title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipG


title: H1N1 O- CA BAL 16187 d14

status: Public on Jun 06 2012

type: RNA

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
For the creation of the normalized data, the limma package was used. Background correction was performed (method=normexp, offset=1).

molecule: total RNA

organism: Macaca mulatta

source_name: Ilhem H1N1 O- CA BAL 16187 d14

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: The study was carried out in strict accordance with the recommendations described in the Guide for the Care and Use of Laboratory Animals of the National Institute of Health, the Office of Animal Welfare and the United States Department of Agriculture. All animal work was approved by the Oregon National Primate Research Center (ONPRC) Institutional Animal Care and Use Committee, which is accredited by the American Association for Accreditation of Laboratory Animal Care (PHS/OLAW Animal Welfare Assurance # A3304-01). All procedures were carried out under Ketamine anesthesia by trained personnel under the supervision of veterinary staff and all efforts were made to ameliorate the welfare and to minimize animal suffering in accordance with the “Weatherall report for the use of non-human primates” recommendations. Animals were housed in adjoining individual primate cages allowing social interactions, under controlled conditions of humidity, temperature and light (12-hour light/12-hour dark cycles). Food and water were available ad libitum. Animals were monitored and fed commercial monkey chow, treats and fruit twice daily by trained personnel. Environmental enrichment consisted of commercial toys. Sixteen female rhesus macaques (Macaca Mulatta) 10-12 (Adult) and 20-24 years (Old/Aged) of age were used in these studies. Animals were infected using a combinatory of intra-tracheal (4ml), intranasal (0.5 ml/nostril), and conjunctival (0.5 ml/eyelid) routes for a total dose of 7x106 TCID50 dose. Microarray analysis was performed on Bronchoalveolar lavage (BAL) samples collected on days 0, 4, 7, 10 and 14.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Microarray analysis was performed on Bronchoalveolar lavage (BAL) samples collected on days 0, 4, 7, 10 and 14.  Note: One of the Day 0 array did not pass QC metrics so for this animal the average of the other Day 0 samples from that group was utilized.1 million BAL cells were resuspended in Trizol (Invitrogen) and frozen until RNA was extracted.

tag: age

value: 20-24 years old

tag: gender

value: female

tag: time (post-infection)

value: day 14

tag: infection

value: A/California/04/2009 H1N1

tag: sample type

value: bronchial lavage

tag: subject


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipG

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with TAS.

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

scan_protocol: Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The data were processed with Tiling Array Software (TAS) using standard parameters according to Kampa et al. ("Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.". Genome Research, 14:331-42, 2004.). In order to identify highly expressed segments we set bandwith=35, i.e. on average the probe intensities are smoothed by calculating the Hodges-Lehman estimator over 3 probes, and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal length of segments to be reported as highly expressed was set to minrun=90. Perfect match (PM) and mismatch (MM) probe intensities were utilized in using an intensity threshold of 150. Differentially expressed segments were identified with the following parameters: Signal intensities of chips of the same type were normalized across the two different biological conditions and log fold changes were calculated. We set bandwith=150 and the maximal gap between probes to be included in a differentially expressed interval was set to maxgap=40. The minimal length of differentially expressed segments was set to minrun=90. Here we use a q-value < 0.05 which results in an FDR of 18%. To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, we identify highdiff intervals by intersecting intervals identified as differentially expressed with those intervals deemed as 'expressed' in at least one of the compared biological states.

label: biotin

organism: Homo sapiens

source_name: Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle

label_protocol: 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.

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

tag: cell line

value: HFF

tag: data processing

value: TAS


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipG

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression data was processed with MAT.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 5e-2 which yielded the best results from the set of tested parameter values.

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle

value: MAT


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipH

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression data was processed with our novel permutation approach TileShuffle.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle

value: TileShuffle


title: HFF cells residing in G0 phase, biological replicate 1

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. HFF cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle.

hyb_protocol: nONCOchip 1.0 arrays were proceed using the Agilent Hybridization Kit, Agilent Hybrization-Chambers and an commercial Hyb-Oven according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling Kit).

scan_protocol: Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 100%, PMT: 300/400, resolution: 5µm, Focus: 0µm, Lines to Average: 2, Wavelength: 532nm, Filter: Standard Green.

data_processing: The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Expression levels were normalized (quantile normalization) and a linear model was fitted using the R package limma in order to identify differentially expressed probes. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

label_protocol: 1µg RNA were analyzed on nONCOchip 1.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protokoll).

tag: cell type

tag: cell cycle


title: Low density associated fibroblasts #3

city: San Francisco

first: RosaAnna

last: DeFilippis

state: CA

address: 513 Parnassus Ave

department: Pathology

institute: University of California San Francisco

description: gene expression data

hyb_protocol: Following fragmentation, 10ug of cRNA was hybridized to Affymetrix HU133 plus 2 chips following manufactorer's instructions in GeneChip Expression Analysis Technical Manual 701021 Rev. 3.

scan_protocol: Gene chips were scanned using the affymetrix Gene Chip Scanner 3000 (GCS3000).

data_processing: The dataset was processed using Affymetrix GCOS 1.4 software.

source_name: mammary fibroblast from woman with low MD

label_protocol: 1 ug of total RNA was used make to amplified and biotinylated cRNA using Ambion's Message Amp II kit according to the manufacturer's instructions.

growth_protocol: Fibroblasts were cultured in RPMI-1640 with L-glutamine, 25 mM Hepes and 10% FBS.

extract_protocol: Total RNA was isolated from cell pellets using Qiagen's Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Fibroblasts were trypsinized, counted on a hemacytometer and 7.4x10^5 - 1x10^6 cells pelleted down. Cell pellets were washed 1x in cold 1x PBS, repelleted in microcentrifugre tubes and snap frozen.

tag: source tissue

value: mammary gland

value: fibroblast

tag: phenotype

value: low mammographic density


title: Low density associated fibroblasts #4

description: gene expression data


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipH


title: Low density associated fibroblasts #5

description: gene expression data


title: HFF cells using TAS (G1 phase) ChipG

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression data was processed with TAS.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with Tiling Array Software (TAS) using standard parameters according to Kampa et al. ("Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.". Genome Research, 14:331-42, 2004.). We set bandwith=35, i.e. on average the probe intensities are smoothed by calculating the Hodges-Lehman estimator over 3 probes, and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal length of segments to be reported as highly expressed was set to minrun=90. Perfect match (PM) and mismatch (MM) probe intensities were utilized in using an intensity threshold of 150.

tag: phase


title: HFF cells using TAS (G0 phase) ChipG

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression data was processed with TAS.


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipH

description: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with MAT.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 5e-2 which yielded the best results from the set of tested parameter values. Differentially expressed segments were identified with the following parameters: We set bandwith=150 and the maximal gap between probes to be included in a differentially expressed interval was set to maxgap=40. The minimal length of differentially expressed segments was set to minprobe=3. Here we use a q-value < 1e-6 which results in an FDR of 17%. To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, we identify highdiff intervals by intersecting intervals identified as differentially expressed with those intervals deemed as 'expressed' in at least one of the compared biological states.


title: Low density associated fibroblasts #1

description: gene expression data


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipL

description: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with our new permutation approach TileShuffle.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.). Analysis of differential expression was performed with the same parameters, except of 100000 permutations, aiming at accommodating the more rugged nature of expression difference signal. Here we use variant B to detect differentially expressed segments, i.e. it is assumed that entire windows are either up- or downregulated between two conditions and converse behaviour of neighboring probes is a consequence of non-specific hybridization. In order to correct for this bias, the presumed direction of regulation is initially assigned to each window on the basis of the sign of its expression scores. Subsequently, all converse probes, i.e. probes with negative log-fold change within positive windows or vice versa, are ignored and neither permuted nor incorporated into the score calculation for differential expression. Consequently, positive and negative windows are compared to different background distributions. To asses the significance of a window score a one-tailed empirical p-value is estimated (according to the corresponding background distribution) and corrected for multiple testing, similar to the one-state analysis. Here we use a q-value < 0.1 which results in an FDR of 18%. To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, TileShuffle takes regions found to be significantly high expressed in at least one of the compared states as input for the two-state analysis, and assesses differential expression solely on the expressed segments.


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipH


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipL

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression data was processed with our novel permutation algorithm TileShuffle.


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipL


title: PA049_367_080522

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

hyb_protocol: The Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridised for 16 hours in a 45°C incubator, rotated at 60rpm according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc.)

scan_protocol: Fluidics Station 450 and GeneChip® Scanner 3000 7G

data_processing: Robust multi-array average (RMA)

source_name: Fresh frozen human lung cancer tumor tissue; microdissected

label_protocol: GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 5)

extract_protocol: For the whole tissue samples, 2µg of total RNA from each sample was used to prepare biotinylated fragmented cRNA. From each of the microdissected samples, 20ng of total RNA was used to prepare biotinylated fragmented cRNA using a two-cycle amplification step according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

tag: tissue

value: microdissected non-small cell lung cancer

tag: patient id

tag: extraction


title: PA049_296_071219

value: 20ng of total RNA was used to prepare biotinylated fragmented cRNA using a two-cycle amplification step according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA)


title: PA049_319_071219


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipH

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression data was processed with MAT.


title: PA049_234_080522


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipL


title: HFF cells using TAS (G0 phase) ChipH


title: HFF cells using TAS (G1 phase) ChipH


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipL


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipL


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipF


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipK


title: Low density associated fibroblasts #2

description: gene expression data


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipK


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipF


title: FB placenta replication1

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

description: RNA amplification, cDNA synthesis, labeling was performed using GeneChip®3’ IVT Express Kit  following the instructions described in GeneChip®3’ IVT Express Kit user manual [(P/N 702646 Rev. 8) (Affymetrix Inc)].

hyb_protocol: Array hybridization was performed after mixing appropriative amount of hybridization components, fragmented and labelled cRNA, control oligonucleotide B2 (3 nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix , DMSO and RNAse free water.The hybridization mix was heated to 99°C for 5 min followed by heating at  45°C for 5 min. Following this the samples were hybridized to the GeneChip® Bovine Genome Array (Affymetrix, CA, USA) for 16 h at 45°C. Three biotin labeled cRNA hybridizations were performed for  each samples of each category (SCNT, IVP, AI and FB)

scan_protocol: After 16 h of hybridization, the arrays washing and staining was performed using the Fluidics Station 450/250 integrated as recommended in GeneChip® expression wash, stain and scan user manual (P/N 702731 (Affymetrix). The arrays were then scanned using affymetrix®GeneChip™3000 slide scanner (Affymetrix, CA, USA).

data_processing: The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma) . The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA).  For this, we used R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).

organism: Bos taurus

source_name: Fibroblasts used as a donor cells  for the production of Somatic cell nuclear transfer embryos 1

label_protocol: The cRNA  was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual

extract_protocol: Total RNA was isolated from 15 mg samples of IVP, NT or AI placentas and 4x106 Donor cells (fibroblast cells) using miRNeasy mini kit (QIAGEN GmbH, Hilden, Germany).


title: PA049_13_071219


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipL


title: FB placenta replication2

source_name: Fibroblasts used as a donor cells  for the production of Somatic cell nuclear transfer embryos 2


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipF


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipK


title: PA025_296A_081211

source_name: Fresh frozen human lung cancer tumor tissue

value: non-small cell lung cancer

value: 2µg of total RNA was used to prepare biotinylated fragmented cRNA.


title: FB placenta replication3

source_name: Fibroblasts used as a donor cells  for the production of Somatic cell nuclear transfer embryos 3


title: PA025_367A_070907


title: PA025_319A_070914


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipK


title: HFF cells using TAS (G1 phase) ChipL


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipF


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipF


title: AI placenta replication1

source_name: Placenta from pregnancies established after the transfer of in vivo produced embryos at day 50 of gestation 1

value: placenta

tag: treatment

value: transfer of in vivo produced embryos


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipK


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipF


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipN


title: AI placenta replication3

source_name: Placenta from pregnancies established after the transfer of in vivo produced embryos at day 50 of gestation 3


title: AI placenta replication2

source_name: Placenta from pregnancies established after the transfer of in vivo produced embryos at day 50 of gestation 2


title: HFF cells using TAS (G0 phase) ChipL


title: NT placenta replication3

source_name: Placenta from pregnancies established after the transfer of  embryos produced by somatic cell nuclear transfer at day 50 of gestation 3


title: IVP placenta replication3

source_name: Placenta from pregnancies established after the transfer of in vitro fertilzed and in vitro culture embryo at day 50 of gestation 3


title: NT placenta replication2

source_name: Placenta from pregnancies established after the transfer of  embryos produced by somatic cell nuclear transfer at day 50 of gestation 2


title: IVP placenta replication2

source_name: Placenta from pregnancies established after the transfer of in vitro fertilzed and in vitro culture embryo at day 50 of gestation 2


title: PA025_234A_070912


title: IVP placenta replication1

source_name: Placenta from pregnancies established after the transfer of in vitro fertilzed and in vitro culture embryo at day 50 of gestation 1


title: PA025_13A_070509


title: NT placenta replication1

source_name: Placenta from pregnancies established after the transfer of  embryos produced by somatic cell nuclear transfer at day 50 of gestation 1


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipN

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipF

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipN


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipK


title: HFF cells using TAS (G1 phase) ChipF


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipN

source_name: Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle


title: HFF cells using TAS (G0 phase) ChipF


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipK


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipN


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipN


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipM


title: HFF cells using TAS (G0 phase) ChipK


title: Methyl-Cytosine IPP from LP Hypothalamus 155 MBH-LP-155

type: genomic

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

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

data_processing: A scaled log2 ratio was calculated for each feature, and subjected to a 750pb window one-sided Kologorov-Smirnov (KS) test. The KS test determines if the probes have a more significant intensity versus the rest of the array. A negative log10 p-value is reported (e.g. 2 equals a p-value of 0.01).

molecule: genomic DNA

organism: Rattus norvegicus

label_protocol: For each of the nine samples, base Cy3 labeled DNA was co-hybridized with Immunoprecipitated Cy5 labeled DNA, and raw signals were detected for all chip features on both channels.

extract_protocol: Rats were anesthetized and brains were rapidly removed. The hypothalamus was dissected away from the rest of the brain and flash frozen. Total RNA and DNA was isolated from each sample using AllPrep DNA/RNA Mini Kit-Qiagen (Valencia, CA). 2000ng of genomic DNA was digested over night with MseI.  After Qiagen PCR cleanup, 150 ng of DNA  were run in a 1% agarose gel to chek digestion efficiency. 500ng of digested DNA were Ipp over night using the Methylamp Kit from Epigentek. 50ng of digested DNA were kept as input material. Ipp and input material were amplified using the WGA2 whole genome amplification Kit from SIGMA. After Qiagen PCR cleanup,  ~25ng of DNA were run in a Agilent DNA chip. Input and methyl Cytosine IPP samples  were subjected to hybridization with the Roche NimbelGen rat Meth 385K Arr Del array (RN34 CpG Island).

tag: strain

value: Sprague Dawley

tag: age

value: 31 days

tag: reproductive stage

value: late proestus

value: Methyl-Cytosine IPP

value: hypothalamus

source_name: Input DNA from LP Hypothalamus 155

value: input DNA


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipM

value: HFF


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipN

value: MAT


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipM

value: TileShuffle


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipM

value: TAS


title: HFF cells using TAS (G1 phase) ChipN


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipM


title: HFF cells using TAS (G1 phase) ChipK


title: HFF cells using TAS (G0 phase) ChipN


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipE


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipM


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipM


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipE


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipE


title: HFF cells using TAS (G1 phase) ChipM


title: Methyl-Cytosine IPP from LP Hypothalamus 162 MBH-LP-162

source_name: Input DNA from LP Hypothalamus 162


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipE


title: Methyl-Cytosine IPP from LJ Hypothalamus 135 MBH-LJ-135

value: 28 days

value: late juvenile

source_name: Input DNA from LJ Hypothalamus 135


title: Methyl-Cytosine IPP from LP Hypothalamus 151 MBH-LP-151

source_name: Input DNA from LP Hypothalamus 151


title: HFF cells using TAS (G0 phase) ChipM


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipE


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipD


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipE


title: Methyl-Cytosine IPP from LJ Hypothalamus 131 MBH-LJ-131

source_name: Input DNA from LJ Hypothalamus 131


title: Methyl-Cytosine IPP from EJ Hypothalamus 166 MBH-EJ-166

value: 21 days

value: early juvenile

source_name: Input DNA from EJ Hypothalamus 166


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipD


title: Methyl-Cytosine IPP from LJ Hypothalamus 134 MBH-LJ-134

source_name: Input DNA from LJ Hypothalamus 134


title: H3K27me3 in Ring1A-KO ESCs (OHT-)_Promoter 1

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

hyb_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

scan_protocol: ChIP-v1_10_Apr08, Agilent DNA Microarray Scanner G2505C, Agilent Scan Control (Ver. A.8.4.1)

data_processing: Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

organism: Mus musculus

source_name: Input DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells (OHT-untreated)

growth_protocol: ES cells were cultured in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.

extract_protocol: ES cells were subjected to ChIP assay using antibodes. Catalogue number of antibodies were Millipore 07-449 for H3K27me3, Millipore 05-678 for H2AK119u1, Abcam ab18255 for H2A and Sigma F1804 for Flag tag. Antibody against Ring1B, equivalent to MBL D139-3, was developed by our laboratory using published protocol by Atsuta et al (Hybridoma, 2001). Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously (van Bakel et al., 2008).

treatment_protocol: ES cells were treated with 1 % formaldehyde/PBS for 10 min at room temperature. Cells were washed with PBS, collected and resuspended in swelling buffer [20 mM Hepes (pH 7.8), 1.5 mM MgCl2, 10 mM KCl, 0.1 % NP-40, and 1 mM DTT] by pipetting and then kept on ice for 10 min. After Dounce homogenizing 10-20 times, the cells were centrifuged and then the pellets were resuspended in RIPA buffer [20 mM Tis-HCl (pH 8.0), 1 mM EDTA, 140 mM NaCl, 1 % Triton X-100, 0.1 % SDS, and 0.1 % deoxycholic acid] containing protease inhibitors and sonicated into fragments with an average length of 0.3-0.5 kb. After centrifugation, the supernatants were subjected to IP with specific antibodies as previously described (Orlando et al., 1997)

value: ES cells

source_name: Immunoprecipitated DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells (OHT-untreated)

tag: antibody

tag: antibody vendor

value: Millipore 07-449


title: H3K27me3 in Eed-KO ESCs_Promoter 1

description: H3K27me3 in Eed-KO ESCs_Promoter 1

source_name: Input DNA from Eed-KO ES cells

label_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

value: Eed-KO

source_name: Immunoprecipitated DNA from Eed-KO ES cells


title: Methyl-Cytosine IPP from EJ Hypothalamus 168 MBH-EJ-168

value: Sprague Dawley

tag: sample type

source_name: Input DNA from EJ Hypothalamus 168


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipD

tag: cell line


title: 3xFlag-Ring1A in Ring1A-KO ESCs (OHT-)_Promoter 1

source_name: Input DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing 3xFlag-Ring1A (OHT-untreated)

value: ES cells expressing 3xFlag-Ring1A

value: OHT-untreated

source_name: Immunoprecipitated DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing 3xFlag-Ring1A (OHT-untreated)

value: Sigma F1804


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipE

tag: data processing


title: 3xFlag-Ring1A in Ring1A/B-KO ESCs (OHT+ day2)_Promoter 1

source_name: Input DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing 3xFlag-Ring1A 2 days after the start of OHT treatment

tag: cell type

value: OHT-treated

source_name: Immunoprecipitated DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing 3xFlag-Ring1A 2 days after the start of OHT treatment


title: HFF cells using TAS (G1 phase) ChipE

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipD

source_name: Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle


title: H2A in Ring1A-KO ESCs (OHT-)_Promoter 1

description: H2A in Ring1A-KO ESCs (OHT-)_Promoter 1

value: Abcam ab18255


title: 3xFlag-Ring1A in Ring1A-KO ESCs (OHT-)_Promoter 2


title: 3xFlag-Ring1A in Ring1A/B-KO ESCs (OHT+ day2)_Promoter 2


title: H3K27me3 in Ring1A-KO ESCs (OHT-)_Promoter 2


title: H2AK119u1 in Ring1A-KO ESCs (OHT-)_Promoter 1 (rep 2)

value: Millipore 05-678


title: H2A in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 1

source_name: Input DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells 2 days after the start of OHT treatment

source_name: Immunoprecipitated DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells 2 days after the start of OHT treatment


title: Ring1B in Ring1A-KO ESCs (OHT-)_Promoter 1 (rep 2)

value: against Ring1B

value: in house


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipD

value: HFF

value: MAT


title: H2A in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 2


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipD


title: Ring1B in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 1 (rep 2)


title: Methyl-Cytosine IPP from EJ Hypothalamus 165 MBH-EJ-165

value: Methyl-Cytosine IPP

value: hypothalamus

source_name: Input DNA from EJ Hypothalamus 165

value: input DNA


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipD

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: H2AK119u1 in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 1 (rep 2)

value: ES cells


title: H2AK119u1 in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 1 (rep 1)


title: H2A in Ring1A-KO ESCs (OHT-)_Promoter 2

description: H2A in Ring1A-KO ESCs (OHT-)_Promoter 2


title: H2AK119u1 in Ring1A-KO ESCs (OHT-)_Promoter 2 (rep 2)


title: H3K27me3 in Eed-KO ESCs_Promoter 2

description: H3K27me3 in Eed-KO ESCs_Promoter 2

value: Millipore 07-449


title: H2AK119u1 in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 2 (rep 2)


title: H2AK119u1 in Ring1A-KO ESCs (OHT-)_Promoter 1 (rep 1)


title: HFF cells using TAS (G0 phase) ChipD


title: Human D54 shRNA 3

city: nashville

first: Miaojun

last: Han

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University

description: D54 transfected TIP-1 shRNA

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Vanderbilt Microarray Core Facility(FGSR).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Fresh typsined cells seeding in DMEM/F12 and culture cellls overnight for RNA extract.

extract_protocol: RNA was isolated from 10^6 cells in 10-cm dish with Ambion RNAqueous Kit, according to the manufacturer’s instructions.

value: Glioma cell

tag: transfection

value: shRNA TIP-1


title: HFF cells using TAS (G1 phase) ChipD


title: Human D54 shRNA 2

description: D54 transfected TIP-1 shRNA


title: Ring1B in Ring1A-KO ESCs (OHT-)_Promoter 1 (rep 1)


title: Ring1B in Ring1A-KO ESCs (OHT-)_Promoter 2 (rep 2)


title: Ring1B in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 2 (rep 2)


title: Human D54 shRNA 1

description: D54 transfected TIP-1 shRNA


title: Ring1B in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 1 (rep 1)


title: Human D54 control 2

description: D54 transfected control shRNA

value: control shRNA


title: Human D54 control 1

description: D54 transfected control shRNA


title: gran_t=0_rep4

status: Public on Jun 05 2012

city: Nijmegen

first: Stan

middle: de

last: Kleijn

address: Kapittelweg 29

department: Laboratory of pediatric infectious diseases

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Affymetrix expression console core RMA sketch
probe group file: HuEX-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: LPS infusion blood

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

extract_protocol: Qiagen Rneasy total RNA isolation

value: isolated circulating neutrophils

tag: time point (hours)


title: gran_t=4_rep4


title: gran_t=6_rep4


title: gran_t=2_rep4


title: gran_t=6_rep3


title: gran_t=4_rep3


title: gran_t=2_rep1


title: Ring1B in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 2 (rep 1)


title: H2AK119u1 in Ring1A/B-dKO ESCs (OHT+ day2)_Promoter 2 (rep 1)


title: H2AK119u1 in Ring1A-KO ESCs (OHT-)_Promoter 2 (rep 1)


title: slide 15-lumiestrone experiment

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

description:
Sexually inactive male goldfish were injected i.p. with lumiestrone (0.5 µg/g) or control vehicle (in charcoal-stripped peanut oil; 5 µL/g). Animals were anaesthetized in MS222, and livers were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #15

hyb_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers.  Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes.  Normalization was performed using LOWESS and scale methods using the Alien Spot Report Genes 1-10 (Stratagene).

organism: Carassius auratus

source_name: vehicle control

extract_protocol: RNeasy Mini Plus kit (Invitrogen)

tag: Sexually inactive male adult goldfish;  liver tissue

source_name: luminestrone-injected (0.5 ug/g)


title: gran_t=0_rep3


title: slide 20-lumiestrone experiment

description:
Sexually inactive male goldfish were injected i.p. with lumiestrone (0.5 µg/g) or control vehicle (in charcoal-stripped peanut oil; 5 µL/g). Animals were anaesthetized in MS222, and livers were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #20

label_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)


title: gran_t=4_rep2


title: gran_t=2_rep3


title: gran_t=2_rep2


title: gran_t=0_rep1


title: gran_t=6_rep2


title: slide 43-lumiestrone experiment

description:
Sexually inactive male goldfish were injected i.p. with lumiestrone (0.5 µg/g) or control vehicle (in charcoal-stripped peanut oil; 5 µL/g). Animals were anaesthetized in MS222, and livers were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #43


title: gran_t=4_rep1


title: gran_t=6_rep1


title: slide 2-lumiestrone experiment

description:
Sexually inactive male goldfish were injected i.p. with lumiestrone (0.5 µg/g) or control vehicle (in charcoal-stripped peanut oil; 5 µL/g). Animals were anaesthetized in MS222, and livers were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #2


title: gran_t=0_rep2


title: HFF cells using TAS (G0 phase) ChipE

tag: phase


title: Ring1B in Ring1A-KO ESCs (OHT-)_Promoter 2 (rep 1)

source_name: Input DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells (OHT-untreated)

source_name: Immunoprecipitated DNA from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells (OHT-untreated)


title: M24met_control_1

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

description: M24 Co_1

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: RMA normalization using R 2.9 and BioC 2.4

source_name: M24met melanoma cell-line

label_protocol: biotin (GeneChip Expression 3´Amplification One-Cycle Target Labeling and Control Reagents (30Rxn)

growth_protocol: Control and Wnt-1 overexpressing human melanoma cell-lines (A375 and M24met) were injected into the right flank of SCID mice. Primary tumors were removed after a mean tumor volume of 400m3 and RNA was prepared. For Affymetrix chips, 5µg of RNA were reverse transcribed into second strand cDNA. Preparation of cRNA, hybridization to Human Genome U133 Plus 2.0 (Affymetrix) were carried out according to the manufacturer’s protocols (www.affymetrix.com).

extract_protocol: SCID mouse-derived samples  were homogenized with RLT lysis buffer using a mixer mill MM200. Total RNA was extracted using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Where indicated, animals were fed with CsA (50mg/kg/day) via a gauge

value: M24met melanoma cell-line

tag: genotype/variation

value: wild type

value: control


title: M24met_control_2

description: M24 Co_2


title: M24met_Wnt1_3

description: M24 Wnt1_3

value: Wnt-1 overexpressing


title: A375 control+CsA -3

source_name: A375 melanoma cell-line

value: A375 melanoma cell-line

value: animals were fed with CsA (50mg/kg/day)


title: A375 control+CsA -4


title: A375 Wnt1+CsA-3

description: A375 Wnt1-CsA_3


title: M24met_Wnt1_4

description: M24 Wnt1_4


title: M24met_Wnt1_2

description: M24 Wnt1_2


title: M24met_Wnt1_1

description: M24 Wnt1_1


title: M24met_control_5

description: M24 Co_5


title: M24met_Wnt1_5

description: M24 Wnt1_5


title: M24met_control_4

description: M24 Co_4


title: A375 Wnt1+CsA-2

description: A375 Wnt1-CsA_2


title: A375 control+CsA -2


title: M24met_control_3

description: M24 Co_3


title: A375 Wnt1-3

description: A375 Wnt1_3


title: A375 Wnt1-2

description: A375 Wnt1_2


title: A375 Wnt1+CsA-1

description: A375 Wnt1-CsA_1


title: A375 control-4

description: A375 Co_4


title: A375 Wnt1-1

description: A375 Wnt1_1


title: A375 control-2

description: A375 Co_2


title: A375 control-1

description: A375 Co_1


title: A375 control+CsA -1


title: A375 control-3

description: A375 Co_3


title: Memory P14 CD8+ T cell rep#3

city: ATLANTA

first: Tuoqi

last: Wu

state: GA

address: 1510 Clifton Rd, Room G211

institute: Emory University

description: miRNA expression data of memory P14 CD8+ T cells

hyb_protocol: ~45 ul of each target was loaded on the 8 plex gasket slide. miRNA array slide was placed on the gasket slide per Agilent Protocol. The chamber was assembled and incubated at 55C 20 RPM for a 20 hours hybridization.

scan_protocol: Samples were scanned with Agilent C Scanner at Vanderbilt University Microarray core according to manufacturer's instructions

data_processing: The raw data were normalized by 90th percentile shift, baseline transformed using GeneSpring GX11.5.

source_name: Memory P14 CD8+ T cells

label_protocol: 100 ng total RNA was dephosphorylated at the 5' by Calf Intestinal Alkaline Phosphatase, denatured, and labeled with Cyanine3-pCp using T4 DNA ligase.

extract_protocol: Total RNA were prepared using miRNeasy Kit (Qiagen) according to manual.

treatment_protocol: P14 cells were collected from P14 transgenic mice and tranferred to C57BL6 recipients. Chimeras were infected with LCMV Armstrong.

value: CD8+ T cells


title: Replication timing of Tc1 MEFs, average of 2 biological replicates

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

description: Whole mouse genome

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (6 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the entire mouse genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing:
NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245]. Human syntenic sequence positions were obtained for each probe using the Lift Genome Annotation tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver) with accepted default parameters. We analyzed all mouse array probes within regions syntenic to human chromosome 21. Data for other mouse regions were not relevant to this study.
This single Sample represents two biological replicates with dye swap.  The first is comprised of 304067_Tc1MEF1_635.pair (early replicating) and 334246_Tc1MEF2_532.pair (late replicating) raw data files.  The second is 304067_Tc1MEF1_532.pair (early replicating) and 334246_Tc1MEF2_635.pair (late replicating).

label: Cy5, Cy3

source_name: Early-replicating DNA of Tc1 MEFs replicate 1

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245]. For complete extraction protocol, please refer to PubMed ID: 21637205.

value: MEFs

tag: dna replication status

value: Early-replicating DNA

label: Cy3, Cy5

source_name: Late-replicating DNA of Tc1 MEFs replicate 1

value: Late-replicating DNA


title: Replication timing of Tc1 CD4+ T lymphocytes, average of 2 biological replicates

description: Mouse genomic data

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 3.5 kb across the entire mouse genome.

data_processing:
NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245]. Human syntenic sequence positions were obtained for each probe using the Lift Genome Annotation tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver) with accepted default parameters. We analyzed all mouse array probes within regions syntenic to human chromosome 21. Data for other mouse regions were not relevant to this study.
This single Sample represents two biological replicates with dye swap.  The first is comprised of 470851_Tc1Tcell1_532.pair (early replicating) and 470851_Tc1Tcell1_635.pair (late replicating) raw data files.  The second is 470851_Tc1Tcell2_532.pair (early replicating) and 470851_Tc1Tcell2_635.pair (late replicating).

source_name: Early-replicating DNA of Tc1 CD4+ T lymphocytes replicate 1

value: T cells

source_name: Late-replicating DNA of Tc1 CD4+ T lymphocytes replicate 1


title: Memory P14 CD8+ T cell rep#1


title: Memory P14 CD8+ T cell rep#2


title: peritumor derived γδT_rep8

city: Shanghai

first: Yong

last: Yi

address: 180 Fenglin Road

country: China

institute: Liver Cancer Institute

description: Gene expression of peritumor-derived γδT cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 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: the arrays were scanned by the Agilent Scanner G2505B.

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: Human paired peritumor-derived γδT cells, replicated 8

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA were extracted from freshly purified γδ T cells using Trizol reagent (Invitrogen) following the manufacturer's recommendation. Sample RNA Quality Control was performed with using Bioanalyzer 2100 to evaluate the RNA integrity from all samples. The NanoDrop ND-1000 was used for accurately measuring RNA concentrations (OD260), protein contamination (ratio of OD260/OD280) and organic compound contamination (ratio of OD260/OD230).

treatment_protocol: Freshly acquired HCC tissue and paired peritumor liver tissue were minced into small pieces of ~1mm3, then digested in an enzyme cocktail (1mg/ml collagenase type IV, 0.02mg/ml DNase in HBSS with 10% FBS) for 1 hour at 37°C. After filtration and extensive wash, the cells were subjected to discontinous density gradient centrifugation in Percoll. After removal of dead cells and incubation with components of TCRγ/δ isolation kit (Mitenyi Biotec), γδ T cells were positively selected from the single-cell suspension using autoMACS Separator (Miltenyi Biotec) with recommended programs.

tag: tissue

value: Peritumor liver tissue

tag: gender

value: male


title: peritumor derived γδT_rep4

source_name: Human paired peritumor-derived γδT cells, replicated 4


title: Day 8 effector P14 CD8+ T cell rep#4

description: miRNA expression data of day 8 effector P14 CD8+ T cells

source_name: Day 8 effector P14 CD8+ T cells


title: peritumor derived γδT_rep6

source_name: Human paired peritumor-derived γδT cells, replicated 6


title: peritumor derived γδT_rep7

source_name: Human paired peritumor-derived γδT cells, replicated 7


title: peritumor derived γδT_rep3

source_name: Human paired peritumor-derived γδT cells, replicated 3


title: M1

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: The transcriptomes of young male and (in estrus) female hypothalami were profiled and compared to learn about the sex dichotomy of the cytoskeletal genomic fabric.

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two rats were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Male hypothalamus

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: All animals were housed individually at Albert Einstein College of Medicine Animal Facility and maintained on a 14-h light, 10-h dark cycle (lights on at 0600 h) with free access to chow and water. Animals were handled according to the NIH guidelines for animal experimentation. All procedures had prior approval from the local animal ethics committee.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA) following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)  Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)    Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

tag: strain

value: Strain:Sprague Dawley (Taconic Farms, Germantown, NY)

value: 3–4 months

tag: Sex

value: hypothalamus


title: peritumor derived γδT_rep1

source_name: Human paired peritumor-derived γδT cells, replicated 1


title: peritumor derived γδT_rep10

source_name: Human paired peritumor-derived γδT cells, replicated 10


title: F4

source_name: Female hypothalamus

tag: age

value: female (in estrus)


title: M3


title: M2


title: peritumor derived γδT_rep5

source_name: Human paired peritumor-derived γδT cells, replicated 5


title: M4


title: Day 8 effector P14 CD8+ T cell rep#2


title: Day 8 effector P14 CD8+ T cell rep#3


title: HCC derived γδT_rep10

description: Gene expression of HCC-derived γδT cells

source_name: Human HCC-derived γδT cells, replicate 10

value: Hepatocellular carcinoma


title: peritumor derived γδT_rep9

source_name: Human paired peritumor-derived γδT cells, replicated 9


title: Day 8 effector P14 CD8+ T cell rep#1


title: HCC derived γδT_rep9

source_name: Human HCC-derived γδT cells, replicate 9


title: HCC derived γδT_rep8

source_name: Human HCC-derived γδT cells, replicate 8


title: Day 5 effector P14 CD8+ T cell rep#4

description: miRNA expression data of day 5 effector P14 CD8+ T cells

source_name: Day 5 effector P14 CD8+ T cells


title: Day 5 effector P14 CD8+ T cell rep#3


title: Day 5 effector P14 CD8+ T cell rep#2


title: eXEN2

city: Hinxton

first: Isheng

middle: Jason

last: Tsai

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Trust Sanger Institute

hyb_protocol: Illumina direct hybridization protocol

scan_protocol: Illumina bead array reader scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: embryo derived XEN_XEN_rep2

label_protocol: biotinylated cRNA was prepared using the Illumina Total Prep 96 RNA Amplification kit from Ambion (Life Technologies)

growth_protocol: Established cXEN and embryo-derived XEN cells were grown in standard XEN. mESCs were grown in standard mESC media (serum and LIF) for 2 days prior to collecting RNA.

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase I treatment  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Untreated - cell were grown in standard XEN or mESC maintenance media.

value: embryo-derived extraembryonic endoderm (XEN) cell line


title: F1


title: eXEN1

source_name: embryo derived XEN_XEN_rep1


title: F2


title: HCC derived γδT_rep7

source_name: Human HCC-derived γδT cells, replicate 7


title: F3


title: cXEN2

source_name: converted XEN cells_XEN_rep2

value: converted XEN (cXEN) cell line


title: Naïve P14 CD8+ T cell rep#3

description: miRNA expression data of naïve P14 CD8+ T cells

source_name: Naïve P14 CD8+ T cells


title: Day 5 effector P14 CD8+ T cell rep#1


title: HCC derived γδT_rep6

source_name: Human HCC-derived γδT cells, replicate 6


title: Naïve P14 CD8+ T cell rep#2


title: cXEN3

source_name: converted XEN cells_XEN_rep3


title: cXEN1

source_name: converted XEN cells_XEN_rep1


title: HCC derived γδT_rep4

source_name: Human HCC-derived γδT cells, replicate 4


title: HCC derived γδT_rep3

source_name: Human HCC-derived γδT cells, replicate 3


title: peritumor derived γδT_rep2

source_name: Human paired peritumor-derived γδT cells, replicated 2


city: Barcelona

first: Perla

last: Kaliman

address: Corsega 176 bajos

country: Spain

institute: IDIBAPS

description:
Cortex from adult exercise female SAMP8 mice, biological replicate 13
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]

hyb_protocol: Total RNA (500 ng) was labeled with Cy3 dye using the Quick Amp Labeling Kit, One-Color from Agilent. Fluorescently labeled samples were hybridized to the microarray slide with 60-mer probes. Hybridization and wash processes were performed according to the manufacturer’s instructions.

scan_protocol: Hybridized microarrays were scanned using an Axon 4000B scanner.

data_processing: GenPix Pro 6.0 extraction software was used for the detection of signals. Background correction and normalization were done with Bioconductor's package limma using method's minimum and quantile respectively.

source_name: Whole cortex exercised

extract_protocol: Total RNA was prepared using the mirVana™ RNA Isolation Kit (Applied Biosystems) following the manufacturer's recommendations. The yield, purity and quality of RNA were determined spectrophotometrically (NanoDrop, USA) and using the Bioanalyzer 2100 capillary electrophoresis (Agilent Technologies).

treatment_protocol: Cortex were rapidly frozen after the sacrifice of the animals.

tag: treatment

value: exercised

value: brain cortex

value: female

value: adult


description:
Cortex from adult exercise female SAMP8 mice, biological replicate 15
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: mESC3

value: embryonic stem (ES) cell line


title: HCC derived γδT_rep1

source_name: Human HCC-derived γδT cells, replicate 1


title: Naïve P14 CD8+ T cell rep#1

value: CD8+ T cells


description:
Cortex from adult exercise female SAMP8 mice, biological replicate 14
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: HCC derived γδT_rep2

source_name: Human HCC-derived γδT cells, replicate 2


title: mESC2


title: control for late gestation ethanol treatment 2

city: London

first: Katarzyna

last: Janus

address: 1151 Richmond Street

institute: University of Western Ontario

hyb_protocol: 5.5 ug of single-stranded cDNA was hybridized for 16 hours at 45 degrees C to the array.  Liquid handling steps were performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 using Command Console v1.1

data_processing: The data were analyzed with Partek Genomics Suite software v6.6.  Probes  were quantile-normalized using the GeneChip-Robust Multiarray Averaging and log2 transformed. All other settings were left as default.

source_name: brain, saline-treated, P70 male

label_protocol: Single-stranded cDNA was synthesized using 200 ng of total RNA using Ambion WE Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and labelled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Mice were raised in standard same-sex housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature).  Mice were sacrificed at postnatal day 70.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and cleaned using Rneasy Mini kit (QIAGEN).

treatment_protocol: At postntatal day 70, mice were sacrificed by CO2 asphyxiation and whole brain tissue were dissected using RNAse-free tools.  Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.

value: postnatal day 70

value: brain

value: saline on gestational days 14 and 16


title: HCC derived γδT_rep5

source_name: Human HCC-derived γδT cells, replicate 5

value: male


description:
Cortex from adult exercise female SAMP8 mice, biological replicate 11
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


description:
Cortex from adult sedentary female SAMP8 mice, biological replicate 10
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]

source_name: Whole cortex sedentary

value: sedentary


title: Sorted 8h TVC cells using Mesp-promoter, replicate 4

city: Tucson

first: Bradley

middle: J

last: Davidson

state: AZ

department: Molecular Cardiovascular Research Program

institute: University of Arizona

description:
Exp3849_BD-8H sort 11
Gene expression data from sorted cells.

hyb_protocol: Hybridization to the Ciona intestinalis custom-design GeneChipTM was conducted using standard Affymetrix procedures at the University of Arizona Genomics Core (http://www.azcc.arizona.edu/research/shared-services/gss).

scan_protocol: Slides were scanned on a GeneChip Scanner 3000 7G.

data_processing: Raw expression data sets (CEL files) were read and analyzed using R Programming tools and the Affy and LIMMA libraries provided by the Bioconductor community. Custom probe sets for Ciona were background subtracted and normalized using the Affy RMA function. The 3 or 4 biological replicas for each experimental condition were then fitted to a linear statistical model. Lists of probes that varied significantly between comparisons of interest including fold change and probability of fold change corrected for false discovery rate were obtained using LIMMA functions. The resulting lists were then annotated using community-provided spreadsheets (Smyth, 2005).

label: Digoxigenin

organism: Ciona intestinalis

source_name: B7.5 cell lineage

label_protocol: Total RNA (1µl) were analyzed on the BioAnalyzer machine using the Eukaryote total RNA Pico Series II kit following the manufacturer's recommendations (Agilent Technologies, #5067-1513). RNA amplification and probe synthesis were performed using the Affymetrix Eukaryotic Target Preparation protocol (Two-Cycle Target Labeling kit, Affymetrix, #900494), with modifications. Briefly, 500 cells equivalent of total RNA were used for first strand cDNA synthesis using the Sensiscript reverse transcriptase (Qiagen, #205211) and a published T7-polyT oligonucleotide (S5) in 20µl. Half of the first-strand cDNA synthesis reaction (10µl) was used for subsequent second-strand synthesis, amplification and probe synthesis.

growth_protocol: Ciona intestinalis adults were purchased from M-REP (San Diego). Fertilization, dechorionation and electroporation were performed as previously described (Corbo, J. C., Levine, M., Zeller, R. W., 1997. Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development. 124, 589-602 (PMID 9043074)). Embryos were staged according to the developmental timeline established in Hotta, K., Mitsuhara, K., Takahashi, H., Inaba, K., Oka, K., Gojobori, T., Ikeo, K., 2007. A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva. Dev Dyn. 236 (PMID 17557317).

extract_protocol: Sorted samples were collected in 500µl RNAlater buffer (Ambion, #7020), kept at 4°C overnight and frozen at -80°C until RNA extraction. Total RNA extraction was performed using the RNAqueous-micro kit (Ambion, #1931). Frozen samples were thawed at room temperature, 500µl CMF-ASW was added and cells were pelleted by centrifugation for 4 minutes, 4000rpm, at 4°C. The supernatant was quickly removed and replaced with 200µl lysis buffer. Cells were lysed by thorough vortexing. RNA extraction was performed as per manufacturer recommendations and eluted in 2x6.5µl of pre-warmed (70°C) elution buffer.

treatment_protocol: Fluorescent-activated sorting of Mesp-GFP-labeled B7.5 founder lineage cells was performed using the FACSAria (BD Bioscienes, San Jose, CA) sorter as previously described (Christiaen et al., 2008) with modifications appropriate for stringent exclusion of YFP-labeled cells and cell clusters as appropriate for this instrument (performed at AZCC/ARL-Division of Biotechnology Cytometry Core Facility funded by the Cancer Center Support Grant, CCSG - CA 023074).

value: B7.5 founder trunk ventral cell lineage

tag: co-electroporated construct


title: ethanol-treated during late gestation 2

source_name: brain, ethanol-treated, P70 male

value: ethanol on gestational days 14 and 16


title: mESC1


title: Sorted 8h TVC cells using Mesp-promoter coelectroporated with a dominant-negative FGF receptor, replicate 3

description:
Exp3850_BD-FGFRdn 11
Gene expression data from sorted cells.

source_name: B7.5 cell lineage, dominant-negative FGF-receptor

value: dominant-negative FGF-receptor


title: Dicer KD biological  metformin treated replicate 2

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

description: microRNA expression after DICER protein silencing plus metformin treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to AgilentMicroarrays  for 17 hours at 65ÂC 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 37ÂC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: breast cell lines control,  treated, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: SUM159 were grown in DMEM/F-12 supplemented with 5% FBS, Insulin 5ug/ml (SIGMA) and Hydrocortisone 0.5 ug/mL (SIGMA). The cells were stably infected with PLKO1-based lentiviral vectors. PLKO.1-shdicer  was a gift of Dr. Stefano Piccolo (Padua, ITALY)(Martello et al, 2010). The CONTROL scrambled-shRNA consisted of an shRNA insert that contains 4 base pair mismatches to any known human or mouse gene in the same backbone vector (PLKO.1) (SIGMA- SHC002).

extract_protocol: Total RNA from breast cancer cell lines was extracted by TRI Reagent lysis reagent (Ambion) according to manufacturer's instructions.

treatment_protocol: logaritmically growing SUM159 cells stably expressing a control shRNA or a dicer-targeting shRNA treated with vehicle (PBS) or metformin (0.5mM) for 24 hrs.

tag: knockdown

value: Dicer shRNA

value: 0.5 mM metformin


title: Dicer KD biological metformin treated replicate 3

source_name: breast cell lines control,  treated, replicate 3

tag: cell line


title: Sorted 8h TVC cells using Mesp-promoter coelectroporated with a dominant-repressive ETS1/2, replicate 4

description:
Exp3851_BD-EtsW 7
Gene expression data from sorted cells.

source_name: B7.5 cell lineage, dominant-repressive ETS1/2

value: dominant-repressive ETS1/2


title: control for late gestation ethanol treatment 1


title: ethanol-treated during late gestation 1


description:
Cortex from adult sedentary female SAMP8 mice, biological replicate 8
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: Control biological  metformin treated replicate 3

description: microRNA expression after scramble silencing plus metformin treatment

source_name: breast cell lines control,  untreated, replicate 3

value: control shRNA


title: Sorted 8h TVC cells using Mesp-promoter coelectroporated with a dominant-repressive ETS1/2, replicate 3

description:
Exp3838_BD-EtsW 6
Gene expression data from sorted cells.


description:
Cortex from adult sedentary female SAMP8 mice, biological replicate 6
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]

value: brain cortex


title: Sorted 8h TVC cells using Mesp-promoter, replicate 3

description:
Exp3836_BD-8h Sort 10
Gene expression data from sorted cells.


description:
Cortex from adult sedentary female SAMP8 mice, biological replicate 9
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]

value: female


title: HUES NEURO_1

city: barcelona

first: Alessandra

last: Giorgetti

address: doctor aiguader 88

institute: CMRB

description: Gene expression data from HUES6-neurons1

hyb_protocol: Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

value: HUES-neurons

tag: condition/variation

value: Control

tag: time


description:
Cortex from adult sedentary female SAMP8 mice, biological replicate 7
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]

value: adult


title: Dicer KD biological  metformin treated replicate 1

source_name: breast cell lines control,  treated, replicate 1


title: Ctr positive 2

description: Gene expression data from HUES6-NPC

tag: cell type

value: HUES-NPCs


description:
Cortex from adult sedentary female SAMR1 mice, biological replicate 5
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: Sorted 8h TVC cells using Mesp-promoter coelectroporated with a dominant-negative FGF receptor, replicate 2

description:
Exp3659_BD-fgfrdn 51007
Gene expression data from sorted cells.


description:
Cortex from adult sedentary female SAMR1 mice, biological replicate 4
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: Sorted 8h TVC cells using Mesp-promoter coelectroporated with a dominant-repressive ETS1/2, replicate 2

description:
Exp3658_BD-Etsw 51007
Gene expression data from sorted cells.


title: HUES NEURO_2

description: Gene expression data from HUES6-neurons2


title: Sorted 8h TVC cells using Mesp-promoter coelectroporated with a dominant-negative FGF receptor, replicate 1

description:
Exp3656_BD-fgfrdn 5407
Gene expression data from sorted cells.


description:
Cortex from adult sedentary female SAMR1 mice, biological replicate 3
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: CBCL10t3

description: Gene expression data from CB-derived neurons

source_name: CB-neurons 1

value: CB-iNCs

value: Differentiated


title: Ctr positive 1

description: Gene expression data from HUES6-NPC


title: CBCL13t3

source_name: CB-neurons 3


description:
Cortex from adult sedentary female SAMR1 mice, biological replicate 2
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: CBCL12t3

source_name: CB-neurons 2


title: Sorted 8h TVC cells using Mesp-promoter coelectroporated with a dominant-repressive ETS1/2, replicate 1

description:
Exp3655_BD-Etsw 5407
Gene expression data from sorted cells.


title: Sorted 8h TVC cells using Mesp-promoter, replicate 1

description:
Exp3654_BD-8h sort 5407
Gene expression data from sorted cells.


description:
Cortex from adult sedentary female SAMR1 mice, biological replicate 1
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]


title: Whole embryo cells at 8h, replicate 3

description:
Exp3608_BD-8Hwhole_4
Gene expression data from whole embryos at 8h development.

source_name: whole embryo at 8h development

value: whole embryo


title: CBCL12t2

description: Gene expression data from induced CB-derived neural cells

source_name: CB-iNC 2

value: Transfected


title: Sorted 8h TVC cells using Mesp-promoter, replicate 2

description:
Exp3657_BD-8h sort 51007
Gene expression data from sorted cells.

value: B7.5 founder trunk ventral cell lineage


title: CBCL10t2

source_name: CB-iNC 1


title: Whole embryo cells at 8h, replicate 2

description:
Exp3607_BD-8Hwhole_3
Gene expression data from whole embryos at 8h development.


title: Dicer KD biological replicate 3

description: microRNA expression after DICER protein silencing

source_name: breast cell lines DICER ko, replicate 3

value: PBS


title: Control biological replicate 3

description: microRNA expression after scramble silencing

source_name: breast cell lines control, replicate 3


title: Dicer KD biological replicate 2

source_name: breast cell lines DICER ko, replicate 2


title: Dicer KD biological replicate 1

source_name: breast cell lines DICER ko, replicate 1


title: Control biological replicate 1

source_name: breast cell lines control, replicate 1


title: Control biological replicate 2

source_name: breast cell lines control, replicate 2


title: Control biological metformin treated  replicate 1

description: microRNA expression after scramble silencing plus metformin treatment

source_name: breast cell lines control,  untreated, replicate 1


title: Control biological  metformin treated replicate 2

source_name: breast cell lines control,  untreated, replicate 2


title: non-transduced rep#3

description: Gene expression data of LCMV specific P14 effector CD8+ T cells without miR-17-92a over-expression

hyb_protocol: After fragmentation, 12.5 ug RNA were incubated with Mouse Genome 430 2.0 at 45C 60 RPM for 16 hrs.

scan_protocol: Samples were scanned using GeneChip Scanner 3000 7G with AutoLoader at Vanderbilt University Microarray core according to manufacturer's instructions

data_processing: Data analysis was performed using GenePattern with the robust multi-chip averaging method (RMA).

source_name: non-transduced

label_protocol: In vitro transcription was performed with 50-250 ng of RNA input.

extract_protocol: According to manual of Qiagen Rneasy plus mini kit.

treatment_protocol: P14 cells were collected from P14 transgenic mice and tranferred to C57BL6 recipients. Chimera mice were infection with 200,000 pfu LCMV Armstrong i.p.. The P14 CD8+ T cells were sorted on day 8 post-infection.

value: CD8+ T cells


title: non-transduced rep#1


title: CBCL13t2

source_name: CB-iNC 3


title: Whole embryo cells at 8h, replicate 1

description:
Exp3578_BD-8Hwhole_2
Gene expression data from whole embryos at 8h development.


title: miR-17-92a over-expression rep#3

description: Gene expression data of LCMV specific P14 effector CD8+ T cells with miR-17-92a over-expression

source_name: miR-17-92a over-expression


title: non-transduced rep#2

description: Gene expression data of LCMV specific P14 effector CD8+ T celsl without miR-17-92a over-expression


description:
Cortex from adult exercise female SAMP8 mice, biological replicate 12
Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]

source_name: Whole cortex exercised

value: exercised


title: CB4

description: Gene expression data from CB CD133+ cells

source_name: CB CD133+ cells 1

value: Untreated


title: HN12 cell, mesenchymal phenotype and high invasive capacity cell

first: zhiyuan

last: zhang

address: 639 zhizaoju Road

institute: Shanghai Jiaotong University

description: natural mesenchymal phenotype and high invasive capacity cell, derived from a nodal metastasis in the patient from whom the HN4 cells originated

hyb_protocol: Hybridization of the mix of Hy5™-labeled sample and Hy3™-labeled reference RNAs to the arrays at 56 ºC for 16 hours followed by washing was performed by Exiqon® (Vedbaek, Denmark) on an HS Pro instrument (Tecan®, Männedorf, Switzerland). The 6th generation miRCURY™ LNA microRNA arrays (Exiqon®, Vedbaek,Denmark) that were used have approx. 2383 locked nucleic acid oligonucleotide probes on quadruplicate 100 µM-sized probe-spots to detect all human, mouse and rat microRNAs, respectively, of miRbase v.16.respectively, of miRbase v.16.

scan_protocol: Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent®, Santa Clara, USA) by Exiqon® (Vedbaek, Denmark).

data_processing: Data processing was done in R (version 2.12.1) using the limma (version 3.4.5) Bioconductor package. The 'normexp' method with offset=10 was used for background-correction, and followed with within-array global 'loess' normalization, with span=1/3 and values from probe-spots with flag-values >1 ignored, and then, between-array 'Rquantile' normalization. For probe-set summarization, the median of the values from multiple spots was used when the ratio of the maximum and minimum values was > 1.5; else, the mean was used. The ratios of the summarized normalized Hy5/Hy3 (test/reference) signal-intensities were log2-transformed.

source_name: HN12 cell line

label_protocol: One µg total RNA from sample and reference was labeled with Hy5™ and Hy3™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Total RNA was purified using the miRNA isolation kit . The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

source_name: common reference pool

value: Multiple

value: Mixed


title: TGF beta treated HN4 cell

description: HN4 cell line treated with TGF beta

source_name: HN4 cell line

value: epithelial phenotype and low invasive capacity cell, derived from a primary squamous cell carcinoma of the tongue


title: miR-17-92a over-expression rep#4


title: CB6

source_name: CB CD133+ cells 3


title: HN4 cell, epithelial phenotype and low invasive capacity cell

description: epithelial phenotype cell, untreated


title: CGH: Richland vs. Wm82-ISU-01

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

organism: Glycine max

source_name: Richland, Leaf tissue

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

extract_protocol: Qiagen DNeasy

value: single plant leaf tissue

tag: cultivar

value: Richland

source_name: Wm82-ISU-01, Leaf tissue


title: CGH: Archer-SGC-01 vs. M92-220

source_name: Archer-SGC-01, Leaf tissue

source_name: M92-220, Leaf tissue


title: CGH: Essex vs. Wm82-ISU-01

source_name: Essex, Leaf tissue

value: Essex


title: miR-17-92a over-expression rep#1


title: CGH: Kingwa vs. Williams

source_name: Kingwa, Leaf tissue

value: Kingwa

source_name: Williams, Leaf tissue

value: Williams


title: miR-17-92a over-expression rep#2


title: CB5

description: Gene expression data fromCB CD133+ cells

source_name: CB CD133+ cells 2