title: hMSC-WNT3a_24HRS

first: Sapna

last: Vijayakumar

address: 1425 Madison Ave

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description: Gene expression data from hMSCs

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: GCOS:default analysis, global normalization

label_protocol: Standard affymetrix protocol

growth_protocol: Standard tissue culture conditions (DMEM/10% FBS)

extract_protocol: RNA extraction was done using Qiagen's RNA extraction kit

treatment_protocol: recombinant WNT3a from R&D was used for treating cells grown in 10cm culture dish.

tag: cell

value: Mesenchymal Stem Cell

tag: time

value: 24 hr


title: Colon with SL1344 infection at 8hr biological rep3

status: Public on Feb 16 2011

type: RNA

city: Rochester

first: Jun

last: Sun

state: MN

address: 575 Elmwood Ave

country: USA

institute: university of rochester

description: Gene expression data from colon mucosa with salmonella SL1344 infection at 8hr

hyb_protocol: Mouse cDNA was hybridized to the Mouse Gene 1.0 ST array, a microarray chip containing 28,000 sequenced mouse genes

scan_protocol: the array was washed and stained with streptavidin-phycoerythrin, and scanned in a proprietary Affymetrix scanner, according to the GeneChip® Whole Transcript Sense Target Labeling Assay manual.

data_processing: The data were processed with Expression Console (Affymetrix) using the PLIER algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Animal experiments were performed using specific-pathogen-free female C57BL/6 mice (Taconic, Hudson, NY) that were 6-7 weeks old.  Water and food were withdrawn 4 h before oral gavage with 7.5 mg/mouse of streptomycin. Afterwards, animals were supplied with water and food. Twenty hours after streptomycin treatment, water and food were withdrawn again for 4 hours before the mice were infected with 1x107 CFU of S. Typhimurium (100µl suspension in HBSS) or treated with sterile HBSS (control) by oral gavage as previously described

tag: strain

tag: sex

value: female

tag: tissue

value: intestinal colon mucosa


title: B6_biol_repl2

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Biological replicate 2 of 3.

hyb_protocol: Following fragmentation, 7.5 ug of single-stranded DNA was hybridized for 16 hr at 45C on  Affymetrix GeneChip® Mouse Tiling 2.0R B Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Sequences of the 25 nt long probes were aligned to the chromosomal positions (UCSC genome build mm9) using MUMmer(http://mummer.sourceforge.net/). Only probes with one perfect match and no near-match (match of 23 or 24 nts) were left. We also filtered out the probes arising from the reverse strand and/or matching chromosomes other than X,Y,2 or the mitochondrial genome. Intensities of remaining probes were quantile normalized and analyzed using R (http://www.r-project.org/). Chromosomal localizations of individual probes with normalized log2 intensities are in the resulting BED files. LogFC values of Spr v. B6 comparison together with P values were calculated using limma package from Biconductor (www.bioconductor.org). The P values were adjusted using Benjamini & Hochberg correction. Chromosomal localizations of the probes together with logFC and adjusted P values are in the Spr_v_B6.bed file, which is linked to the Series GSE19633 record as a supplementary file.

organism: Mus musculus domesticus

label_protocol: 2 ug total RNA was used to prepare biotinylated single-stranded target by modification of the Affymetrix protocol (Whole Transcript (WT) Double-Stranded Target Assay Manual, 702179 Rev. 3, Affymetrix), where the synthesis of second-strand cDNA was omitted in the final step.

extract_protocol: Total RNA was isolated from the testes of individual mice using the RNeasy Mini kit (Qiagen) according to manufacturer's instructions.

tag: gender

value: male

tag: age

value: 2 months

value: testes


title: hMSC-WNT3a_6HRS

city: New York

description: Gene expression data from hMSCs

organism: Homo sapiens

tag: treatment

value: 6 hr


title: hMSC-Control

description: Gene expression data from hMSCs

source_name: hMSC-Control


title: B6_biol_repl1

description: Biological replicate 1 of 3.


title: Colon with SL1344 infection at 8hr biological rep1

source_name: colon mucosa with salmonella SL1344 infection at 8hr


title: 0hr control young replicate 2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Gene expression data from liver of 0h control young mice.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C to Affymetrix GeneChip Mouse Expression U74Av2 arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Raw signal intensites were normalized using the RMA algorithm implemented with R and BioC (justRMA function).

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Male mice of the CB6F1 hybrid strain at 5-6 months of age, and at 25-27 months of age were obtained from Jackson Laboratories, and the National Institute on Aging, respectively.

extract_protocol: Total RNA was isolated using the RNeasy mini columns from Qiagen.

treatment_protocol: Mice were anesthetized by use of an intraperitoneal injection of avertin followed by supplementary inhalation of isoflurane.  Partial hepatectomy was performed by surgical removal of 70% of the liver mass.  Liver tissue was collected at  0, 0.5, 1, 2 and 4 hour(s) following surgery.

value: 5-6 months

tag: time (hours)


title: 0hr control young replicate 3


title: Colon with SL1344 infection at 8hr biological rep2


title: Control at 8hr biological rep3

description: Gene expression data from colon mucosa at 8hr

source_name: colon mucosa at 8hr


title: 0hr control young replicate 1


title: Control at 8hr biological rep1


title: Control at 8hr biological rep2


title: Colon with SB1117 infection at 4day biological rep3

description: Gene expression data from colon mucosa with salmonella SB1117 infection at 4day

source_name: colon mucosa with salmonella SB1117 infection at 4days


title: leaf_R_0H_rep3

status: Public on Feb 15 2011

city: BEIJING

first: mingming

last: xin

address: YUAN MING YUAN WEST ROAD 2, HAIDIAN DISTRICT

department: plant genetics and breeding

country: China

institute: China Agricultrual University

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

scan_protocol: GeneChips were scanned using the Genechip® 3000 Scanner

data_processing: The chip images were scanned and extracted using default settings and the CEL files were produced with the Affymetrix GeneChip Operating Software (GCOS 1.2). The resulting CEL files were imported into the Bioconductor (version 1.8)  in R 2.3.0 statistical environment. Subsequent background adjustment, normalization of the raw data and estimation of probe sets signal intensities were done using GC-RMA method.

organism: Triticum aestivum

source_name: 2 week-old wheat leaves before powdery mildew infection

label_protocol: The biotin labelled cRNA was made using the GeneChip® IVT Labelling Kit (Affymetrix, CA, USA).

growth_protocol: Hexaploid wheat (Triticum aestivum L.) line 8866 (S)(susceptible to wheat powdery mildew) and its near-isogenic resistant line Pm30 (R) were grown in a growth chamber at a relative humidity of 75% and 26/20℃ day and night temperature with light intensity of 3000 lx. 2 week-old plants were used for all experiments.

treatment_protocol: One isolate of the powdery mildew fungus Erysiphe graminis f. sp. tritici (Egt) (Isolate E09) was maintained on the susceptible wheat cultivar  by weekly transfer to new plants. Inoculations were performed at a density of 100-150 conidia/mm2 by brushing plants. Leaves were collected at 12 hours after infection.

tag: line

value: pm30 (resistant to wheat powdery mildew， also designed as ‘R’)

value: two-week old

value: leaf

tag: infection

value: control

value: 0 hours


title: leaf_S_0H_rep2

value: 8866 (susceptible to wheat powdery mildew,also designed as ‘S’)


title: leaf_R_0H_rep2


title: leaf_R_12H_rep3

source_name: 2 week-old wheat leaves 12 hours after powdery mildew infection

value: powdery mildew

value: 12 hours


title: leaf_R_0H_rep1


title: leat-S_12H_rep3

source_name: 2 week-old wheat leaves  12 hours after powdery mildew infection


title: leaf_S_0H_rep3


title: leaf_S_0H_rep1


title: leaf_R_12H_rep1


title: leaf_R_12H_rep2


title: leat-S_12H_rep2


title: ELF-MF exposure group, biological rep2

city: Hangzhou

first: Guangdi

last: Chen

state: Zhejiang

address: 388 Yuhangtang

department: School of Medicine

institute: Zhejiang University

description: Gene expression data from yeast cells after 0.4 mTELF-MF exposure for 6 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45ºC on Human Genome GeneChip HG-U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: The data were analyzed with GeneChip Operating Software 1.0 (GCOS 1.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was arbitrarily set to 500.

organism: Saccharomyces cerevisiae

source_name: Yeast cells, 0.4 mT ELF-MF exposed for 6 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The strain Saccharomyces cerevisiae S288C (No. 201388) was obtained from the American Type Culture Collection (ATCC, Rockville, MD) and grown in 5% YPD (Yeast Extract/Peptone/Dextrose) medium (Clontech, Palo Alto, CA) supplemented with or without 1.5% agar (Invitrogen, Carlsbad, CA) at 30oC in humidified air. A single clone was selected and cultured overnight at 230 rpm. Prior to EMF exposure, cells were seeded onto individual 100 mm Petri dishes (Orange Scientific, Braine-I’Alleud, Belgium) for ELF-MF exposure or 35 mm Petri dishes (NUNC, Roskilde, Denmark) for RF-EMF exposure from a single “parental” flask at an optical density of 0.2 at 600 nm, determined by a Smart SpecTM3000 spectrophotometer (Bio-Rad Laboratories, Hercules, CA).

treatment_protocol: The yeast cells were exposed to 0.4 mT 50 Hz ELF-MF or 1800 MHz RF-EMF at a specific absorption rate of 3.5 W/kg for 6 hours.


title: RF-EMF control group, biological rep2

description: Gene expression data from yeast cells after RF-EMF sham exposure for 6 hours

source_name: Yeast cells, RF-EMF sham exposed for 6 hours


title: ELF-MF exposure group, biological rep1


title: A549 miR-328 Replicate 2

city: Phoenix

first: Julianna

last: Ross

state: AZ

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

description:
Biological replicate 2 of 2.  miR-328 overexpressing cells.
A549 miR-328 Replicate 2_LogRatio

hyb_protocol: Approximately 800ng of both Cy5-labeled experimental cRNA and Cy3-labeled universal reference RNA were hybridized to each microarray (adjusting for labeling efficiency).

scan_protocol: Images were captured using an Agilent DNA microarray scanner set at default settings for gene expression.

data_processing: Scanned images were processed using Feature Extractor v. 10.5.1.1. By applying a LOWESS (locally weighted linear regression) correction for dye-bias, background noise was subtracted from spot intensities. To filter the preprocessed data, genes with a background signal higher than feature signal were removed.

source_name: A549 cells with miR-328 vector

label_protocol: A quick-amplification kit (Agilent, Santa Clara, CA) was used to amplify and label 500 ng target mRNA species to complementary RNA (cRNA) for oligo microarrays according to the manufacturer’s protocol. For each array, experimental samples were run in duplicate along with a commercial universal reference RNA (Stratagene, La Jolla, CA) were labeled with cyanine 5-CTP and cyanine-3-CTP (Perkin Elmer, Boston, MA), respectively. cRNA concentration and labeling efficiency was measured spectrophotometrically.

growth_protocol: For each experimental sample, 3 x 10^5 cells were seeded in duplicate using standard growth conditions and grown for 24 hours before total RNA isolation.

extract_protocol: Total RNA was isolated according to manufacturer’s protocol (mirVana miRNA Isolation Kit, Ambion, Austin, TX). Total RNA yield was assessed using a NanoDrop 2000c (Thermo Scientific, Wilmington, DE), and quality was assessed on a BioAnalyzer 2400 using a BioAnalyzer RNA 6000 Nano LabChip Kit (Agilent Technologies, Palo Alto, CA).

tag: cell line

value: NSCLC Cell Line A549

tag: protocol

value: miR-328 overexpression

source_name: Universal reference RNA

tag: reference

value: Universal reference RNA


title: RF-EMF control group, biological rep1


title: ELF-MF control group, biological rep2

description: Gene expression data from yeast cells after ELF-MF sham exposure for 6 hours

source_name: Yeast cells, ELF-MF sham exposed for 6 hours


title: ELF-MF control group, biological rep1


title: Tat-SF1 shRNA B_rep2

city: Durham

first: Heather

last: Miller

email: hnb3@duke.edu, hbmiller@ncsu.edu

state: NC

address: Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University

description: 1292_2787_13860_GH2_HuEx-1+0-st-v1_2.CEL_Expression

hyb_protocol: Microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450.

scan_protocol: Genechip scanner 3000 7G was used.

data_processing: The input files were normalized with full quantile normalization (Irizarry et al 2003). For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points. Next, the 6,553,590 probes were manipulated into the analysis values as follows. Probes with GC count less than 6 and greater than 17 were excluded from the analysis. Probe scores were then transformed by taking the Natural Logarithm of 0.1 plus the probe score. Background CorrectionExon arrays do not use individual mis-match probes. Background is established from a pool of probes designed for that purpose. Background probes are stratified by CG content and are defined in the HumanExon10ST_antigenomic.bgp file. BGP files can also be downloaded from www.affymetrix.com. Each probe score was corrected for background by subtracting the median expression score of background probes with similar GC content. The HumanExon10ST array contains 1,404,693 probe-sets (typically, but not always, groups of four probes). Probe-set Expression Scores and Annotation FilteringThe expression score for a probe-set was defined to be the median of its probe expression scores and probe-sets with fewer than 3 probes (that pass all of the tests defined above) are excluded from further analysis. Exon Array Probes are designed off of genomic sequence and hence the reliability of probes and probe-sets correspond to the quality of their parent genomic annotations. Probe-set reliability is ranked from more to less reliable as Core, Extended, or Full. For example 'Core' probe-sets include probe-sets that correspond to high quality genomic features like RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org) transcripts while 'full' and 'extended' probe-sets match less reliable annotations like EST hits and gene prediction algorithms. For this analysis, only 'Core' probe-sets were analyzed.Probe-set Presence/Absence and the Removal of Non-expressed Probe-setsNon-expressed probes can cause tests for alternative splicing to find false positives (because they cause 'non-parallel' expression patterns across the gene). A probe-set is judged to be expressed above background if for any group: Integral from T0 to Infinity of the standard normal distribution less than Significance (0.001)    Where  T0 equals Sqr(GroupSize) (T minus P) divided by Sqr(Pvar), GroupSize equals Number of CEL files in the group, T equals average of probe scores in probe-set, P equals average of background probes averages of GC content, and Pvar equals sum of background probe variances divided by (Number of probes in probe-set) to the second power.  Hence, we test that the average of probe-sets in a group is greater than the average expression of background probes of similar GC content as the probe-set probes as the center of background for the probe-set and derive its dispersion from the background probe-set variance.  Low-variance probe-sets are excluded from the analysis via a Chi-Square test. A probe-set is considered to be low-variance if its transformed variance is to the left of the 90 percent confidence interval of the Chi-Squared distribution with (N-1) degrees of freedom.(N-1) * Probe-set Variance / (Gene Probe-set Variance) ~ Chi-Sq(N-1) where N is the number of input CEL files, (N-1) is the degrees of freedom for the Chi-Squared distribution, and the 'probe-set variance for the gene' is the average of probe-set variances across the gene. Although, in practice, this method works well, it should be noted that the Chi-Square test of variance is usually applied to test a variance against a constant value and we are using it to test probe-set variance against a random variable (probe-set variance across gene) ; furthermore, the probe-set and probe-set across gene are not independent.

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

growth_protocol: T-Rex-293 cells stably expressing a plasmid encoding GFP were grown in DMEM (high glucose) with 10% tetracycline-tested FBS, plus 1% L-glutamine plus 1% pen/strep.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen), followed by DNase treatment (Ambion).

treatment_protocol: T-Rex-293 cells stably expressing a plasmid encoding GFP were induced with 2.5ug/mL tetracycline for 72 hours for expression of either an empty vector, an shRNA specific to GFP, or an shRNA specific to Tat-SF1.

tag: file number

tag: genome/variation

value: Tat-SF1 knockdown by shRNA


title: Ovarian Cancer Sample (JB 993)

first: Douglas

last: Levine

state: NY

address: 1275 York Ave.

department: Surgery

institute: MSKCC

description: MicroRNA labelling

hyb_protocol: miRNA Complete Labeling and Hybridization Kit (Agilent)

scan_protocol: manufacturer’s instructions using Feature Extraction 9.5 (Agilent)

data_processing: Quantile normalized, log2 transformed, signal intensity with negative values set to zero

source_name: Tumor RNA

extract_protocol: mirVana™ microRNA isolation kit (Ambion)

value: Ovarian Cancer

tag: vital status

value: Dead

tag: recurred

value: yes

tag: os

tag: pfs

tag: age at dx

tag: histology

value: Serous


title: RF-EMF exposure group, biological rep1

description: Gene expression data from Yeast cells after exposure to RF-EMF at SAR of 3.5 W/kg for 6 hours

source_name: Yeast cells, RF-EMF exposed at SAR of 3.5 W/kg for 6 hours

tag: strain


title: Ovarian Cancer Sample (JB 95)

description: MicroRNA labelling

label_protocol: miRNA Complete Labeling and Hybridization Kit (Agilent)

tag: tissue


title: Ovarian Cancer Sample (JB 94)

description: MicroRNA labelling

value: Alive


title: Ovarian Cancer Sample (JB 958)

description: MicroRNA labelling

value: no


title: RF-EMF exposure group, biological rep2


title: Undifferentiated E14_U1

city: Manchester

first: Crispin

address: Wilmslow Road

department: Applied computational Biology

country: United Kingdom

institute: Paterson Institute for Cancer Research

hyb_protocol: Arrays were washed, stained with streptavidin-phycoerythrin. Full details of the protocol can be found in: http://bioinformatics.picr.man.ac.uk/mbcf/downloads/GeneChip_Hyb_Wash_Scan_Protocol-CR-UK_v2.pdf

scan_protocol: Arrays were scanned using an Affymetrix GeneChip scanner.  Full details of the protocol can be found in: http://bioinformatics.picr.man.ac.uk/mbcf/downloads/GeneChip_Hyb_Wash_Scan_Protocol-CR-UK_v2.pdf

data_processing: Data were analysed using the RMA implentation in the 'affy' BioConductor package.

source_name: E14 TG2a

label_protocol: RNA that passed the above criteria was prepared for microarray analysis, hybridised to the arrays and scannced by the Molecular Biology Core Facility, PICR. Before proceeding with labelling for microarray analysis, RNA quality and concentration was determined using an Agilent Bioanylyser (Agilent Technologies). In all cases satisfactory RNA integrity was observed. Biotinylated target RNA, for hybridisation to microarrays was prepared with minor modifications to the manufacturer’s instructions (Affymetrix). Spike controls were added to 10µg fragmented cRNA before overnight hybridisation to arrays.  Full details of the protocol can be found in: http://bioinformatics.picr.man.ac.uk/mbcf/downloads/GeneChip_Target_Prep_Protocol-CR-UK_v3.pdf

growth_protocol: Cells were grown in Falcon tissue culture flasks (Becton Dickinson) in a humidified atmosphere of 5% CO2 at 37°C. Tissue culture flasks were prepared for culture of ES cells by coating with 0.1% gelatin (Sigma) overnight at 4ºC. E14TG2a embryonic stem cells were grown in Knockout Dulbecco's modified Eagle's medium (DMEM; Invitrogen) supplemented with 10% Hyclone foetal calf serum (DMEM-FCS; Perbio) or 10% serum replacement (DMEM-SR; Invitrogen), 2mM L-glutamine, 1% non-essential amino acids (eBioscience), nucleosides [6 ml of the following solution/500 ml DMEM: adenosine (80 mg), guanosine (85 mg), cytidine (73 mg), uridine (73 mg) and thymidine (24 mg) dissolved in 100 ml double distilled water; Sigma], 2-mercaptoethanol (50 µM; Invitrogen) and leukaemia inhibitory factor (LIF; 1000 units/ml of ESGRO; Chemicon Int.).  Media was changed daily. Cells were passaged every other day: growth medium was aspirated and cells washed in PBS. Cells were incubated with 1x trypsin-EDTA (Sigma) for 10s and incubated at 37ºC for 1 minute. Cells were resuspended in growth media and passaged 1:6. For differentiation of ES cells, cells were trypsinised and washed as described above. Cells were resuspended in media which was not supplemented with LIF and plated at the 4 x104 cells/cm2 . Media was changed daily. Cells were not passaged during differentiation.

extract_protocol: Prior to RNA extraction and subsequent processing, all apparatus and working surfaces were cleaned using RNaseZap (Ambion), to reduce the possibility of RNA degradation. After FACS sorting, cells were centrifuged (5 minutes, 350g) and resuspended in trizol (Invitrogen). RNA was extracted according to the manufacturer’s instructions. Briefly, cells suspended in trizol were incubated at room temperature for 5 minutes in RNA free 1.5 ml eppendorfs (Starlab). 0.2 ml chloroform (VWR) was added per 1ml trizol, shaken and incubated at room temperature for 2 minutes. Samples were centrifuged again (12000g, 15 minutes, 4˚C) and the upper aqueous phase transferred to a clean eppendorf and 0.5 ml propan-2-ol (VWR) per 1 ml trizol added. This was incubated at room temperature for 10 minutes, then centrifuged (12000g, 10 minutes, 4˚C). The supernatant was discarded and the RNA pellet resuspended in 75% ethanol (75% absolute ethanol, VWR, in RNase free water, Ambion). This was stored at -80˚C until ready for further analysis. When ready for further analysis the sample was removed from the freezer,  centrifuged (7500g, 5 minutes, 4˚C) and supernatant removed. The pellet was allowed to air dry and resuspended in RNase free water. RNA was then cleaned using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. 50 μl RNase free water (Qiagen) was used in the final elution from the column. RNA concentration was determined using a Nanodrop spectrophotometer with supplied Nanodrop 2.4.7c software (National Instruments). A260/280 ratios were calculated, and RNA samples with concentrations (determined using the Beer-Lambert law, with 40ng-cm/ml at λ=260nm used as the molar extinction coefficient of RNA) greater than 300ng/ml, and A260/280 ratios between 1.80 and 2.10 were deemed suitable for further analysis.

treatment_protocol: Cells were trypsinised, washed twice in PBS and resuspended at 2 x 106 cells/ml in FACS buffer (0.1% sodium azide, Sigma; 0.2% bovine serum albumin, Sigma; in PBS). Cells were labelled with antibodies at 4˚C for 1 hour at (unless stated otherwise) the following concentrations: mouse IgM anti-SSEA-1 directly conjugated to phycoeryithrin (PE; Santa Cruz) 2 mg/ml; mouse IgM conjugated PE isotype control (Santa Cruz) 2 mg/ml; 9A7 (rat IgG2A anti-m5T4) 20 μg/ml; rat IgG2A isotype control (eBioscience). 9A7 labelled cells were washed twice in 100μl FACS buffer, resuspended in the original volume of FACS buffer and incubated for 1 hour at 4˚C with rabbit anti-rat immunolglobulins directly conjugated to fluorescein isothiocyanate (FITC, 100 μg/ml, Dako Cytomation). Cells were washed twice and fixed as for SSEA-1 labelled cells. After fixing cells were analysed using FACScan flow cytometer running CellQuest software. A total of 20,000 events were collected and WinMDI 2.8 software (The Scripps Research Institute) was used to produce histograms of results. Live cells (prior to fixation) were gated using forward and side scatter, and this population used for analysis. Typically the gate was set so that it contained the upper 2.5% of the cells incubated with isotype control antibody. This was not practical in all cases due to long “tails” of the negative control histogram. In these instances the gated region was set based on the shape of the histogram. Fluorescence activated cell sorting (FACS): Cells were labelled with 9A7 as described for flow cytometry but the labelling incubation time was reduced to 45 minutes. Cells were not fixed but instead were filtered through a 30μm pre-separation filter (Miltenyi). Cells were sorted (into FACS buffer at 4˚C) using a FACSVantage SE cell sorter, having gated for live cells based upon forward and side scatter, and gating for cells with the same fluorescence intensity as the isotype control incubated cells (5T4 negative cells) and cells with higher fluorescence intensity than isotype control incubated cells (5T4 positive cells).

tag: differentiation status

value: Undifferentiated

tag: cell type

value: 5T4 negative TG2a cell


title: Undifferentiated E14_U2


title: Differentiated E14_D2

value: Differentiated

value: 5T4 positive TG2a cell


title: Differentiated E14_D1


title: Ovarian Cancer Sample (JB 892)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 891)

description: MicroRNA labelling


title: Differentiated E14_D3


title: Undifferentiated E14_U3


title: Ovarian Cancer Sample (JB 919)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 951)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 866)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 820)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 928)

description: MicroRNA labelling

value: #NULL!


title: Ovarian Cancer Sample (JB 720)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 712)

description: MicroRNA labelling


title: Tat-SF1 shRNA A_rep2

description: 1292_2787_13857_AB2_HuEx-1+0-st-v1.CEL_Expression


title: leat-S_12H_rep1

tag: line

value: 8866 (susceptible to wheat powdery mildew,also designed as ‘S’)

tag: age

value: two-week old

value: leaf

value: powdery mildew

tag: time


title: Ovarian Cancer Sample (JB 710)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 877)

description: MicroRNA labelling


title: Tat-SF1 shRNA B_rep1

description: 1292_2787_13859_GH1_HuEx-1+0-st-v1_2.CEL_Expression

tag: cell line


title: Ovarian Cancer Sample (JB 6)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 511)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 5)

description: MicroRNA labelling


title: Tat-SF1 shRNA A_rep1

description: 1292_2787_13856_AB1_HuEx-1+0-st-v1.CEL_Expression


title: Ovarian Cancer Sample (JB 362)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 40)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 35)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 3051)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 242)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 323)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 337)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 2186)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 2160)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 264)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 2133)

description: MicroRNA labelling


title: GFP shRNA_rep2

description: 1292_2787_13854_GFP2_HuEx-1+0-st-v1.CEL_Expression

source_name: Control

value: Control


title: Ovarian Cancer Sample (JB 2061)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 2059)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 2025)

description: MicroRNA labelling


title: Tat-SF1 shRNA A_rep3

description: 1292_2787_13858_AB3_HuEx-1+0-st-v1_2.CEL_Expression

value: Tat-SF1 knockdown by shRNA


title: Ovarian Cancer Sample (JB 2113)

description: MicroRNA labelling

value: Ovarian Cancer


title: Ovarian Cancer Sample (JB 2011)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1944)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1957)

description: MicroRNA labelling

value: Dead


title: Ovarian Cancer Sample (JB 1924)

description: MicroRNA labelling

value: yes


title: Ovarian Cancer Sample (JB 1939)

description: MicroRNA labelling

value: Serous


title: GFP shRNA_rep1

description: 1292_2787_13853_GFP1_HuEx-1+0-st-v1.CEL_Expression


title: Tat-SF1 shRNA B_rep3

description: 1292_2787_13861_GH3_HuEx-1+0-st-v1_2.CEL_Expression


title: GFP shRNA_rep3

description: 1292_2787_13855_GFP3_HuEx-1+0-st-v1.CEL_Expression


title: Ovarian Cancer Sample (JB 1900)

description: MicroRNA labelling

value: Alive


title: Ovarian Cancer Sample (JB 1841)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1535)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1650)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1585)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1598)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1340)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1796)

description: MicroRNA labelling

value: no


title: Ovarian Cancer Sample (JB 1654)

description: MicroRNA labelling


title: Empty Vector_rep2

description: 1292_2787_13851_Empty2_HuEx-1+0-st-v1.CEL_Expression


title: Ovarian Cancer Sample (JB 126)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1209)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1412)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 118)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1196)

description: MicroRNA labelling


title: Empty Vector_rep1

description: 1292_2787_13850_Empty1_HuEx-1+0-st-v1.CEL_Expression


title: Ovarian Cancer Sample (JB 1117)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1504)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 11)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 107)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1013)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1045)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1037)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1001)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1133)

description: MicroRNA labelling


title: Ovarian Cancer Sample (JB 1063)

description: MicroRNA labelling


title: SMALLINT_FETAL15WK_PT30_146_412_1_1

type: genomic

city: SAN DIEGO

first: GULSAH

last: ALTUN

state: CA

address: 3030 Science Park Rd. 3rd floor, room 3020

institute: THE SCRIPPS RESEARCH INSTITUTE

description: Genomic DNA extracted was genotyped using HumanOmni1-Quad BeadChip Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: Scanned on a BeadArray Reader (Illumina) using standard Illumina Protocol.

data_processing: We have used the Illumina Genome Studio software version 2010.2 to generate the SNP calls.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Small Intestine

label_protocol: standard Illumina protocol

extract_protocol: Qiagen DNeasy Blood and Tissue Kit

value: Tissue

tag: passage number


title: STOMACH_FETAL14WK_PT32_101_414_1_1

source_name: Stomach


title: SPLEEN_FETAL14WK_PT32_91_414_1_1

source_name: Spleen


title: STOMACH_ADULT_PT1_101_29_1_5


title: Mixed_50HDF51_50HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 50:50 ratio


title: SPLEEN_ADULT_PT2_91_30_1_1


title: LYMPHNODE_ADULT_PT1_100_29_1_8

source_name: LymphNode


title: TONGUE_FETAL15WK_PT26_139_407_1_2

source_name: Tongue


title: SPLEEN_ADULT_PT1_91_29_1_7


title: URETER_ADULT_PT1_92_29_1_2

source_name: Ureter


title: Mixed_70HDF51_30HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 70:30 ratio


title: URETER_ADULT_PT2_92_30_1_1


title: Mixed_60HDF51_40HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 60:40 ratio


title: STOMACH_FETAL15WK_PT30_101_412_1_1


title: Mixed_10HDF51_90HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 10:90 ratio


title: Mixed_20HDF51_80HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 20:80 ratio


title: Mixed_80HDF51_20HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 80:20 ratio


title: PLACENTA_15WK_PT30_108_412_1_1

source_name: Placenta


title: LUNG_FETAL14WK_PT32_94_414_1_1

source_name: Lung


title: PANCREAS_ADULT_PT1_220_29_1_6

source_name: Pancreas

value: unknown


title: SKMUSCLE_ADULT_PT1_97_29_1_7

source_name: Muscle


title: Mixed_30HDF51_70HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 30:70 ratio


title: PLACENTA_14WK_PT32_108_414_1_1


title: LYMPHNODE_ADULT_PT2_100_30_1_1


title: LUNG_ADULT_PT2_94_30_1_1


title: STOMACH_FETAL15WK_PT26_101_407_1_2


title: SKMUSCLE_ADULT_PT2_97_30_1_1


title: PANCREAS_ADULT_PT2_220_30_1_1


title: Mixed_40HDF51_60HDF51IPS11_323_932_1_1

source_name: Mixure of HDFs and undifferentiated HDFs, 40:60 ratio


title: LUNG_FETAL15WK_PT30_94_412_1_1


title: LUNG_ADULT_PT1_94_29_1_7


title: HEART_FETAL14WK_PT32_111_414_1_1

source_name: Heart


title: KIDNEY_FETAL15K_PT30_143_412_1_1

source_name: Kidney


title: LIVER_FETAL_14WK_PT32_147_414_1_1

source_name: Liver


title: BRAINCXPT77_21_631_2_1


title: BRAINCXPT78_21_632_2_1


title: BRAINCBPT77_21_631_1_1


title: BRAINCBPT78_21_632_1_1


title: BRAINCXPT71_21_625_2_1


title: VENT_FETAL15WK_PT30_111_412_2_1

source_name: HEART, Ventricle


title: BRAINCXPT73_21_627_2_1


title: BRAINCXPT74_21_628_2_1


title: BRAINCBPT74_21_628_1_1


title: BRAINCBPT79_21_633_1_1


title: KIDNEY_FETAL14K_PT32_143_414_1_1


title: DIAPHRAGM_ADULT_PT1_93_29_1_6

source_name: Diaphragm


title: BRAINCBPT72_21_626_1_1


title: BRAINCBPT73_21_627_1_1


title: BRAINCBPT71_21_625_1_1


title: DIAPHRAGM_ADULT_PT2_93_30_1_1


title: BLOOD_PT9_107_366_7_1

source_name: Blood


title: BLOOD_PT8_107_365_6_1


title: BRAINCXPT72_21_626_2_1


title: BLOOD_PT6_107_363_2_1


title: BLOOD_PT5_107_362_1_1


title: BLOOD_PT3_107_35_5_1


title: HEART_ADULT_PT1_102_29_1_6

source_name: HeartRightAtrium


title: BLOOD_PT4_107_361_4_1


title: BLOOD_PT7_107_364_3_1


title: BRAINCXPT79_21_633_2_1


title: ADIPOSE_ADULT_P1_98_30_1_1

source_name: Adipose


title: BLOOD_PT12_107_369_10_1


title: ADRENAL_ADULT_PT2_95_30_2_1

source_name: Adrenal


title: BLOOD_PT13_107_370_12_1


title: BLOOD_PT11_107_368_9_1


title: BLOOD_PT21_107_371_11_1


title: BLADDER_ADULT_PT2_99_30_1_1

source_name: Bladder


title: BLADDER_ADULT_PT1_99_29_1_7


title: HBVSMC266_203_556_1_1

value: Primary Cell


title: ADIPOSE_ADULT_PT1_98_29_1_6


title: HBdSMC265_212_565_1_1


title: ADRENAL_FETAL14WK_PT32_95_414_1_1


title: HSkMC268_208_561_1_1


title: HDK85P3_257_689_1_2

source_name: Keratinocyte


title: AORTA_ADULT_PT2_96_30_1_1

source_name: Aorta


title: ADRENAL_ADULT_PT1_95_29_1_7


title: ADRENAL_FETAL15WK_PT30_95_412_1_2


title: KERA1P4_137_400_3_1


title: HPAv263_217_570_1_1


title: HESMC267_207_560_1_1


title: AORTA_ADULT_PT1_96_29_1_7


title: KDIB2P2_251_669_1_2


title: SC33FIBRO_65_228_3_1

source_name: Postmortem-derived primary dermal fibroblasts


title: HUVECBF4P4_169_250_2_1


title: HDK85P3_257_689_1_1


title: BLOOD_PT10_107_367_8_1


title: HUVECBF5P4_170_251_2_1


title: SC01GLIA_61_224_3_1

source_name: Postmortem-derived primary astrocytes


title: SC11GLIA_67_230_3_1


title: MRC5P5_312_891_3_1

source_name: Fetal Lung Fibroblast


title: IMR90_129_382_3_1

source_name: Fibroblast, lung


title: HPLF260_206_559_1_1


title: HDF58P7_194_462_1_2

source_name: Fibroblast


title: HS27_49_323_1_1

source_name: Human foreskin fibroblasts


title: HDF70P8_222_575_1_1


title: HDF51P7_166_411_1_2


title: HDF51P7_166_411_4_2

source_name: fibroblast


title: HDF69P5_201_544_1_1


title: HDF84P3_255_687_2_2


title: HDF258_204_557_1_1


title: HDF51P11_166_436_1_2


title: HDF68P5_200_543_1_1


title: HDF_HSP_P33_40_167_1_1

source_name: Human dermal fibroblasts, neonatal


title: HDF259_205_558_1_1


title: HDF57P12_193_461_1_2


title: HDF86P3_258_690_1_1


title: SC30FIBRO_63_226_3_1


title: HCFaa1_216_569_1_1


title: HCF1_215_568_1_1


title: HASMC264_214_567_1_1


title: CCD1079SK_128_380_3_1

source_name: Human Foreskin Fibroblast


title: HRCEpiC255_210_563_1_1


title: HANSE21DIFF5D_191_299_1_2

value: Somatic Stem Cell


title: HREpiC256_211_564_1_1


title: HDF_HSP_P12_40_164_1_1


title: HANSE20HDIFF5D_190_298_1_2


title: HIBEpiC254_213_566_1_1


title: SM2_72_237_2_1


title: HANSE22HDIFF5D_192_300_2_4


title: HRPTEpiC257_209_562_1_1

source_name: Renal Proximal Tubular Epithelial_Cells


title: SM3_71_236_3_1


title: HANSE22HP3_192_300_1_4


title: SC27NSC_125_375_1_2


title: SC23NSC_62_225_3_1


title: HANSE20H_190_295_1_4


title: SC31MSC_64_227_3_1

source_name: Bone marrow-derived mesenchymal stem cells, CD105+, CD34-


title: HANSE21_191_296_1_1


title: SC41MSC_66_229_3_1


title: HMSCad251_219_572_1_1


title: HMSCbm252_218_571_1_1


title: PELP11_60_223_1_18

source_name: Differentiated hESC, fibroblasts


title: WA07P95CMD7_47_187_1_1

source_name: Differentiated hESC, cardiomyocyte, day 7


title: ES4CL3P19_132_389_3_1B

source_name: Undifferentiated hiPSC, generated from hESC line differentiated into fibroblast-like cells

value: HIPSC


title: WA07P40OPC_48_180_1_4

source_name: Differentiated hESC, oligodendrocyte precursor cells


title: ES4CL4P19_133_391_3_1


title: WA07P95CMD2_47_186_1_1

source_name: Differentiated hESC, cardiomyocyte precursors, day 2


title: WA07P34MNPD29_47_402_1_2

source_name: Differentiated hESC, motor neuron precursors, day 29


title: PELP13_60_421_1_2


title: ES4CL3P19_132_389_3_1A


title: WA07P96CMD2_47_189_1_1


title: ES4CL1P18_130_384_3_1


title: ES4CL4P18_133_390_3_1


title: GOTTESFELD4078.1A2P27_302_782_3_1

source_name: Undifferentiated hiPSC, generated from human dermal fibroblasts, Friedrich's ataxia


title: GOTTESFELD3816.5P14_300_780_3_1


title: GOTTESFELD4078.1B3P20_301_781_3_1


title: IMR90C4P27_135_394_3_1B

source_name: Undifferentiated hiPSC, generated from lung epithelial fibroblasts


title: K4AMKIPS4F1P15_138_401_1_2B

source_name: Undifferentiated hiPSC, generated from primary keratinocytes


title: TH1.24SOX2P34_309_888_3_1

source_name: Undifferentiated hiPSC, generated from human dermal fibroblasts, beta thalassemia, with persistent exogenous SOX2 expression


title: KIPS4F8P27_250_668_1_2


title: KIPS4F1P32_249_667_1_2


title: HFIB2IPS5P69FF_85_420_1_2

source_name: Undifferentiated hiPSC, generated from human dermal fibroblasts


title: K4AMKIPS4F1P15_138_401_1_2A


title: IMR90C4P27_135_394_3_1A


title: HDF68IPS10P4_233_599_1_1


title: TH1.52OCT4P30_308_887_3_1

source_name: Undifferentiated hiPSC, generated from human dermal fibroblasts, beta thalassemia, with persistent exogenous OCT4/POU5F1 expression


title: ES4CL2P17_131_387_3_1


title: WA07P96CMD7_47_190_1_1


title: HDK68IPS1_221_574_1_1


title: HDF68IPS4P4_230_596_1_1


title: HDF51IPS6P33_157_647_1_2


title: HDF51IPS7P5_158_442_1_1


title: HDF58IPS44P7_198_537_3_1


title: HDF57IPS45P7_199_538_3_1


title: IMR90C2P27_134_392_3_1


title: TH1.60OCT4SOX2P38_311_890_3_1

source_name: Undifferentiated hiPSC, generated from human dermal fibroblasts, beta thalassemia, with persistent exogenous OCT4/POU5F1 and SOX2 expression


title: HDF51IPS5P34_156_646_1_1


title: HDF51IPS9P33_160_649_1_3


title: HDF51IPS7P33_158_648_1_1


title: HDF51IPS3P8_155_456_3_2


title: GOTTESFELD8.2A4RP28_299_779_3_1


title: HDF51IPS9P7_160_473_1_1


title: HDF51IPS6P5_157_441_1_1


title: 36-7 M.mulatta Ovul Follicle 36h postovul

city: Beaverton

first: fuhua

last: xu

state: OR

address: 505 NW 185th Ave

institute: Oregon National Primate Research Center

description: Gene expression data from CL during luteal development (luteinization), i.e. just after ovulation when the cellular constituents remaining from the preovulatory follicle are transformed into the CL.

hyb_protocol: Labeled target is fragmented at 95C in the presence of high magnesium concentration.  The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Ten micrograms of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.cel files).  Image inspection was performed manually immediately following each scan.

data_processing: The processed image files (.cel) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.

label: Biotin

organism: Macaca mulatta

source_name: Follicle collected at 36 hour post-hCG treatment

label_protocol: Messenger RNA is amplified and labeled from 2 micrograms of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix).  In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using RNeasy spin columns (Qiagen) following manufacturer instructions.

treatment_protocol: Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. When estradiol levels reached 100 ~ 120 pg/ml, a GnRH antagonist (Acyline, 0.1 ml/kg) plus recombinant (r)-human (h) FSH and r-hLH (30 IU each) were administered at 16:00 that day (day 1) and at 08:00 next day (day 2). At 16:00 on day 2, 1000 IU r-hCG was injected to initiate ovulatory events. The ovary bearing the large dominant follicle (ruptured) was removed from anesthetized animals by laparotomy at 36 h post-hCG treatment, and the follicle was separated from the ovary, immediately frozen in liquid nitrogen, and stored at -80¡ãC until total RNA was extracted. Daily blood samples were collected until the day of surgery.

tag: gender

value: female

value: Follicle

tag: reproductive state

value: controlled ovulation


title: 36-6 M.mulatta Ovul Follicle 36h postovul


title: HDF51IPS5P6_156_440_1_1


title: HDF51IPS3P6_155_439_1_1


title: 36-5 M.mulatta Ovul Follicle 36h postovul


title: HDF51IPS1P25_153_738_1_1


title: 36-8 M.mulatta Ovul Follicle 36h postovul


title: 36-3 M.mulatta Ovul Follicle 36h pre-ovul

treatment_protocol: Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. When estradiol levels reached 100 ~ 120 pg/ml, a GnRH antagonist (Acyline, 0.1 ml/kg) plus recombinant (r)-human (h) FSH and r-hLH (30 IU each) were administered at 16:00 that day (day 1) and at 08:00 next day (day 2). At 16:00 on day 2, 1000 IU r-hCG was injected to initiate ovulatory events. The ovary bearing the large dominant follicle (unruptured) was removed from anesthetized animals by laparotomy at 36 h post-hCG treatment, and the follicle was separated from the ovary, immediately frozen in liquid nitrogen, and stored at -80¡ãC until total RNA was extracted. Daily blood samples were collected until the day of surgery.


title: HDF51IPS1P6_153_437_1_1


title: 36-4 M.mulatta Ovul Follicle 36h pre-ovul


title: HDF51IPS3P12_155_490_3_2


title: 36-2 M.mulatta Ovul Follicle 36h pre-ovul


title: HDF51IPS13P14_164_502_3_2


title: HDF51IPS3P34_155_645_1_4


title: HDF51IPS14P8_165_472_1_1


title: HDF51IPS11P33_162_650_1_1


title: HDF51IPS2P34_154_644_1_2


title: 24-3 M.mulatta Ovul Follicle 24h post-hCG

source_name: Follicle collected at 24 hour post-hCG treatment

treatment_protocol: Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. When estradiol levels reached 100 ~ 120 pg/ml, a GnRH antagonist (Acyline, 0.1 ml/kg) plus recombinant (r)-human (h) FSH and r-hLH (30 IU each) were administered at 16:00 that day (day 1) and at 08:00 next day (day 2). At 16:00 on day 2, 1000 IU r-hCG was injected to initiate ovulatory events. The ovary bearing the large dominant follicle was removed from anesthetized animals by laparotomy at 24 h post-hCG treatment, and the follicle was separated from the ovary, immediately frozen in liquid nitrogen, and stored at -80¡ãC until total RNA was extracted. Daily blood samples were collected until the day of surgery.


title: 24-4 M.mulatta Ovul Follicle 24h post-hCG


title: HDF51IPS11P8_162_475_3_2


title: WA09P92_87_313_2_1

source_name: Undifferentiated hESC

value: HESC


title: HDF51IPS12P6_163_447_1_1


title: C14P32_310_889_3_1


title: HDF51IPS11P14_162_501_3_2


title: HDF51IPS14P27_165_592_1_2


title: 36-1 M.mulatta Ovul Follicle 36h pre-ovul


title: 24-2 M.mulatta Ovul Follicle 24h post-hCG


title: HDF51IPS13P34_164_652_1_1


title: HDF51IPS13P8_164_471_3_2


title: WA09P50_87_312_2_1


title: HDF51IPS10P37_161_900_1_2


title: NSC253IPSCP23_314_893_3_1

source_name: Undifferentiated hiPSC generated from neural stem cell line


title: 12-4 M.mulatta Ovul Follicle 12h post-hCG

source_name: Follicle collected at 12 hour post-hCG treatment

treatment_protocol: Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. When estradiol levels reached 100 ~ 120 pg/ml, a GnRH antagonist (Acyline, 0.1 ml/kg) plus recombinant (r)-human (h) FSH and r-hLH (30 IU each) were administered at 16:00 that day (day 1) and at 08:00 next day (day 2). At 16:00 on day 2, 1000 IU r-hCG was injected to initiate ovulatory events. The ovary bearing the large dominant follicle was removed from anesthetized animals by laparotomy at 12 h post-hCG treatment, and the follicle was separated from the ovary, immediately frozen in liquid nitrogen, and stored at -80¡ãC until total RNA was extracted. Daily blood samples were collected until the day of surgery.


title: 24-1 M.mulatta Ovul Follicle 24h post-hCG


title: HDF51IPS10P6_161_445_1_1


title: WA09P49MGKSRFF_87_146_4_1


title: 12-2 M.mulatta Ovul Follicle 12h post-hCG


title: 12-1 M.mulatta Ovul Follicle 12h post-hCG


title: 12-3 M.mulatta Ovul Follicle 12h post-hCG


title: 0-4 M.mulatta Ovul Follicle 0h

source_name: Follicle collected at 0 hour post-hCG treatment

treatment_protocol: Blood samples were collected daily by saphenous venipuncture starting six days after onset of menses. Serum was separated and samples were assayed daily for estradiol concentrations. When estradiol levels reached 100 ~ 120 pg/ml, a GnRH antagonist (Acyline, 0.1 ml/kg) plus recombinant (r)-human (h) FSH and r-hLH (30 IU each) were administered at 16:00 that day (day 1) and at 08:00 next day (day 2). At 16:00 on day 2, the ovary bearing the large dominant follicle was removed from anesthetized animals by laparotomy, and the follicle was separated from the ovary, immediately frozen in liquid nitrogen, and stored at -80¡ãC until total RNA was extracted. Daily blood samples were collected until the day of surgery.


title: HDF51IPS2P6_154_438_1_2


title: 0-5 M.mulatta Ovul Follicle 0h


title: 0-6 M.mulatta Ovul Follicle 0h


title: WA09P46POLYNEOPTFF_87_144_1_1


title: WA09P77C1_87_676_1_1

source_name: Undifferentiated hESC, cultured from single-cell clone


title: HDF51IPS12P33_163_651_1_3


title: 0-2 M.mulatta Ovul Follicle 0h


title: 0-3 M.mulatta Ovul Follicle 0h


title: 0-1 M.mulatta Ovul Follicle 0h

description: Gene expression data from preovulatory follicle.


title: WA09P41FF_87_304_7_2


title: OCI-Ly10 panobinostat 48h_methlyation data

first: Matko

last: Kalac

address: 522 1st Avenue

department: NYU Cancer Institute

institute: NYU Medical Center

scan_protocol: standard Illumina protocol

data_processing: Methylation scores represented as â values are generated for each site using BeadStudio 3.2 software (© Illumina, Inc. 2003-2008) and are computed based on the ratio of methylated to methylated plus unmethylated signal outputs. Thus the â values range from 0 (unmethylated) to 1 (fully methylated) on a continuous scale. Intra-array normalisation was performed by the Illumina BeadStudio3.2 software. The resulting â-valued data matrix was normalised further using a quantile-normalization strategy, designed to reduce unwanted inter-array variation using CLCBio Genomics Workbench 3 software package (version 3.7.1).

source_name: DLBCL patient

growth_protocol: cells were grown in IMDM (Ly1 and Ly10) or RPMI (Su-DHL6) medium with 10% fetal bovine serum. Fresh medium was added every 2-3 days and the cells were kept at a cell concentration of 0.5-1 x 106/mL.

extract_protocol: Total DNA was isolated using phenol chloroform method

treatment_protocol: Cells were treated with panobinostat alone, decitabine alone or their combination. Following 48h of incubation with the drugs total DNA was isolated.

value: Diffuse large B-cell lymphoma

tag: agent

value: panobinostat


title: Su-DHL6 combination 48h_methlyation data

value: decitabine and panobinostat


title: Su-DHL6 control 48h_methlyation data

value: DMSO control


title: Su-DHL6 panobinostat 48h_methlyation data


title: OCI-Ly10 combination 48h_methlyation data


title: Su-DHL6 decitabine 48h_methlyation data

value: decitabine


title: OCI-Ly10 decitabine 48h_methlyation data


title: WA09P39HDFPOLY_87_142_1_1


title: OCI-Ly10 control 48h_methlyation data


title: WA09P40KSR_87_137_1_1


title: OCI-Ly1 panobinostat 48h_methlyation data


title: OCI-Ly1 combination 48h_methlyation data


title: WA09P39POLY_87_139_1_1


title: OCI-Ly1 decitabine 48h_methlyation data


title: WA01P51_3_3_3_1


title: WA07P95_47_188_1_1


title: OCI-Ly1 control 48h_methlyation data


title: WA09P39NEOPT_87_138_1_1


title: WA07P56_47_177_1_1


title: Su-DHL6 decitabine 48h

data_processing: Expression intensity measures went through background correction, log2 transformation, and quantile normalization methods executed by BeadStudio 3.2. software. Unsupervised clustering of gene expression data by principal component analysis was performed with the use of GenePattern software

extract_protocol: Total RNA was isolated using TRIZOL reagens

treatment_protocol: Cells were treated with panobinostat alone, decitabine alone or their combination. Following 48h of incubation with the drugs total RNA was isolated.


title: WA01 _3_686_1_2


title: WA07P35_47_176_1_5


title: Su-DHL6 combination 48h


title: WA01 _3_686_2_2


title: UC06P71POLYNEOPT_39_157_1_1


title: OCI-Ly10 combination 48h


title: Su-DHL6 panobinostat 48h


title: Su-DHL6 control 48h


title: UC06P61KSR_39_158_1_1


title: OCI-Ly10 panobinostat 48h


title: OCI-Ly10 decitabine 48h


title: UC06P59_39_316_1_1


title: UC06P61NEOPT_39_159_1_1


title: SIVF050P9_280_750_1_3


title: SIVF049P9_279_749_1_3


title: SIVF048P13_278_748_1_3

source_name: Undifferentiated hESC, Trisomy 5


title: OCI-Ly10 control 48h


title: OCI-Ly1 panobinostat 48h


title: SIVF046P11_287_757_1_3


title: OCI-Ly1 combination 48h


title: UC06P70POLY_39_156_1_1


title: OCI-Ly1 decitabine 48h


title: SIVF044P13_285_755_1_3


title: SIVF047P10_288_758_1_3


title: SIVF045P13_286_756_1_3


title: OCI-Ly1 control 48h


title: NESG1-negative C6-5-8F NPC cells rep2

city: guangzhou

first: weiyi

last: fang

address: tonghe road

institute: cancer institute

description:
C6-2
Gene expression data from NESG1-negative expression NPC 5-8F cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at -80℃ on GeneChip U133_Plus_2 (GPL570 platform)Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: NPC 5-8F cells with NESG1-negative expression

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

growth_protocol: 4 NPC cells, including two from NESG1-negative C6-Ctr cells and two from NESG1-expressing 2F4 cells were cultured by 10% newborn calf serum (NBCS)

treatment_protocol: 4 NPC cells were harvested by trizol and preserved at -80℃

value: NPC 5-8F cells

tag: genotype/variation

value: control


title: UC06P112_39_317_1_1


title: SIVF041P17_282_752_1_3


title: SIVF043P12_284_754_1_3


title: NESG1-negative C6-5-8F NPC cells rep1

description:
C6-1
Gene expression data from NESG1-negative expression NPC 5-8F cells


title: NESG1-overexpressed 2F4-5-8F NPC cells rep2

description:
2F4-2
Gene expression data from NESG1-overexpressed NPC 5-8F cells

source_name: NPC 5-8F cells with NESG1 overexpression

value: NESG1 overexpression


title: SIVF028P28_276_746_1_3


title: NESG1-overexpressed 2F4-5-8F NPC cells rep1

description:
2F4-1
Gene expression data from NESG1-overexpressed NPC 5-8F cells


title: SIVF029P28_277_747_1_3


title: SIVF040P17_281_751_1_3


title: SIVF026P30_298_778_1_2


title: SIVF027P31_297_777_1_3


title: FIB-4Fs_2

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStadio

source_name: fibroblasts, SPI1, CEBPA, MNDA, IRF8,lentivirus vector transduced

label_protocol: Biotinylated cRNA were prepared with the Illumina RNA Amplification kit (Ambion) for Illumina arrays

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

value: fibroblast

tag: tissue derived

value: skin

value: Male


title: SIVF042P13_283_753_1_3


title: FIB_SPI1_rep2

description: Replicate 2

source_name: fibroblasts, SPI1 lentivirus vector transduced


title: FIB-4Fs_1

description: Replicate 1


title: FIB_SPI1_rep3

description: Replicate 3


title: FIB_SPI1_rep1

description: Replicate 1


title: SIVF024P28_294_774_1_3

source_name: Undifferentiated hESC, Turner's Syndrome


title: FIB-4Fs_3

description: Replicate 3


title: FIB_mock_rep2

description: Replicate 2

source_name: fibroblasts, mock lentivirus vector transduced


title: FIB_mock_rep1

description: Replicate 1


title: MON_rep3

description: Replicate 3

source_name: CD14+ monocytes

value: CD14+ cells

value: Peripheral blood


title: SIVF022P48_121_768_1_3


title: SIVF023P23_122_353_4_1


title: SIVF024P15_294_772_1_3


title: MON_rep2

description: Replicate 2


title: MON_rep1

description: Replicate 1


title: S23_rep4

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 8 - 15 k format for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intesities. In limma, the edwards method for background correction was used (offset = 30), and global loess normalization (MAANOVA) was done.

organism: Folsomia candida

source_name: 30 animals, natural soil

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil: 20 adult animals were incubated per container to lay eggs for 2 days; the container contained a plaster of Paris base mixed with charcoal. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle.

extract_protocol: Total RNA was extracted from all animals (~30 per jar) using the SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil (both field soils and control soils at 50% water holding capacity). Exposure was done at same conditions as incubation. After exposure, the animals were extracted from soil with tap water via flotation, put in 1.5 mL tubes and frozen in liquid N2.

value: 23 days

tag: soil

value: natural


title: FIB_mock_rep3

description: Replicate 3


title: FIB_rep3

description: Replicate 3

source_name: dermal fibroblasts


title: SIVF020P82_289_762_1_2


title: FIB_rep2

description: Replicate 2


title: S04_rep4


title: FIB_rep1

description: Replicate 1


title: SIVF020HDP52_119_350_4_1

source_name: Undifferentiated hESC, Huntington's Disease


title: SIVF019P81_118_761_1_2

source_name: Undifferentiated hESC


title: S09_rep4


title: SIVF019P53_118_349_4_1


title: S12_rep3


title: SIVF019P67_118_776_1_3


title: Cervical cancer-lymph node positive-38-57

city: Groningen

first: Maartje

last: Noordhuis

department: Gynecologic Oncology

institute: University Medical Center Groningen

description: Gene expression data from cervical cancer tissue of patient with pelvic lymph node metastasis

hyb_protocol: Labelled RNA samples were hybridized according to a randomized design to the human genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). The microarrays were loaded with 200 μl of hybridization cocktail solution and then placed in Genechip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm at 45 °C for 16 h.

scan_protocol: After hybridization, the arrays were washed on Genechip Fluidics Station 400 (Affymetrix) and scanned using Genechip Scanner 3000 (Affymetrix) according to the manufacturers’ procedure. Labeling of the RNA, quality control, the microarray hybridization and scanning were performed by ServiceXS (Leiden, the Netherlands ) according to Affymetrix standards.

data_processing: Processing of CEL files was performed with Affymetrix Expression Console software. Probe set expression summary was done using the Robust Multi-array Average (RMA) algorithm. Quality of the microarray data was checked using histograms, box plots and a RNA degradation plot. Principal component analysis (PCA) was performed for controlling the quality of the hybridizations.

source_name: Early stage cervical cancer

label_protocol: For labelling, 10 μg of total RNA was amplified by in vitro transcription using T7 RNA polymerase, according to standard Affymetrix protocols.

extract_protocol: From the frozen biopsies, four 10 mm thick sections were cut and used for standard RNA isolation. After cutting, a 3 mm thick section was stained with hematoxylin/eosin for histological examination and only tissues with >80% tumor cells were included. RNA was isolated with TRIzol reagent (Invitrogen, Breda, the Netherlands) according to manufacturer's protocol. RNA was treated with DNAse and purified using the RNeasy mini-kit (Qiagen, Westburg, Leusden, the Netherlands). The quality and quantity of the RNA was determined by Agilent Lab-on-Chip analysis.

treatment_protocol: Primary treatment consisted of type 3 radical hysterectomy and pelvic lymph node dissection. In case of poor prognostic factors, such as lymph node metastases or positive resection margins, patients were treated with adjuvant radiotherapy or chemoradiation.

tag: pelvic lymph nodes

value: Positive

tag: age at diagnosis

tag: figo stage


title: SIVF017P67_292_769_1_2

value: HESC


title: S27_rep3


title: S08_rep4


title: S24_rep3


title: S02_rep2


title: Cervical cancer-lymph node positive-36-50


title: S05_rep4


title: Cervical cancer-lymph node positive-37-56


title: SIVF014P42_295_773_1_3


title: SIVF018HDP44_117_347_4_1


title: SIVF018P72_293_770_1_2


title: SIVF022P19_121_352_4_1


title: S11_rep3


title: S26_rep4


title: Cervical cancer-lymph node positive-35-46


title: SIVF017HDP43_116_346_4_1


title: Cervical cancer-lymph node positive-39-59


title: S01_rep3


title: S10_rep4


title: SIVF011P28_273_743_1_2


title: SIVF006P24_114_355_3_1


title: Cervical cancer-lymph node positive-33-38


title: S23_rep3


title: Cervical cancer-lymph node positive-34-45


title: S07_rep4


title: SIVF006P22_114_344_4_1


title: S11_rep2


title: SIVF015P18_274_744_1_2


title: S26_rep3


title: S10_rep3


title: S09_rep3


title: SLCZ_rep4

source_name: 30 animals, control soil


title: SIVF007P21_115_345_4_1


title: S03_rep4


title: Cervical cancer-lymph node positive-30-26


title: SIVF005P24_123_354_4_1


title: SIVF005P44_123_767_1_2


title: S08_rep3


title: S04_rep3


title: SIVF004P43_291_766_1_3


title: S06_rep3


title: S09_rep2


title: SIVF002P17_136_398_3_1


title: SIVF003P22_113_343_4_1


title: Cervical cancer-lymph node positive-29-25


title: Cervical cancer-lymph node positive-27-21


title: S05_rep3


title: SIVF021P49_120_764_1_2

source_name: Undifferentiated hESC, Trisomy 21


title: S03_rep3


title: S25_rep4


title: Cervical cancer-lymph node positive-26-15


title: S01_rep2


title: S24_rep2


title: S25_rep3


title: S06_rep2


title: S03_rep2


title: S07_rep3


title: Cervical cancer-lymph node positive-25-10


title: Cervical cancer-lymph node positive-24-09


title: Cervical cancer-lymph node positive-23-07


title: SIVF001P41FF_112_341_4_1


title: SIVF001P45FF_112_342_4_1


title: S26_rep2


title: SIVF021P19_120_351_4_1


title: S01_rep1


title: S06_rep4


title: SIVF001P18_112_396_3_1


title: S07_rep2


title: S10_rep2


title: SIVF001P39FF_112_340_4_1


title: Cervical cancer-lymph node positive-28-23


title: Cervical cancer-lymph node positive-21-04


title: Cervical cancer-lymph node positive-22-05


title: S08_rep2


title: MIZ6P27NEOPT_38_162_1_1


title: S24_rep1


title: S25_rep2


title: S03_rep1


title: S04_rep2


title: S12_rep2


title: Cervical cancer-lymph node negative-20-62

description: Gene expression data from cervical cancer tissue of patient with no pelvic lymph node metastasis

value: Negative


title: Cervical cancer-lymph node positive-32-37


title: SLCZ_rep3


title: SIVF002P50_290_763_1_3


title: Cervical cancer-lymph node negative-19-54


title: S27_rep2


title: Cervical cancer-lymph node negative-18-53


title: Cervical cancer-lymph node negative-17-52


title: S09_rep1


title: S23_rep2


title: S05_rep2


title: SIVF016P19_275_745_1_3


title: Cervical cancer-lymph node negative-16-51


title: MIZ6P18_38_610_1_1


title: S07_rep1


title: Cervical cancer-lymph node negative-15-48


title: Cervical cancer-lymph node negative-14-44


title: S04_rep1


title: S02_rep1


title: S05_rep1


title: S27_rep1


title: MIZ4P65POLYNEOPTFF_37_157_1_1


title: S25_rep1


title: Cervical cancer-lymph node negative-13-43


title: S11_rep1


title: S06_rep1


title: S26_rep1


title: Cervical cancer-lymph node positive-31-28


title: Cervical cancer-lymph node negative-11-35


title: MIZ4P62HDFPOLYNEOPT_37_156_1_1


title: S10_rep1


title: Cervical cancer-lymph node negative-10-34


title: S08_rep1


title: S12_rep1


title: Cervical cancer-lymph node negative-12-36


title: SLZC_rep2


title: S23_rep1


title: MIZ4P60POLY_37_150_1_1


title: S13_rep4


title: Cervical cancer-lymph node negative-09-33


title: MIZ4P62HDFPOLY_37_154_3_1


title: Cervical cancer-lymph node negative-08-32


title: S15_rep4


title: SIVF007P23_115_356_3_1


title: MIZ6P27KSR_38_161_1_1


title: S16_rep4


title: MIZ4P53KSR_37_147_1_1


title: S18_rep4


title: Cervical cancer-lymph node negative-07-27


title: MIZ4P53NEOPT_37_148_5_1


title: S21_rep4


title: S17_rep4


title: S20_rep4


title: S28_rep4


title: Cervical cancer-lymph node negative-06-20


title: Cervical cancer-lymph node negative-05-18


title: MIZ4P33_37_319_1_1


title: MIZ1P89_110_318_1_1


title: S21_rep3


title: SLCC_rep3


title: Cervical cancer-lymph node negative-04-13


title: S16_rep3


title: MIZ13P50_238_613_1_1


title: Cervical cancer-lymph node negative-03-11


title: MIZ1P41_110_612_1_1


title: S19_rep4


title: S15_rep3


title: Cervical cancer-lymph node negative-02-02


title: Cervical cancer-lymph node negative-01-01


title: SLCC_rep1


title: S13_rep3


title: MEL3P34_126_376_3_1


title: MEL4P35_127_378_3_1


title: HUVEC_Ad.HLX_32h

city: Wien

first: Julia

last: Testori

address: Lazarettgasse 19

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Medical University Vienna

description: Gene expression data

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed using RMA (Robust multiarray average) Signal extraction and normalization.

source_name: HUVEC, infected Adenovirus HLX, 32h

label_protocol: Affymetrix protocol

tag: Human umbilical vein endothelial cells, passage 5


title: MEL4P36_127_379_3_1


title: S15_rep1


title: S17_rep3


title: S28_rep3


title: HUVEC_Ad.HLX_16h

description: Gene expression data

source_name: HUVEC, infected Adenovirus HLX, 16h


title: MEL2P16_36_134_4_1


title: S21_rep2


title: S16_rep2


title: HUVEC_Ad.HLX_8h

description: Gene expression data

source_name: HUVEC, infected Adenovirus HLX, 8h


title: MEL2P13_36_131_4_1


title: HUVEC_Ad.HLX_4h

description: Gene expression data

source_name: HUVEC, infected Adenovirus HLX, 4h


title: S21_rep1


title: S15_rep2


title: S20_rep3


title: HUVEC_noninfected

description: Gene expression data

source_name: HUVEC, not infected


title: S20_rep1


title: S13_rep2


title: MEL1P51_35_122_4_1


title: MIZ4P63POLYNEOPT_37_152_1_1


title: HUVEC_Ad.con_32h

description: Gene expression data

source_name: HUVEC, infected Adenovirus control, 32h


title: MIZ6P87_38_611_1_1


title: S18_rep3


title: MEL1P62FF_35_130_4_1


title: MIZ4P88_37_320_1_1


title: S20_rep2


title: S19_rep3


title: S28_rep2


title: S19_rep2


title: SLCC_rep2


title: HUVEC_Ad.con_8h

description: Gene expression data

source_name: HUVEC, infected Adenovirus control, 8h

treatment_protocol: The cells were infected by adding 40 MOI of CsCl-purified Adenovirus.


title: HUVEC_Ad.con_16h

description: Gene expression data

source_name: HUVEC, infected Adenovirus control, 16h


title: S18_rep2


title: S28_rep1


title: S17_rep1


title: HUVEC_Ad.con_4h

description: Gene expression data

source_name: HUVEC, infected Adenovirus control, 4h


title: S02_rep4


title: S16_rep1


title: S12_rep4


title: HUES16P21_70_233_3_1


title: S17_rep2


title: HUES13P21_69_232_3_1


title: MEL1P62FF_35_127_4_1


title: 2_CD34+_12h_TCDD+

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of highly purified CD34+ cells from normal donor 2 after in vitro TCDD exposure.

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr 30 minutes at 45°C on GeneChip HG-U133A Array. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The HG-U133A arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: The data were analyzed with GeneChip Operating Software (GCOS version 1.4) using Affymetrix default analysis settings and global scaling as normalization.

source_name: CD34+ cells from normal donor after in vitro TCDD exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 micrograms of total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (GibcoBRL). RNA was purified using the RNeasy® Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol:
The hematopoietic progenitor CD34+ cells were separated from the leukapheresis of normal donors stimulated with G-CSF using the immunonomagnetic MACS Miltenyi method. The cells harvested by apheresis were layered on a Ficoll-Paque gradient (specific gravity 1.077 g/ml; Nycomed Pharma AS, Oslo, Norway) in order to separate the low density mononuclear cells (LD-MNCs), and the samples were washed twice in Hanks' balanced salt solution (HBSS). The LD-MNCs were incubated with the QBEND10 monoclonal antibody directed against the CD34 antigen for 15 minutes at 4°C, and were then washed and incubated with immunomagnetic beads (Miltenyi Biotech, Bergisch Gladbach, Germany) against QBEND10 for a further 15 minutes at 4°C. For the flow cytometry analysis, CD34-phycoerythrin (CD34-PE) conjugated antibody (HPCA-2, Becton Dickinson, Mountain View, CA, USA) was added to the cells for 15 minutes at 4°C. At the end of the separation, the cells were counted and assessed for viability by means of trypan blue dye exclusion, and their purity was determined by means of flow cytometry. All of these steps were performed under aseptic conditions. The mean purity of the CD34+ cells after immunomagnetic separation was 96.0%.

The highly purified human CD34+ cells were exposed to 20 nM TCDD for 12h in vitro.

value: hematopoietic progenitor CD34+ cells

tag: treatment

value: in vitro TCDD exposure

tag: normal donor 2


title: 5_CD34+_12h_TCDD-

description: Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 5.

source_name: CD34+ cells from untreated normal donor

treatment_protocol: The hematopoietic progenitor CD34+ cells were separated from the leukapheresis of normal donors stimulated with G-CSF using the immunonomagnetic MACS Miltenyi method. The cells harvested by apheresis were layered on a Ficoll-Paque gradient (specific gravity 1.077 g/ml; Nycomed Pharma AS, Oslo, Norway) in order to separate the low density mononuclear cells (LD-MNCs), and the samples were washed twice in Hanks' balanced salt solution (HBSS). The LD-MNCs were incubated with the QBEND10 monoclonal antibody directed against the CD34 antigen for 15 minutes at 4°C, and were then washed and incubated with immunomagnetic beads (Miltenyi Biotech, Bergisch Gladbach, Germany) against QBEND10 for a further 15 minutes at 4°C. For the flow cytometry analysis, CD34-phycoerythrin (CD34-PE) conjugated antibody (HPCA-2, Becton Dickinson, Mountain View, CA, USA) was added to the cells for 15 minutes at 4°C. At the end of the separation, the cells were counted and assessed for viability by means of trypan blue dye exclusion, and their purity was determined by means of flow cytometry. All of these steps were performed under aseptic conditions. The mean purity of the CD34+ cells after immunomagnetic separation was 96.0%.

tag: cell type

value: untreated

tag: normal donor 5


title: HES4P59_34_120_4_1


title: S24_rep4

source_name: 30 animals, natural soil

tag: age


title: 4_CD34+_12h_TCDD+

description: Gene expression profiling data of highly purified CD34+ cells from normal donor 4 after in vitro TCDD exposure.

tag: normal donor 4


title: S19_rep1


title: S18_rep1


title: HUES7P21_68_231_3_1

tag: passage number


title: HES4P29_34_274_1_1


title: 4_CD34+_12h_TCDD-

description: Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 4.


title: 3_CD34+_12h_TCDD+

description: Gene expression profiling data of highly purified CD34+ cells from normal donor 3 after in vitro TCDD exposure.

tag: normal donor 3


title: SLCC_rep4


title: 3_CD34+_12h_TCDD-

description: Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 3.


title: HES4P56_34_116_4_1


title: 1_CD34+_12h_TCDD+

description: Gene expression profiling data of highly purified CD34+ cells from normal donor 1 after in vitro TCDD exposure.

tag: normal donor 1


title: S13_rep1


title: HES2P55_32_114_4_1


title: HES3P60_33_119_4_1


title: HES3P31_33_276_1_1


title: HES2P92_32_110_4_1


title: S02_rep3


title: 1_CD34+_12h_TCDD-

description: Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 1.


title: SLCZ_rep1


title: S27_rep4


title: S11_rep4


title: BCL6 ChIP-chip in NALM1 cells + 10µM STI571 (24h)  replicate 2

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description:
NALM1_S_r2_WC13
BCL6 ChIP-chip in NALM1 cells  treated with 10uM STI571 (24h)  replicate 2
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody

hyb_protocol: Standard Nimblegen protocol.

scan_protocol: Standard Nimblegen protocol.

data_processing:
Take all the probes in the promoter region and perform Log2 transformion of IP/INPUT(Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter.
The analysis method (script) was published in Ci et al. Blood. 2009 May 28;113(22):5536-48. PMID: 19307668.

source_name: genomic DNA [input]

label_protocol: described in www.nimblegen.com

extract_protocol: sonicated genomic DNA, then purify by qiagen column

value: Ph+ ALL cell line NALM-1

tag: agent

tag: chip antibody

value: none, input DNA

source_name: BCL6 ChIP DNA from ph+ ALL cell line [IP]

extract_protocol: chromatinIP products which are genomic regions bound by BCL6, then purify by qiagen column.

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody lot #

tag: chip antibody catalog #


title: BCL6 ChIP-chip in BV173 cells + 10µM STI571 (24h)  replicate 2

description:
BV173_S_r2_WC15
BCL6 ChIP-chip in BV173 cells treated with 10uM STI571 (24h)  replicate 2
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody

value: Ph+ ALL cell line BV-173


title: BCL6 ChIP-chip in BV173 cells - STI571  replicate 2

description:
BV173_C_r2_WC14
BCL6 ChIP-chip in BV173 cells cultured in absence of STI571 replicate 2
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody

value: control


title: BCL6 ChIP-chip in NALM1 cells - STI571  replicate 2

description:
NALM1_C_r2_WC12
BCL6 ChIP-chip in NALM1 cells cultured in absence of STI571 replicate 2
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: S01_rep4

tag: soil


title: HES3P54_33_112_4_1

description: Genomic DNA extracted was genotyped using HumanOmni1-Quad BeadChip Genotyping BeadChips (Illumina).

source_name: Undifferentiated hESC


title: BCL6 ChIP-chip in Tom1 cells - STI571  replicate 2

description:
TOM1_C_r2_WC10
BCL6 ChIP-chip in Tom1 cells cultured in absence of STI571 replicate 2
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody

value: Ph+ ALL cell line TOM-1


title: BCL6 ChIP-chip in BV173 cells + 10µM STI571 (24h)  replicate 1

description:
BV173_S_r1_WC9
BCL6 ChIP-chip in BV173 cells  treated with 10uM STI571 (24h)  replicate 1
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: ESIH3_31_106_1_1

value: unknown


title: ESIH3P114_31_109_1_1


title: BCL6 ChIP-chip in Tom1 cells + 10µM STI571 (24h)  replicate 2

description:
TOM1_S_r2_WC11
BCL6 ChIP-chip in Tom1 cells  treated with 10uM STI571 (24h)  replicate 2
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: BCL6 ChIP-chip in NALM1 cells - STI571  replicate 1

description:
NALM1_C_r1_WC6
BCL6 ChIP-chip in NALM1 cells cultured in absence of STI571 replicate 1
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: HES2P105_32_135_4_1


title: FES29P39_24_94_1_1


title: siliques WT, hypoxia, biological rep1

city: Gatersleben

first: Johannes

last: Thiel

address: Corrensstrasse 3

country: Germany

institute: IPK-Gatersleben

description: Gene expression data after treatment

hyb_protocol: After fragmentation, cRNA was hybridized to GeneChip Arabidopsis ATH1 Genome Array according to Affymetrix standard protocol at RZPD. Gene Chips were washed and stained using fluidics protocol EUKGE-WS2V4_450.

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

data_processing: Data were processed with the Affymetrix MicroArray Suite software package (MAS 5.0) and analyzed using Bioconductor packages in R. Data were normalized using the Robust Multi-array Average (RMA) method.

organism: Arabidopsis thaliana

source_name: Arabidopsis siliques after hypoxia treatment (1h)

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix) at the RZPD Deutsches Ressourcenzentrum für Genomforschung GmbH (Berlin, Germany).

growth_protocol: Plants were grown at 22°C under 16/8-h photoperiod, a relative air humidity of 60% and an approximate light intensity of 100-150 µmol photons m-2 second-1.

extract_protocol: Total RNA was isolated from siliques using GENTRA kit (Biozym, Germany) according to the manufacturer´s instructions. RNA was further purified using RNeasy Kit (Quiagen) and subjected to DNAse digestion (Quiagen) according to the manufacturer´s instructions.

treatment_protocol: Complete plants (45 DPG) were aerated with a gas mixture containing 10.5% oxygen (composed of a 1:1 mixture of ambient gas and N2) or ambient gas containing 21% oxygen for control samples in darkness for 1 hour. Plants were decapitated and immediately frozen in liquid nitrogen. About 70-80 siliques were dissected in liquid nitrogen for one biological replicate.

tag: genotype

value: 11/12 days after pollination corresponding to mid phase of seed maturation

tag: tissue

value: silique

value: hypoxia


title: BCL6 ChIP-chip in Tom1 cells + 10µM STI571 (24h)  replicate 1

description:
TOM1_S_r1_WC5
BCL6 ChIP-chip in Tom1 cells  treated with 10uM STI571 (24h)  replicate 1
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: BCL6 ChIP-chip in Tom1 cells - STI571  replicate 1

description:
TOM1_C_r1_WC4
BCL6 ChIP-chip in Tom1 cells cultured in absence of STI571 replicate 1
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: ESI053P37_30_105_5_1


title: HES2P28_32_273_1_1


title: BCL6 ChIP-chip in NALM1 cells + 10µM STI571 (24h)  replicate 1

description:
NALM1_S_r1_WC7
BCL6 ChIP-chip in NALM1 cells  treated with 10uM STI571 (24h)  replicate 1
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: BCL6 ChIP-chip in BV173 cells - STI571  replicate 1

description:
BV173_C_r1_WC8
BCL6 ChIP-chip in BV173 cells cultured in absence of STI571 replicate 1
chip-on-chip is performing in three Ph+ ALL cell lines (BV-173, NALM-1 and TOM-1) in duplicate by BCL6 antibody


title: siliques WT, control, biological rep2

description: Gene expression data after treatment

source_name: Arabidopsis siliques after control treatment (1h)

tag: treatment


title: siliques WT, control, biological rep1

description: Gene expression data after treatment


title: siliques WT, control, biological rep3

description: Gene expression data after treatment


title: miHO1_2

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

institute: MFPL

description: EM_12112008_4_BIL_(HuGene-1_0-st-v1).CEL

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA was computed in R/Bioconductor (http://www.R-project.org)

source_name: BeWo choriocarcinoma cells

label_protocol: Affymetrix

growth_protocol: Total RNAs of LMP or miHO-1 BeWo cells (24 hours after seeding), and a minimum of two consecutive cell passages of each BeWo cell line were isolated and 200ng of total RNA were then used for preparation of labeled cDNA for hybridization to human Gene Level 1.0 ST arrays(Affymetrix).

extract_protocol: Trizol followed by RNeasy Mini kit (Qiagen)

treatment_protocol: no treatment

value: BeWo choriocarcinoma cells


title: miHO1_1

description: EM_01282009_1_BIL_(HuGene-1_0-st-v1).CEL


title: FES22P44_23_92_1_1


title: auxin and brassinazole-treated seedlings, biological rep3

city: Seoul

first: Sunghwa

last: Choe

address: Gwanak-Gu Shillim-Dong

department: Biological sciences

country: South Korea

institute: Seoul National University

description: Gene expression data

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2002, Affymetrix).

growth_protocol: Arabidopsis seedlings (Columbia ecotype) were grown for 10 d on 1× MS agar-solidified media under long-day conditions (16:8, white light and dark cycle).

extract_protocol: Total RNAs isolated from each batch were prepared from 3 replicate seedlings using an RNeasy plant mini kit (Qiagen, Germany). The integrities and concentrations of the total RNAs were assessed using a Nanodrop spectrophotometer (Thermo, USA) and by gel electrophoresis before being pooled together.

treatment_protocol: The seedlings were then transferred to 2 different liquid media containing either 10–7 M 2,4-D or 10–7 M 2,4-D plus 10–6 M brassinazole. After 8 h of treatment, the seedlings were blotted with paper towels to remove excess media and subject to total RNA isolation.

tag: Arabidopsis Columbia seedlings at 10 days after germination, Ecotype

value: Columbia


title: CSC14P26_197_524_1_2

tag: cell type

value: HESC


title: auxin and brassinazole-treated seedlings, biological rep2

description: Gene expression data


title: LMP_2

description: EM_12112008_3_BIL_(HuGene-1_0-st-v1).CEL


title: CM7P19_243_621_1_1


title: H3K4ac set1D on WT exp2

city: Montréal

first: Benoit

last: Guillemette

state: Qc

address: 2950, chemin de Polytechnique

department: IRIC

country: Canada

institute: Université de Montréal

hyb_protocol: Approximately 7.5µg per sample of labeled/fragmented DNA was hybridized per array using the Affymetrix GeneChip Hybridization, Wash, and Strain kit. Hybridization was done using a GeneChip Hybridisation oven, washes were done in a GeneChip Fluidics Stations F450.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G with autoloader

data_processing:
Data were processed with the Affymetrix Tiling Analysis Software - Version 1.1 using the Two sample comparison analysis in Intensities, exported in .BAR files, Signal scale was set to log2, and probe bandwidth was set to 200bp. PM values only were considered.
The corresponding RPT .txt files were converted to .WIG files for uploading into the UCSC Genome Browser and Galaxy for further analyses.

source_name: H3K4ac (home antibody) ChIP DNA from set1D yeast cells

label_protocol: ChIP samples were amplified using random primers and Sequenase with the addition of dUTP following the protocol supplied from Affymetrix. Amplified samples (8μg of DNA) were enzymatically fragmented and labeled using the WT Double Stranded DNA Terminal Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

growth_protocol: 200ml of yeast cells were grown up to mid-log phase (o.d. 600 of  0.6-0.8) in YPD

extract_protocol: Cells were treated with 1% formaldehyde directly added to the media at room temperature for 10 minutes. Formaldehyde was quenched with 0.125 M of glycine and cells were washed three times in cold water. Pellets (approximately 1.2x109 cells) were resuspended in 1.2 ml of lysis buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM EDTA, 1mM PMSF, 30mM sodium butyrate, complete EDTA-free protease inhibitor cocktail, Roche), and split into three tubes. After adding one volume of glass beads to each sample, cells were disrupted using a bead beater (Disruptor Genie, Scientific Industries) at maximal speed for 2h at 4°C. After removing the glass beads, the lysates were transferred to fresh tubes and sonicated for 15 minutes (30 seconds ON, 30 seconds OFF) at high intensity in a Bioruptor (Diagenode) connected to a water cooler at 4°C. Lysates were clarified by centrifugation and pooled into a 2 ml tube. After addition of 800µl of fresh lysis buffer and mixing, lysates were clarified again by centrifugation. 4µl of lysate (1% of the whole cell extract, WCE) was kept aside as an input control. For immunoprecipitation, aliquots of 400µl were prepared for each ChIP and mixed with the appropriate antibody: either 5µl of anti-H3K4ac, 5µl of anti-H3-C (Abcam ab1791), 3µl of anti-H3K4me3 (Abcam ab8580) for at least 1h at 4°C. Before use, Dynabeads M-280 coupled to sheep anti-rabbit IgG (InVitrogen) (30µl per ChIP) were washed in lysis buffer containing 5 mg/ml bovine serum albumin. The beads were added to each lysate and incubated at 4°C for at least 1h. Beads were washed twice with lysis buffer, twice with lysis buffer containing 500mM NaCl, twice in wash buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% Nonidet-P40, 0.5% Na-deoxycholate, 1mM EDTA) and once in TE (10mM Tris-HCl pH 8.0, 1mM EDTA). To elute the DNA, 100µl of a 10% Chelex 100 (Biorad) suspension in water was added to the beads (as well as to the 1% WCE) and incubated at 100°C for 10 minutes. Tubes were then cooled and treated with 0.2 µg/µl ribonuclease A at 50°C for 30 min, followed by 0.2 µg/µl proteinase K at 50°C for 30 min. Samples were incubated again at 100°C for 10 min to inactivate the proteinase K and then cooled down and spun down to get rid of debris. 80µl of each supernatant was kept at ‑20°C for qPCR or ChIP-chip analysis.

tag: strain

value: BY4741 set1D::KAN-MX

tag: antibody

source_name: H3K4ac (home antibody) ChIP DNA from WT (BY4741) yeast cells


title: auxin and brassinazole-treated seedlings, biological rep1

description: Gene expression data


title: ESI051P37_29_104_3_1


title: set1D H3K4ac on H3 exp2

source_name: non modified H3 (Abcam 1791) ChIP DNA from set1D yeast cells

tag: vendor

value: Abcam 1791


title: LMP_1

description: EM_12112008_1_BIL_(HuGene-1_0-st-v1).CEL


title: auxin-treated seedlings, biological rep2

description: Gene expression data


title: WT H3K4ac on H3 exp1

source_name: non modified H3 (Abcam 1791) ChIP DNA from WT (BY4741) yeast cells


title: CM8P25_241_618_1_1

tag: passage number


title: WT H3K4me3 on H3 exp1

source_name: H3K4me3 (Abcam ab8580) ChIP DNA from WT (BY4741) yeast cells

value: Abcam ab8580


title: auxin-treated seedlings, biological rep1

description: Gene expression data


title: auxin-treated seedlings, biological rep3

description: Gene expression data


title: S26 in vitro

status: Public on Feb 14 2011

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with MBNI re-mapped CDF files, version 12.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

source_name: in vitro cultured cells

label_protocol: 10 ug of Qiagen-purified total RNA

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

tag: cell line


title: S26 in vivo

source_name: in vivo xenograft tumors


title: WT H3K4ac on H3 exp2


title: S22 in vitro


title: CM1P16_246_624_1_2


title: S18 in vivo


title: CNE2 in vitro

tag: parental line


title: CNE2 in vivo


title: CM8P12_241_619_1_1


title: CM14P87_239_615_1_1


title: CM2P17_245_623_1_1


title: CSC14C1P26_202_550_1_1

source_name: Undifferentiated hESC, cultured from single-cell clone


title: Lig4/P53 KO, rep 5

city: Boston

first: Michael

middle: Richard

last: Green

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from lymphoid tumor

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: Scanned using an Affymetrix GCS3000 scanner

data_processing: Raw data was normalized for batch effects using robust multiarray (RMA) preprocessing with quantile normalization and a median polish using RMA Express, version 1.0.4.

source_name: Lymphoid tumor

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

extract_protocol: Tripure (Roche) isolation of RNA was performed according to the manufacturers protocol. Total RNA was amplified to cRNA using Ovation RNA amplification system V2 (NuGen) according to the manufacturers protocol.

value: Tumor

value: Lig4/p53 double knock-out

value: Lymphoid tumor


title: S22 in vivo


title: Lig4/P53 KO, rep 3


title: Lig4/P53 KO, rep 6


title: S18 in vitro


title: ESI049P38_28_103_4_1


title: Lig4/P53 KO, rep 4


title: Lig4/P53 KO, rep 1


title: Myc/Bcl6, rep 3

value: Myc/Bcl6 dual-transgenic (Pasqualucci et al., Nat. Genet. 2008;40:108-112)

value: Bcl6/Myc dual-transgenic


title: Myc/Bcl6, rep 2


title: Lig4/P53 KO, rep 2


title: Myc/Bcl6, rep 1


title: Plasmablast, rep 3

description: Gene expression data from purified B-cell population

value: Spleen

value: Wild-type


title: CM6P19_244_622_1_1


title: Bcl6 Trans, rep 3

value: Bcl6 transgenic (Catoretti et al., Cancer Cell 2005;7:445-455)

value: Bcl6 knock-in


title: BG01P67FF_53_214_7_6


title: Plasma cell, rep 3

source_name: Purified Plasma cells (B220-low/Cd138-positive/Cd93-negative)

value: Bone Marrow


title: BG02P46_54_215_1_4


title: Plasmablast, rep 4


title: Plasma cell, rep 2

value: Purified Plasma cells (B220-low/Cd138-positive/Cd93-negative)


title: BG01VP53FF_52_213_1_5

source_name: Undifferentiated hESC, variant line


title: Germinal Centre B, rep 1

source_name: Purified Germinal Centre (B220-positive/PNA-high) B-cells


title: Bcl6 Trans, rep 1


title: Bcl6 Trans, rep 2


title: Germinal Centre B, rep 2

value: Purified Germinal Centre (B220-positive/PNA-high) B-cells


title: Germinal Centre B, rep 5


title: Plasma cell, rep 1


title: Marginal Zone B, rep 3

source_name: Purified Marginal Zone (Cd19-positive/Cd21-high/Cd23-low) B-cells


title: Plasmablast, rep 2


title: Germinal Centre B, rep 4


title: Follicular B, rep 3

source_name: Purified Follicular (Cd19-positive/Cd21-intermediate/Cd23-high) B-cells


title: Marginal Zone B, rep 2

value: Purified Marginal Zone (Cd19-positive/Cd21-high/Cd23-low) B-cells


title: Plasmablast, rep 1


title: Follicular B, rep 2

value: Purified Follicular (Cd19-positive/Cd21-intermediate/Cd23-high) B-cells


title: Marginal Zone B, rep 1


title: Follicular B, rep 1


title: CM14P21_239_616_1_1

source_name: Undifferentiated hESC

value: HESC


title: Germinal Centre B, rep 3


title: Transitional B, rep 4

source_name: Purified Transitional (B220-positive/Cd93-positive) B-cells