooled samples


title: ngo0545::km cells replicate 3

description: total RNA from not pooled samples

source_name: ngo0545::km mutant

value: KO of NgoAXP (ngo0545::km)

value: modAXP


title: WILsp034_04.t11.rep2


title: WILsp024_04.t8.rep2

source_name: Grape berry 7 weeks post flowering


title: genomic DNA from PBMC 1

description: smoker PBMC sample

source_name: PBMC 1

tag: gender

value: Smoker


title: CLAsk042.t14r2

source_name: Grape berry skin, 13 weeks post flowering


title: ngo0545::km cells replicate 2

description: total RNA from not pooled samples


title: ngo0545::km cells replicate 4

description: total RNA from not pooled samples


title: WILsp022_04.t8.rep1


title: WILsp031_04.t10.rep2

source_name: Grape berry 9 weeks post flowering


title: WILsp035_04.t12.rep1

source_name: Grape berry 11 weeks post flowering


title: WILsp030_04.t10.rep1


title: WILsp036_04.t12.rep2


title: WILsp054_04.t19.rep2

source_name: Grape berry 18 weeks post flowering


title: WILsp013_04.t5.rep2

source_name: Grape berry 4 weeks post flowering


title: WILsp009_04.t4.rep2

description: Gene expression data from whole berries pooled from several bunches

source_name: Grape berry 3 weeks post flowering


title: ngo0545::km cells replicate 1

description: total RNA from not pooled samples


title: WILsp029_04.t9.rep2

source_name: Grape berry 8 weeks post flowering


title: WILsp018_04.t7.rep1

source_name: Grape berry 6 weeks post flowering


title: WILsp017_04.t6.rep2

source_name: Grape berry 5 weeks post flowering


title: WILsp027_04.t9.rep1


title: WILsp011_04.t5.rep1


title: WILsp014_04.t6.rep1


title: WILsp008_04.t4.rep1


title: WILsp005_04.t2.rep2

source_name: Grape berry 1 week post flowering


title: WILsp020_04.t7.rep2


title: Acini_MECs_TG RL 774-72h 48_WT RL 730-72h 44

status: Public on Feb 12 2017

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

description: TG RL 774-72h 48_WT RL 730-72h 44

hyb_protocol: The labeled cRNA was then hybridized to the 44K Whole Mouse Genome Oligo microarrays (G4122A Agilent Technologies, Palo Alto, CA) using the Agilent Gene Expression Hybridization kit and washed using Agilent Gene Expression Wash Buffers following the provided protocols. Each RANKL (Receptor Activator of NFkB Ligand) treated sample was hybridized against its corresponding untreated sample in a fluor-reversed pair of arrays.

scan_protocol: The chips were scanned on Agilent DNA Microarray Scanner G2565AA.

data_processing:
The data were extracted using the Agilent Feature Extraction (version 9.5.1.1) software using the standard Agilent protocol (GE2-v5_95_Feb07_Feature_Extraction) except with Lowess normalization.
Please note that experiments were performed technically as dual channel (e.g., Cy3 and Cy5-labeled samples hybridized to the same array; total 72 hybridizations) but the results were processed as though they were single channel. Rosetta Resolver ratio split algorithm was used to parse individual Cy3 (Ch1) or Cy5 (Ch2) intensity values and then to combine 4 replicate values for each sample into a single intensity value. Therefore, the normalized_combined_data.txt  (available on the Series records) contains 36 data columns [i.e. (72array X 2 channel)/4 replicates; 2 genotype (WT or TG)  X 3 replicates X 3 timepoints (8 ,24 ,72hr) X 2 treatments (w/&w/o RANKL)]. The matrix table has been generated to contain only the non-control agilent features after removing the bad features from the data set, resulting 41174 data rows.
Avreage intensity ratio-split combined error-weighted normalized values (absolute expression) from 4  replicate experiments for each sample.

label_protocol: 200 ng of total RNA from each sample was amplified and labeled using Agilent Low RNA Input Linear Amplification labeling kit (Agilent Technologies, Palo Alto, CA). Labeled cRNA was generated by the incorporation of Cy3-CTP or Cy5-CTP (Perkin Elmer, Waltham, MA) during in vitro transcription and purified using the RNeasy mini kit (Qiagen, Valencia, CA).

growth_protocol: RNA was collected from WT and MMTV-RANK MECs grown in 3D cultures in differentiation media with or without RANKL.

extract_protocol: RNAeasy Kit (Qiagen).

treatment_protocol: For differentiation assays in 3D cultures, 400,000 primary mammary epithelial cells isolated from pregnant WT and MMTV-RANK females were plated in 6 well plates on top of growth factor reduced GFR-matrigel in growth medium (GM: DMEM F12, FBS 5%, EGF 10 ng/ml, hydrocortisone 0.5 μg/ml, insulin 5 μg/ml, cholera toxin 100 ng/ml and penicilin/streptomiciyn) for 24h and subsequently changed to MECs differentiation medium (DM: DMEM F-12, prolactin 3ug/ml, hydrocortisone 1 μg/ml, ITS (Insulin, transferring, selenium), cholera toxin 100 ng/ml, penicilin/streptomiciyn, and RANKL-LZ (1 μg/ml; Amgen Inc) for the indicated time points (8, 24 and 72h).

tag: strain  background

tag: genotype/variation

value: MMTV-RANK transgenic

value: female

tag: age

value: gestation day 16.5

value: Mammary epithelial cells

tag: exposed to

tag: time point

tag: sample id

value: wild type


title: Acini_MECs_WT RL 730-72h 44_TG RL 774-72h 48

description: WT RL 730-72h 44_TG RL 774-72h 48

value: RANKL (Receptor Activator of NFkB Ligand)


title: Acini_MECs_TG RL 774-8h 16_WT RL 730-8h 12

description: TG RL 774-8h 16_WT RL 730-8h 12


title: Acini_MECs_TG RL 774-24h 32_WT RL 730-24h 28

description: TG RL 774-24h 32_WT RL 730-24h 28


title: Acini_MECs_WT RL 730-24h 28_TG RL 774-24h 32

description: WT RL 730-24h 28_TG RL 774-24h 32


title: WILsp007_04.t3.rep2

source_name: Grape berry 2 weeks post flowering


title: Acini_MECs_TG 774-72h 47_WT 730-72h 43

description: TG 774-72h 47_WT 730-72h 43


title: Acini_MECs_WT RL 730-8h 12_TG RL 774-8h 16

description: WT RL 730-8h 12_TG RL 774-8h 16


title: Acini_MECs_WT 730-72h 43_TG 774-72h 47

description: WT 730-72h 43_TG 774-72h 47


title: WILsp003_04.t1.rep2

description: Gene expression data from flowers at anthesis

source_name: Anthesis flower sample


title: Acini_MECs_WT 730-24h 27_TG 774-24h 31

description: WT 730-24h 27_TG 774-24h 31


title: WILsp006_04.t3.rep1


title: WILsp001_04.t1.rep1


title: WILsp004_04.t2.rep1


title: Acini_MECs_TG 774-24h 31_WT 730-24h 27

description: TG 774-24h 31_WT 730-24h 27


title: Zscan4_Emerald- Replicate 3

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Biological replicate 3 of 3, Cy3 is mouse RNA and Cy5 is mouse reference

hyb_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

scan_protocol: standard protocol

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 28 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
The result is used as the normalized VALUE. More information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.

extract_protocol:
Ch1: The samples were dissolved in the well with TRIzol reagent 1/2 mL. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer. ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.
Ch2: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts.

treatment_protocol: Cells were harvested by treatment with 0.05% Trypsin (GIBCO) and mechanical dispersion to make a single cell suspension. They were then resuspended in cell sorting medium (HyQ IMDM (Hyclone), 1% ES-qualified FBS). Cells were sorted based upon emerald fluorescence. Both positive and negative cells were sorted into cell sorting medium: 60% HyQ IMDM, 35% FCS, 1% Glutamax, 1% Pen/Strep, 1% Non-Essential Amino Acids, 1% Beta-mercaptoethanol, 1% Sodium Pyruvate. The cells were then spun down and immediately fixed them with TRIzol reagent (Invitrogen). I then extracted the RNA following Invitrogen protocol.

tag: strain

value: ES [129.3:zscan4cEmgfp] cells

tag: development stage

value: Embryonic Stem Cells

tag: emerald based sorting

value: Regular Medium

tag: individual identifier

source_name: Universal Mouse Reference

tag: sample type

value: Reference


title: Zscan4_Emerald+ Replicate 1

description: Biological replicate 1 of 3, Cy3 is mouse RNA and Cy5 is mouse reference

tag: cell type


title: Zscan4_Emerald+ Replicate 2

description: Biological replicate 2 of 3, Cy3 is mouse RNA and Cy5 is mouse reference


title: Zscan4_Emerald- Replicate 2


title: Zscan4_RA_Emerald+ Replicate 1

description: Biological replicate 1 of 1, Cy3 is mouse RNA and Cy5 is mouse reference

value: Retinoic Acid


title: Zscan4_Emerald- Replicate 1


title: Acini_MECs_WT 730-8h 11_TG 774-8h 15

description: WT 730-8h 11_TG 774-8h 15


title: Zscan4_RA_Emerald- Replicate 1


title: Acini_MECs_TG 774-8h 15_WT 730-8h 11

description: TG 774-8h 15_WT 730-8h 11


title: Acini_MECs_WT RL 686-72h 42_TG RL 732-72h 46

description: WT RL 686-72h 42_TG RL 732-72h 46


title: Acini_MECs_TG RL 732-24h 30_WT RL 686-24h 26

description: TG RL 732-24h 30_WT RL 686-24h 26


title: Acini_MECs_TG RL 732-8h 14_WT RL 686-8h 10

description: TG RL 732-8h 14_WT RL 686-8h 10


title: Acini_MECs_TG 732-8h 13_WT 686-8h 9

description: TG 732-8h 13_WT 686-8h 9


title: Acini_MECs_TG 732-72h 45_WT 686-72h 41

description: TG 732-72h 45_WT 686-72h 41


title: Acini_MECs_WT 686-24h 25_TG 732-24h 29

description: WT 686-24h 25_TG 732-24h 29


title: Acini_MECs_TG 732-24h 29_WT 686-24h 25

description: TG 732-24h 29_WT 686-24h 25


title: Acini_MECs_WT 686-8h 9_TG 732-8h 13

description: WT 686-8h 9_TG 732-8h 13


title: Acini_MECs_WT 686-72h 41_TG 732-72h 45

description: WT 686-72h 41_TG 732-72h 45


title: Acini_MECs_WT RL 670-24h 18_TG RL 672-24h 20

description: WT RL 670-24h 18_TG RL 672-24h 20


title: Acini_MECs_TG RL 672-72h 36_WT RL 670-72h 34

description: TG RL 672-72h 36_WT RL 670-72h 34


title: Acini_MECs_WT RL 670-72h 34_TG RL 672-72h 36

description: WT RL 670-72h 34_TG RL 672-72h 36


title: Acini_MECs_WT RL 686-24h 26_TG RL 732-24h 30

description: WT RL 686-24h 26_TG RL 732-24h 30


title: Acini_MECs_TG RL 672-24h 20_WT RL 670-24h 18

description: TG RL 672-24h 20_WT RL 670-24h 18


title: Acini_MECs_WT 670-72h 33_TG 672-72h 35

description: WT 670-72h 33_TG 672-72h 35


title: Acini_MECs_WT RL 670-8h 2_TG RL 672-8h 4

description: WT RL 670-8h 2_TG RL 672-8h 4


title: Acini_MECs_TG RL 672-8h 4_WT RL 670-8h 2

description: TG RL 672-8h 4_WT RL 670-8h 2


title: Acini_MECs_WT 670-24h 17_TG 672-24h 19

description: WT 670-24h 17_TG 672-24h 19


title: Acini_MECs_TG 672-24h 19_WT 670-24h 17

description: TG 672-24h 19_WT 670-24h 17


title: Zscan4_Emerald+ Replicate 3


title: Acini_MECs_TG RL 732-72h 46_WT RL 686-72h 42

description: TG RL 732-72h 46_WT RL 686-72h 42


title: Acini_MECs_WT 670-8h 1_TG 672-8h 3

description: WT 670-8h 1_TG 672-8h 3


title: Acini_MECs_TG 774-72h 47_TG RL 774-72h 48

description: TG 774-72h 47_TG RL 774-72h 48


title: Acini_MECs_TG 672-8h 3_WT 670-8h 1

description: TG 672-8h 3_WT 670-8h 1


title: Acini_MECs_TG RL 774-24h 32_TG 774-24h 31

description: TG RL 774-24h 32_TG 774-24h 31


title: Acini_MECs_TG RL 774-8h 16_TG 774-8h 15

description: TG RL 774-8h 16_TG 774-8h 15


title: Acini_MECs_TG RL 774-72h 48_TG 774-72h 47

description: TG RL 774-72h 48_TG 774-72h 47


title: Acini_MECs_TG 774-24h 31_TG RL 774-24h 32

description: TG 774-24h 31_TG RL 774-24h 32


title: Acini_MECs_WT RL 686-8h 10_TG RL 732-8h 14

description: WT RL 686-8h 10_TG RL 732-8h 14


title: Acini_MECs_TG 774-8h 15_TG RL 774-8h 16

description: TG 774-8h 15_TG RL 774-8h 16


title: Acini_MECs_TG 672-72h 35_WT 670-72h 33

description: TG 672-72h 35_WT 670-72h 33


title: Acini_MECs_TG RL 732-8h 14_TG 732-8h 13

description: TG RL 732-8h 14_TG 732-8h 13


title: Acini_MECs_TG 732-72h 45_TG RL 732-72h 46

description: TG 732-72h 45_TG RL 732-72h 46


title: Acini_MECs_TG RL 732-24h 30_TG 732-24h 29

description: TG RL 732-24h 30_TG 732-24h 29


title: Acini_MECs_WT RL 730-72h 44_WT 730-72h 43

description: WT RL 730-72h 44_WT 730-72h 43


title: Acini_MECs_WT 730-72h 43_WT RL 730-72h 44

description: WT 730-72h 43_WT RL 730-72h 44


title: Acini_MECs_TG 732-8h 13_TG RL 732-8h 14

description: TG 732-8h 13_TG RL 732-8h 14


title: Acini_MECs_WT RL 686-24h 26_WT 686-24h 25

description: WT RL 686-24h 26_WT 686-24h 25


title: Acini_MECs_WT RL 730-8h 12_WT 730-8h 11

description: WT RL 730-8h 12_WT 730-8h 11


title: Acini_MECs_WT 730-24h 27_WT RL 730-24h 28

description: WT 730-24h 27_WT RL 730-24h 28


title: Acini_MECs_WT 686-72h 41_WT RL 686-72h 42

description: WT 686-72h 41_WT RL 686-72h 42


title: Acini_MECs_WT 730-8h 11_WT RL 730-8h 12

description: WT 730-8h 11_WT RL 730-8h 12


title: Acini_MECs_WT RL 686-72h 42_WT 686-72h 41

description: WT RL 686-72h 42_WT 686-72h 41


title: Acini_MECs_WT RL 686-8h 10_WT 686-8h 9

description: WT RL 686-8h 10_WT 686-8h 9


title: Acini_MECs_WT 686-8h 9_WT RL 686-8h 10

description: WT 686-8h 9_WT RL 686-8h 10


title: Acini_MECs_TG RL 672-72h 36_TG 672-72h 35

description: TG RL 672-72h 36_TG 672-72h 35


title: Acini_MECs_TG 672-72h 35_TG RL 672-72h 36

description: TG 672-72h 35_TG RL 672-72h 36


title: Acini_MECs_TG 672-24h 19_TG RL 672-24h 20

description: TG 672-24h 19_TG RL 672-24h 20


title: Acini_MECs_TG RL 672-24h 20_TG 672-24h 19

description: TG RL 672-24h 20_TG 672-24h 19


title: Acini_MECs_TG RL 672-8h 4_TG 672-8h 3

description: TG RL 672-8h 4_TG 672-8h 3


title: Acini_MECs_TG 672-8h 3_TG RL 672-8h 4

description: TG 672-8h 3_TG RL 672-8h 4


title: Acini_MECs_WT RL 670-72h 34_WT 670-72h 33

description: WT RL 670-72h 34_WT 670-72h 33


title: Acini_MECs_WT 670-72h 33_WT RL 670-72h 34

description: WT 670-72h 33_WT RL 670-72h 34


title: Acini_MECs_TG RL 732-72h 46_TG 732-72h 45

description: TG RL 732-72h 46_TG 732-72h 45


title: Acini_MECs_TG 732-24h 29_TG RL 732-24h 30

description: TG 732-24h 29_TG RL 732-24h 30


title: Acini_MECs_WT RL 730-24h 28_WT 730-24h 27

description: WT RL 730-24h 28_WT 730-24h 27


title: Acini_MECs_WT 686-24h 25_WT RL 686-24h 26

description: WT 686-24h 25_WT RL 686-24h 26


title: Acini_MECs_WT RL 670-24h 18_WT 670-24h 17

description: WT RL 670-24h 18_WT 670-24h 17


title: Acini_MECs_WT RL 670-8h 2_WT 670-8h 1

description: WT RL 670-8h 2_WT 670-8h 1


title: Acini_MECs_WT 670-24h 17_WT RL 670-24h 18

description: WT 670-24h 17_WT RL 670-24h 18


title: Acini_MECs_WT 670-8h 1_WT RL 670-8h 2

description: WT 670-8h 1_WT RL 670-8h 2


title: SVts8_33.5

city: Setagaya-ku

first: Mizuho

last: Sakaki

state: Tokyo

department: Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

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

scan_protocol: Arrays were imaged using the iScan system with standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.1
The methylation level of each of the >  27,000 CpG sites was calculated using the GenomeStudio Methylation Module 1.9.0 (Illumina). Normalization was performed using Normalization to Internal Controls and Background Subtraction options implemented in the Methylation Module 1.9.0.

source_name: SVts8 cells cultured under 33.5°C

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated using the DNeasy Blood & Tissue (Qiagen) according to the manufacturer’s instructions.

tag: derived cell

tag: cell state

value: proliferating


title: PDL85

source_name: TIG3 cells passaging until PDL85

value: senescence


title: pBabe-puro

source_name: TIG3 cells induced pBabe-puro


title: SVts8_38

source_name: SVts8 cells cultured under 38°C


title: PAO1 treated with sphingomyelin rep.2

city: Fukuoka

first: Nozomu

last: OKINO

state: Fukuoka

address: 6-10-1 Hakozaki, Higashi-ku

department: Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences

institute: Kyushu University

hyb_protocol: cRNA was hybridized to Affymetrix P. aeruginosa Genome Array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PAO1 cultures with addition of 200 µM sphingomyelin

label_protocol: The cRNA was amplified, labeled using Ambion®WT Expression Kit、GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

growth_protocol: P. aeruginosa cells were cultured in 2 ml of PY-medium containing 0.05% sodium taurodeoxycholate, and shaken at 30°C for 8 h.

extract_protocol: Total RNA was isolated from cells using TRI Reagent (Molecular Research Center) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: The cells were stabilized by RNAlater and harvested.


title: pBabe-puro-H-RAS-V12

source_name: TIG3 cells induced pBabe-puro-H-RAS-V12


title: PAO1 untreated rep.3

source_name: P. aeruginosa PAO1 cultures without addition of 200 µM sphingomyelin


title: PAO1 untreated rep.1


title: PAO1 treated with sphingomyelin rep.3


title: PAO1 untreated rep.2


title: PDL36

source_name: TIG3 cells passaging until PDL36


title: PAO1 treated with sphingomyelin rep.1


title: PDL49

source_name: TIG3 cells passaging until PDL49


title: ein2_cd_6_rep3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Transcriptomic profiling of Arabidopsis thaliana mutants in response to combined abiotic stress

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5242).

scan_protocol: Scanned on an Agilent scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX 12 Software. 75th Percentile Shift Normalization

organism: Arabidopsis thaliana

source_name: leaf tissue_cd_6

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop.

extract_protocol: Trizol-RNA extraction

tag: tissue

value: leaf tissue


title: ein2_cd_6_rep2


title: aba1.6_cd_6_rep3


title: aba1.6_cd_6_rep2


title: ein2_cd_6_rep1


title: SBMA;TLS+/- biological rep 1

city: Tokyo

first: Yoshihiro

last: Kino

address: 2-522-1 Noshio, Kiyose

institute: Meiji Pharmaceutical University

hyb_protocol: 5 ug of Fragmented ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed by the RMA algorithm using AltAnalyze software at the default setting.
MoEx-1_0-st-v1.r2.pgf
Mm_gene_extended.mps

source_name: SBMA;TLS+/-, spinal cord at 8 weeks

label_protocol: 100ng of total RNA was used to prepare biotinilated DNA, according Affymetrix recomandations (http://media.affymetrix.com/support/downloads/manuals/wt_expressionkit_manual.pdf). Whole transcript targets were produced using the Ambion WT kit and the Affymetrix kit (The Affymetrix GeneChip® WT Terminal Labeling Kit) to fragment and labelled DNA.

extract_protocol: Samples were dissected and snap-frozen in liquid nitrogen. RNA extraction with Trizol and purification with RNeasy mini kit (Qiagen)

value: SBMA;TLS+/-

value: 8 weeks

value: spinal cord


title: SBMA;TLS+/- biological rep 2


title: SBMA;TLS+/+ biological rep 3

source_name: SBMA;TLS+/+, spinal cord at 8 weeks

value: SBMA;TLS+/+


title: SBMA;TLS+/+ biological rep 2


title: PDL69

source_name: TIG3 cells passaging until PDL69


title: aba1.6_cd_6_rep1


title: SBMA;TLS+/- biological rep 3


title: Col-0_cd_6_rep2 (2)


title: WT;TLS+/- biological rep 3

source_name: WT;TLS+/-, spinal cord at 8 weeks

value: WT;TLS+/-


title: WT;TLS+/- biological rep 2


title: SBMA;TLS+/+ biological rep 1


title: Col-0_cd_6_rep1 (2)


title: WT;TLS+/+ biological rep 2

source_name: WT;TLS+/+, spinal cord at 8 weeks

value: WT;TLS+/+


title: WT;TLS+/- biological rep 1


title: WT;TLS+/+ biological rep 3


title: WT;TLS+/+ biological rep 1