title: Breast biopsy sample_R7347_T62

source_name: Breast biopsy sample_R7347_T62

value: 56 years-old patient

value: Infiltrating ductal carcinoma (IDC) + "in situ" intraductal carcinoma

value: chemotherapy and hormonal therapy

value: free of disease

value: ER+,PR-.


title: Breast biopsy sample_R7176_T52

status: Public on Dec 31 2017

type: RNA

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were pre-hybridized in prewarmed 5X SCC, 0.1% SDS and 0.1% BSA at 42ºC for 45 min, rinsed under milliQ water and spun dry using a centrifuge for 5 min at 1500 rpm. Labeled samples were redissolved in 42ºC prewarmed 12 microliter of Hybridization buffer A (50% formamide, 6X SSC, 0.5% SDS and 5X Denhardt’s applied to a glass coverslip, covered with the spotted glass slide. Arrays were incubated in a corning hybridization chamber for 18 hr at 42ºC in a humid environment (In Slide Out oven, Boeckel). Arrays were washed at room temperature using an orbital shaker for 10 min with a high stringency wash buffer (0.1X SSC, 0.1% SDS), twice for 10 min with a low stringency wash buffer (0.1X SSC), rinsed for 5 min in milliQ water and spun dry for 5 min at 1500 rpm using a centrifuge.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays were scaled so that every array has the same median intensity and same absolute standard deviation, in order to give the same weight to every gene on the array.
After normalization, replicated spots of the same gene were average.

molecule: total RNA

organism: Homo sapiens

source_name: Breast biopsy sample_R7176_T52

label_protocol:
Linear T7-oligodT mediated mRNA amplification (described by Van Gelder et al. 1990 and Eberwine et al. 1992)
3 microgram of the in vitro amplified aRNA samples were reverse transcribed with 4 microliter 5X first strand buffer, 2 microliter 0.1 M DTT, 0.4 microliter low dT-dNTP mix (25 mM dA, dC, dG, 10 mM dT), 1.5 microliter Superscript II (Invitrogen) and 2 microliter 25 mM Cy3-dUTP or Cy5-dUTP (Amersham). The reaction was incubated at 42ºC for 2 hr, chilled on ice and quick spun to bring down condensation. To stop the reaction 1 microliter 1 M NaOH/20 mM EDTA, was added followed by 80 microliter MilliQ-H20 and 10 microliter 3M NaOAc pH 5. Labeled samples were purified with Quiaquick PCR purification columns (Qiagen) and eluted twice with 50 microliter EB (10 mM Tris pH 8.5). Labeling efficiency was calculated by quantification with Nanodrop, obtaining between 50-80 pmol/microliter of Cy3 or Cy5 labeled probes. Labeled samples for the same array were combined, 1 microliter 1 microgram/microliter Human Cot DNA (Invitrogen) was added, and the labeled mix was desiccated by Speed-Vac centrifugation.

extract_protocol:
Frozen tumor samples come from surgical biopsies provided by the Hospital del Mar (Barcelona). Total RNA was prepared by using Ultraspec® RNA isolation system (Biotecx laboratories Inc.) following manufacturer’s instructions.
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

tag: age

value: 58 years-old patient

tag: cancer type

value: Infiltrating ductal carcinoma (IDC)

tag: reproductive stage

value: postmenopausal

tag: tumor stage

tag: depth

value: no vascular invasion

tag: histological grade

tag: treatment

tag: status

tag: marker

tag: receptor

value: ER+,PR+.

source_name: Universal human reference RNA Stratagene® (cat.no.740000)

tag: type

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7145_T53

source_name: Breast biopsy sample_R7145_T53

value: Infiltrante tubular carcinoma (ITC)

value: hormonal therapy


title: Breast biopsy sample_R6280_T44

source_name: Breast biopsy sample_R6280_T44

value: 82 years-old patient

value: Infiltrating lobulillar carcinoma (ILC) + "in situ" ductal carcinoma (IDC)


title: Breast biopsy sample_R6279_T36

source_name: Breast biopsy sample_R6279_T36

value: 66 years-old patient

value: NORMAL BREAST.


title: Breast biopsy sample_R10116_T32

source_name: Breast biopsy sample_R10116_T32

value: 79 years-old patient

value: Papilar carcinoma invasive (IPC)


title: Breast biopsy sample_R10101_T22

source_name: Breast biopsy sample_R10101_T22

value: 54 years-old patient

value: chemotherapy and hormonal therapy


title: Breast biopsy sample_R8150_T17

source_name: Breast biopsy sample_R8150_T17

value: Intraductal carcinoma

value: no vascular invasion,-,no therapy

value: free of disease


title: Breast biopsy sample_R7904_T13

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays

source_name: Breast biopsy sample_R7904_T13

value: 81 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: postmenopausal


title: Breast biopsy sample_R8403_T20

source_name: Breast biopsy sample_R8403_T20

value: 52 years-old patient

value: Infiltrante medular carcinoma (IMC)

value: no vascular invasion

value: chemotherapy

value: ER-,PR-.

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7906_T12

source_name: Breast biopsy sample_R7906_T12

value: 83 years-old patient

value: hormonal therapy

value: ER+,PR+.


title: Breast biopsy sample_R10108_T27

source_name: Breast biopsy sample_R10108_T27

value: 84 years-old patient

value: vascular invasion

value: ER+,PR-.


title: Breast biopsy sample_R10112_T29

source_name: Breast biopsy sample_R10112_T29

value: 61 years-old patient

value: Lobulillar carcinoma

value: no vascular invasion,-

value: chemotherapy and hormonal therapy


title: Breast biopsy sample_R10107_T26

source_name: Breast biopsy sample_R10107_T26

value: 40 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: premenopausal

value: free of disease


title: Breast biopsy sample_R10105_T25

source_name: Breast biopsy sample_R10105_T25

value: 55 years-old patient

value: postmenopausal

value: no vascular invasion


title: Breast biopsy sample_R10115_T31

source_name: Breast biopsy sample_R10115_T31

value: 79 years-old patient

value: Papilar carcinoma invasive (IPC)

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7946_T15

source_name: Breast biopsy sample_R7946_T15

value: 54 years-old patient

value: Infiltrating ductal carcinoma (IDC) + Intraductal carcinoma

value: ER+,PR+.


title: Breast biopsy sample_R7939_T14

source_name: Breast biopsy sample_R7939_T14

value: 63 years-old patient

value: Intraductal carcinoma

value: hormonal therapy

value: ER+,PR-.


title: Breast biopsy sample_R8153_T18

source_name: Breast biopsy sample_R8153_T18

value: 61 years-old patient

value: Infiltrating ductal carcinomarcinoma (IDC)

value: chemotherapy and hormonal therapy

source_name: Universal human reference RNA Stratagene® (cat.no.740000)


title: Breast biopsy sample_R10104_T24

source_name: Breast biopsy sample_R10104_T24

value: 82 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: free of disease


title: Breast biopsy sample_R10113_T30

source_name: Breast biopsy sample_R10113_T30

value: 48 years-old patient

value: premenopausal

value: vascular invasion


title: Breast biopsy sample_R10103_T23

source_name: Breast biopsy sample_R10103_T23

value: 50 years-old patient

value: ER+,PR+ .

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7541_T10

source_name: Breast biopsy sample_R7541_T10

value: 57 years-old patient

value: Infiltrating ductal carcinoma (IDC) + Intraductal carcinoma

value: postmenopausal

value: no vascular invasion

value: ER+,PR+.


title: Breast biopsy sample_R7617_T09

source_name: Breast biopsy sample_R7617_T09

value: 73 years-old patient

value: hormonal therapy


title: Breast biopsy sample_R7692_T07

source_name: Breast biopsy sample_R7692_T07

value: 84 years-old patient

value: Metaplasic carcinoma + Intraductal carcinoma

value: no vascular invasion,_

value: chemotherapy

value: EXITUS

value: ER-,PR- ,


title: Breast biopsy sample_R7553_T04

source_name: Breast biopsy sample_R7553_T04

value: 51 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: premenopausal

value: chemotherapy  NEOADJUVANT

value: with disease

value: ER-,PR-.


title: Breast biopsy sample_R7540_T02

source_name: Breast biopsy sample_R7540_T02

value: 38 years-old patient

value: chemotherapy neoadjuvant

value: ER+,PR- .

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Breast biopsy sample_R7545_T03

source_name: Breast biopsy sample_R7545_T03

value: 65 years-old patient

value: Infiltrating ductal carcinoma (IDC) + Intraductal carcinoma

value: postmenopausal

value: vascular invasion

value: free of disease


title: Breast biopsy sample_R7693_T08

source_name: Breast biopsy sample_R7693_T08

value: 84 years-old patient

value: Metaplasic carcinoma + Intraductal carcinoma

value: no vascular invasion,_

value: chemotherapy

value: EXITUS


title: Breast biopsy sample_R10109_T28

source_name: Breast biopsy sample_R10109_T28

value: 62 years-old patient

value: Medular atypical carcinoma

value: no vascular invasion


title: Breast biopsy sample_R7612_T05

source_name: Breast biopsy sample_R7612_T05

value: 49 years-old patient

value: Infiltrating lobulillar carcinoma (ILC)

value: premenopausal

value: no vascular invasion,-

value: ER+,PR+.


title: Breast biopsy sample_R7614_T06

source_name: Breast biopsy sample_R7614_T06

value: 67 years-old patient

value: Infiltrating ductal carcinoma (IDC)

value: chemotherapy and hormonal therapy

value: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: Liver_47

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: Gene expression data from Liver sample of broiler chickens

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on ChiGene-1_0-st Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

label: biotin

organism: Gallus gallus

source_name: Liver

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: affiliation to dietary treatment

value: H

tag: Sex

value: m

tag: sampling time point

value: day 21


title: Liver_46


title: Liver_41

value: F


title: Liver_27

value: A


title: Liver_26


title: Liver_42


title: Liver_36

value: E


title: Liver_22


title: Liver_16


title: Liver_37


title: Liver_05


title: Liver_17


title: Jejunum_42

description: Gene expression data from Jejunum sample of broiler chickens

source_name: Jejunum


title: Liver_11


title: Liver_12


title: Jejunum_41


title: Hairless vs Control replicate 3

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalised with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.

organism: Drosophila melanogaster

label_protocol: Mix together 25-50 µg total RNA, DEPC MilliQ water and spike mix to a total volume of 28 µl in an RNAse-free 1.5 ml tube. Add 1 µl of 500 ng/µl oligo (dT)23 anchored primer (Sigma). Incubate at 65 °C for 10 minutes in a hot-block to denature RNA tertiary structure, and then place on ice. Add µl of 5x first strand buffer (Invitrogen), 2 µl of low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl of 1 mM Cy3 or Cy5 dCTP (GE Healthcare), 2 µl of 0.1 M DTT (Invitrogen), 0.5 µl of RNAsin (Promega) and 2 µl of Superscript III reverse transcriptase (Invitrogen). Incubate at 42 °C for 1-2 hours. Hydrolyse the remaining RNA by mixing equal volumes of 0.5 M EDTA and 1 M NaOH. Then add 20 µl of this mix to the reaction and incubate at 65 °C for 15 minutes. Bring samples to room temperature and add 25 µl of 1 M Tris-HCl (pH 7.5) to neutralise. Reduce volume of probe to approximately 25 µl, by placing in a speed vac with medium heat. Then combine the Cy3- and Cy5-labelled probe (sample and control) into one 1.5 ml microfuge tube. Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: Kc cells were cultured at 25°C in Shields and Sang M3 insect medium (Sigma, S3652), supplemented with 5% FBS (Sigma, F9665), 1 g/l yeast extract (Oxoid, LP0021), 2.5 g/l bacto-peptone (BD Biosciences, 211677) and 1× Antibiotic-Antimycotic (Gibco, 15240-062)

extract_protocol: Total RNA extracted using Qiagen Rneasy Midi kit (cat N 75142) following manufacturer's instructions

treatment_protocol: Cell were grow in 100mm petri dish until reach 1x10^7 cells, cell where diluted 1 in 10 in 10ml of KC media and incubated in 100mm petri dish supplementing media with 20 μg dsRNA for hairless and White respectively for 72hrs at 25˚C before collection. dsRNA was synthetised using Ambion MEGAshortscript™ T7 Kit (cat N AM1354), the DNA templates where generated by PCR using  the following primers (5’-GAATTAATACGACTCACTATAGGGAGCTGCTAGGTGGGAGCAGTG, 5’-GAATTAATACGACTCACTATAGGGAGCGCCAGTGTGGATATGTACG, 5’- CTAATACGACTCACTATAGGGACCTGATTTTCCAAGCCAT, 5’-CTAATACGACTCACTATAGGGGAAGACGGCTGATGAATGGT) for Hairless and White respectively.

tag: cell line

value: KC167 cells treated with White dsRNA

value: Kc167 cells treated with Hairless dsRNA


title: CD34+ LMAFVAR1IDN DONOR 3

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: GEP of LMAFVAR1IDN-transduced CD34+ HPCs

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were scanned by using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: Cord Blood CD34+ cells

label_protocol: Gene expression profile (GEP) was performed on total RNA derived from five independent experiments.  Briefly, biotinylated aRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the aRNA concentration/quality as well as to optimize the aRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in 24-well plates at 5×105/mL in (a) serum-free medium SYN-H (ABCell-Bio, Paris, France) supplemented with stem cell factor (SCF; 5 ng/mL), thrombopoietin (TPO; 50 ng/ml), interleukin-11 (IL11; 40 ng/ml), interleukin-3 (IL3; 2 ng/ml) and interleukin-6 (IL6; 1 ng/ml; all from Miltenyi).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last nucleofection. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: After 24 hours of culture post-purification, Human CB CD34+ Hematopoietic Progenitor Cells (HPCs) were transduced in 24-wells plates at a density of 5x1052x105/ml in (a) serum-free medium SYN-H (ABCell-Bio, Paris, France) supplemented with SCF (5 ng/mL), THPO (50 ng/mL), IL-11 (40 ng/mL), IL-6 (1 ng/mL) and IL-3 (2 ng/mL; all from Miltenyi) or (b) IMDM (Euroclone) supplemented with 10% FBS (Sigma). SCF (50 ng/mL), Flt3L (50 ng/mL), THPO (20 ng/mL), IL-6 (10 ng/mL), and IL-3 (10 ng/mL; all from Miltenyi). CD34+ cells were transduced by means of three cycles of infection (12 hours each) with viral supernatant in the presence of polybrene (8 µg/ml) in retronectin-coated plates (10 µg/cm2). After transduction, cells were maintained in the same culture conditions reported above for 24 hours. Transduction efficiency was monitored by flow cytometric detection of the NGFR-positive (NGFR+) fraction after labeling with a PE-conjugated anti-NGFR antibody (Miltenyi Biotec). Transduced CD34+ cells were subsequently purified by an immunomagnetic procedure (EasySep “Do-It-Yourself” Selection Kit; StemCell Technologies) by means of a anti-human p75-NGFR mouse monoclonal antibody (BD Biosciences). and seeded in the liquid culture conditions as reported above. After 24 hours of culture post-purification, Human CB CD34+ Hematopoietic Progenitor Cells (HPCs) were transduced in 24-wells plates at a density of 5x1052x105/ml in (a) serum-free medium SYN-H (ABCell-Bio, Paris, France) supplemented with SCF (5 ng/mL), THPO (50 ng/mL), IL-11 (40 ng/mL), IL-6 (1 ng/mL) and IL-3 (2 ng/mL; all from Miltenyi) or (b) IMDM (Euroclone) supplemented with 10% FBS (Sigma). SCF (50 ng/mL), Flt3L (50 ng/mL), THPO (20 ng/mL), IL-6 (10 ng/mL), and IL-3 (10 ng/mL; all from Miltenyi). NGFR-positive (NGFR+) cells were analysed for MAF and expression by Western Blot.

value: LMAFVAR1IDN transduction

tag: retroviral vector transduction

tag: donor


title: Jejunum_47


title: Liver_21


title: Jejunum_36


title: Hairless vs Control replicate 2 (dye-swap)


title: Hairless vs Control replicate 1


title: Jejunum_37


title: CD34+ LXIDN DONOR 3

description: GEP of LXIDN-transduced CD34+ HPCs

value: LXIDN transduction

value: LXIDN


title: Liver_04


title: Hairless vs Control replicate 4 (dye-swap)


title: Jejunum_46


title: Jejunum_27


title: CD34+ LMAFVAR2IDN DONOR 3

description: GEP of LMAFVAR2IDN-transduced CD34+ HPCs

value: LMAFVAR2IDN transduction


title: CD34+ LMAFVAR1IDN DONOR 2


title: CD34+ LXIDN DONOR 2

description: GEP of LXIDN-transduced CD34+ HPCs


title: Jejunum_16


title: Jejunum_17


title: CD34+ LMAFVAR1IDN DONOR 1


title: Jejunum_22


title: Jejunum_21


title: CD34+ LMAFVAR2IDN DONOR 2


title: Jejunum_12


title: Rec-1

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

institute: CRO Aviano

description: Gene expression of MCL cell line models.

hyb_protocol: 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v107_Sep09 and Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.

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

growth_protocol: Six different MCL cell line models (Rec-1, Jeko-1, Mino, JVM-2, JVM-13, and Z-138) were used for GEP studies. MCL cell line models were cultured (1 × 106 cells/ml) in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate (Thermo Fisher Scientific)

extract_protocol: Total RNA was extracted from MCL cell lines using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: not applicable

tag: tissue

value: whole blood


title: JVM-13


title: Jejunum_04


title: genomic DNA from MCF-7 treated Ginsenoside Rg3

type: genomic

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

country: South Korea

institute: dongguk unversity

description:
SAMPLE 2
breast cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC 850K Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Background correction, Extraction of CpGs with detection p-value ≥ 0.05 more than 25% of all samples, and BMIQ normalization

molecule: genomic DNA

source_name: mammary gland, breast; derived from metastatic site: pleural effusion

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from MCF-7 using ZR Dyet DNA/RNA kit (Zymo research) according to standard instructions

tag: cell type

value: epithelial

tag: gender

value: female

tag: disease

value: adenocarcinoma


title: Jejunum_05


title: Jejunum_11


title: Mino

source_name: Mino


title: Jejunum_26


title: Jeko-1


title: MCL_4301

description: Constitutive Gene expression of MCL cells.

source_name: MCL Peripheral Blood (PB). Leukemic cells >90%.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from MCL cells using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Female


title: JVM-2


title: CD34+ LMAFVAR2IDN DONOR 1


title: genomic DNA from MCF-7 treated 0.1% EtOH

description:
SAMPLE 1
breast cancer


title: CD34+ LXIDN DONOR 1

description: GEP of LXIDN-transduced CD34+ HPCs


title: MCL_1201


title: MCL_506

value: Male


title: MCL_3304


title: MCL_2001


title: MCL_410


title: Z-138


title: MCL_412


title: MCL_505


title: MCL_604


title: MCL_703


title: MCL_2901


title: MCL_404


title: MCL_2501


title: MCL_802


title: MCL_507


title: MCL_3701


title: MCL_2301


title: KG1a_LKB1_negative control

city: Shenyang

first: Huihan

last: Wang

address: No. 36 Sanhao Street

country: China

institute: China Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

source_name: KG1a cells with LKB1 gene as negative control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: KG1a cells were maintained in Iscove’s modified Dulbecco’s media supplemented with 10% fetal bovine serum. All of the cells were incubated at 37°C in a humidified atmosphere with 5% CO2.

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

treatment_protocol: We use shRNA to knock down(KD) the expression of LKB1 gene at the human acute myeloid leukemia KG1a cells ,meanwhile build the negative control with normal LKB1 expression.

value: KG1a cells

tag: genotype/variation

value: negative control (NC)

tag: phenotype

value: LKB1 gene normal expression


title: MCL_301


title: MCL_1901


title: MCL_205


title: MCL_2602


title: MCL_707


title: MCL_601


title: MCL_408


title: TUNC1

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

description: This sample is of negative control transfected TU177. It is the first of three negative control biological replicates.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis.

source_name: Human laryngeal squamous carcinoma cells TU177 negative control

label_protocol: For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer.

growth_protocol: TU177 cells were maintained in RPMI1640 supplimented with 10% FBS under 37 ℃, 5% CO2 and 100% humidity.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: TU177 cells were transfected with Hsa-miR-145-5p mimic and negative control oligo  at a final concentration of 50 nM by using lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions for 48 h, respectively.

value: squamous carcinoma cells

tag: transfection

value: Negative control


title: MCL_409


title: MCL_102


title: TUNC2

description: This sample is of negative control transfected TU177. It is the second of three negative control biological replicates.


title: MCL_1701


title: irCCaMK vector_AMF inoculation_6wpi_r3

city: Jena

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description: Utah accession, leaf, elongation stage with AMF

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw intensity data were normalized with the quantile method, and subsequently the low expression probes were after log2 transformation. Differentially expressed probes were filtered after pair-wise comparison (FDR≤0.05, fold change≥ 1.5).

organism: Nicotiana attenuata

source_name: Utah accession, leaf, elongation stage

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

growth_protocol: Empty vector (EV) plants carrying the empty construct [line A-03–9-1 (63)] and plants silenced in the expression of a calcium- and calmodulin-dependent protein kinase (irCCamK [irCCamK 2 line A09-1212-1, (Groten et al., 2015a)] were germinated on Gamborg B5 medium according to (Kruegel et al., 2002). EV and irCCamK plants were grown as two plant communities in 2L pots filled with either living or dead FMM or commercial inoculum. Plants were irrigated with hydroponics fertilizer with 1/10 of the regular inorganic Pi concentration during rosette stage, and starting with the elongation stage with 1/4 Pi concentration.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini Kit columns (Qiagen) according to manufacturer’s protocols, in combination with on-column DNase-I treatment (Qiagen). Aliquots (1 µL) of puriﬁed RNA were pipetted for quantiﬁcation and quality assessment of total RNA using the Agilent 2100 Bioanalyzer system in combination with RNA 6000 n kit (Agilent, Santa Clara, CA). Only RNA that displayed intact 18S and 25S peaks was used for microarray analysis.

treatment_protocol: Experiments were performed with living and dead (autoclaved at 121 °C for 30 min) commercial Rhizophagus irregularis inoculum (Biomyc Vital) which was also diluted 1:10 with autoclaved expanded clay (2-4 mm).

tag: cultivar

value: Utah

value: leaf

tag: Stage

value: elongation

value: irCCaMK


title: TUNC3

description: This sample is of negative control transfected TU177. It is the third of three negative control biological replicates.


title: TU145_3

description: This sample is of miR-145-5p mimic transfected TU177. It is the third of three miR-145-5p overexpressed biological replicates.

source_name: Human laryngeal squamous carcinoma cells TU177 overexpressing miR-145-5p

value: miR-145-5p overexpressed


title: irCCaMK vector_control_6wpi_r2

description: Utah accession, leaf, elongation stage without AMF


title: empty vector_AMF inoculation_6wpi_r3

value: empty vector


title: empty vector_AMF inoculation_6wpi_r1


title: empty vector_control_6wpi_r3


title: KG1a_LKB1_knock down

source_name: KG1a cells with LKB1 gene knock down

value: LKB1_knock down

value: LKB1 gene lower expression


title: empty vector_AMF inoculation_6wpi_r2


title: irCCaMK vector_control_6wpi_r1


title: irCCaMK vector_control_6wpi_r3


title: irCCaMK vector_AMF inoculation_6wpi_r2


title: irCCaMK vector_AMF inoculation_6wpi_r1


title: TU145_2

description: This sample is of miR-145-5p mimic transfected TU177. It is the second of three miR-145-5p overexpressed biological replicates.


title: empty vector_control_6wpi_r2


title: irCCaMK vector_control_2wpi_r1

description: Utah accession, leaf, rosette stage without AMF

source_name: Utah accession, leaf, rosette stage

value: rosette


title: TU145_1

description: This sample is of miR-145-5p mimic transfected TU177. It is the first of three miR-145-5p overexpressed biological replicates.


title: irCCaMK vector_control_2wpi_r2


title: empty vector_control_6wpi_r1


title: empty vector_control_2wpi_r2


title: empty vector_control_2wpi_r1


title: irCCaMK vector_AMF inoculation_2wpi_r3

description: Utah accession, leaf, rosette stage with AMF


title: empty vector_AMF inoculation_2wpi_r3


title: empty vector_control_2wpi_r3


title: irCCaMK vector_AMF inoculation_2wpi_r2


title: empty vector_AMF inoculation_2wpi_r2


title: irCCaMK vector_AMF inoculation_2wpi_r1


title: irCCaMK vector_control_2wpi_r3


title: empty vector_AMF inoculation_2wpi_r1


title: Colon, AOM treated, Cardamonin treatment after tumor formation, biol.rep.1

city: Thycaud

first: Dr. Harikumar

middle: K

last: B

state: Kerala

address: Poojappura

department: Cancer Research Program

country: India

institute: Rajiv Gandhi centre for Biotechnology

description: miRNA expression from AOM and cardamonin treated samples

hyb_protocol: Samples were hybridised using Affymetrix hybridisation kit. Briefly, biotin labelled sample and hybridisation master mix were incubated at 99oC for 5 mins, then at 45oC for 5 mins. 130ul was injected into the array and both septa covered with tough spots. Loaded into hybridisation oven and incubated at 48oC, 60rpm for 16-18hrs

scan_protocol: The chips were then scanned with an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, California, United States).

data_processing: The Data generated from the scan was then analyzed using the Bioconductor packages (Oligo, limma)

label: Biotin

organism: Mus musculus

source_name: Colon, AOM, Cardamonin after tumor formation

label_protocol: Total RNA was used for the reaction, Poly(A) tailing was performed followed by biotin labelling of the RNA. This was done by  Flash Tag Biotin HSR labelling kit by Affymetrix

growth_protocol: Colon collected from mice treated with AOM, followed by Cardamonin simultaneously treated or after tumor development. Colon from normal, healthy mice were used as control.

extract_protocol: Colon dissected and rinsed in 1X PBS, followed by snap freezing in liquid nitrogen. This was ground in liquid nitrogen, and mirVana miRNA isolation kit was used for the subsequent steps.

treatment_protocol: Azoxymethane (AOM) was given intraperitoneally at a dose of 10mg/kg, once every week for 6 weeks. Cardamonin was administered orally, at a dose of 10mg/kg, 5 times every week for 30weeks for simultaneous group. And treatment started at a dose of 10mg/kg, 5times every week from 16th week to 30th week for the ''after tumor formation''group.

tag: strain

value: Colon

tag: treatment regime

value: Treated - Cardamonin after tumor formation


title: Colon, AOM treated, Cardamonin treatment after tumor formation, biol.rep.3


title: Colon, AOM treated, Cardamonin treatment after tumor formation, biol.rep.4


title: M-MØ_5HT_donor2_rep1

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

institute: CSIC

description: Gene expression in M-MØ after 6 hours of 5HT

hyb_protocol: 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe.

label_protocol: For each sample, we have generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA is reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA is synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10^6 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

extract_protocol: Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Macrophages were treatment with 5HT (10uM) during 6h. Before treatment, M-MØ macrophages were maintained in serum-free medium for 48 hours.

tag: subject status

value: healthy donor

value: Monocyte-derived M-CSF macrophages

tag: treated with

value: 10 uM 5HT


title: Colon, AOM treated, Cardamonin simultaneous treatment, biol.rep.2

source_name: Colon, AOM, Cardamonin simultaneous

value: Treated - Cardamonin simultaneous


title: Colon, AOM treated, Cardamonin simultaneous treatment, biol.rep.1


title: Colon, AOM treated, Vehicle control, biological rep.2

description: miRNA expression from AOM treated colon

source_name: Colon, AOM treated

value: Treated - vehicle control


title: Colon, AOM treated, Vehicle control, biological rep.1

description: miRNA expression from AOM treated colon


title: Colon, AOM treated, Cardamonin treatment after tumor formation, biol.rep.2


title: Healthy colon, biological rep.2

description: miRNA expression form normal colon

source_name: Colon, normal

value: Untreated


title: nonviral Keratinocyte iPSC clone 1 p14

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

country: USA

institute: Johns Hopkins School of Medicine

description: Individual sample

hyb_protocol: All arrays were hybridized at 55ºC for 20 hours followed by wash procedure according to the miRNA Microarray System Protocol, Version 1.5, December 2007 (Agilent Technologies).

scan_protocol: Fluorescent signals were obtained by scanning with an Agilent scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Data were acquired with Agilent Feature Extraction 9.5.3.1 software for miRNA microarray. MicroRNA Expression data were extracted from Agilent miRNA Kits by Agilent Feature Extraction software and then Partek and Spotfire were employed for their normalization and analysis. The fluorescent signal data were imported into Partek where duplicate probe information was merged and were then normalized to the 75th percentile. The 75th percentile normalization process is similar to median normalization, above, except that each gene’s 75th percentile value is subtracted rather than its median. (Agilent recommends the 75th percentile based on the observation that about half the microRNAs are not expressed, so the 75th percentile is near the median for those that are).

source_name: nonviral Keratinocyte iPSC clone 1, passage 14

label_protocol: 150 ng total RNA from each sample was labeled using the miRNA Labeling Reagent & Hybridization Kit (Agilent Technologies, Santa Clara, CA) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the miRNeasy Mini Kit (Qiagen) with on-column DNase I digestion.

value: nonviral Keratinocyte iPSC clone 1

tag: passage

tag: sample type

value: non-integrated keratinocyte iPSC generated in the Zambidis laboratory


title: nonviral Keratinocyte iPSC clone 1 p13

description: Individual sample

source_name: nonviral Keratinocyte iPSC clone 3, passage 13

value: nonviral Keratinocyte iPSC clone 3


title: viral fibroblast iPSC line IMR90-4

description: Individual sample

source_name: viral fibroblast iPSC clone iPS(IMR90)-4

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 318:1917-1920. 1997.


title: viral fibroblast iPSC line IMR90-1

description: Individual sample

source_name: viral fibroblast iPSC clone iPS(IMR90)-1


title: nonviral 7F Adult fibroblast iPSC clone 6.1 p12

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) fetal Fibroblast iPSC clone 6.1, passage 12

value: non-integrated fetal Fibroblast iPSC generated in the Zambidis laboratory


title: nonviral 7F Adult fibroblast iPSC clone 6.6 p12

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) fetal Fibroblast iPSC clone 6.6, passage 12


title: Colon, AOM treated, Vehicle control, biological rep.3

description: miRNA expression from AOM treated colon


title: Colon, AOM treated, Cardamonin simultaneous treatment, biol.rep.3


title: nonviral 7F stromal primed cord blood iPSC clone 6.13 p14

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.13, passage 14

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: nonviral 7F stromal primed cord blood iPSC clone 19.11 p14

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 19.11 passage 14


title: nonviral 7F stromal primed cord blood iPSC clone 6.2 p14

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.2, passage 14


title: nonviral 7F stromal primed cord blood iPSC clone 6.11 p14

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.11, passage 14


title: hESC (H9) p45

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 49 (NIH Code WA09)

value: Undifferentiated hESC


title: Healthy colon, biological rep.3

description: miRNA expression form normal colon


title: M-MØ_Control_donor2_rep1

description: Gene expression in M-MØ

value: none (control)


title: Colon, AOM treated, Cardamonin simultaneous treatment, biol.rep.4


title: Healthy colon, biological rep.1

description: miRNA expression form normal colon


title: H170 drug sensitive tissue

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

source_name: human breast cancer tissue

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: MiRNAs were isolated from breast cancer tissues using a miRNeasy FFPE Kit (Bioteke, Beijing, China) according to the manufacturer's instructions.

value: human breast cancer tissue

value: drug sensitive


title: M-MØ_Control_donor1_rep1

description: Gene expression in M-MØ


title: H131 drug sensitive tissue


title: H135 drug sensitive tissue


title: P1-BM-Bulk Reprogrammed Cells

description: Individual sample

source_name: Bone Marrow CD34+ progenitors 3 weeks after transfection with  7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen)


title: P1-CB-Bulk Reprogrammed Cells

description: Individual sample

source_name: Cord Blood CD34+ progenitors 3 weeks after transfection with  7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen)


title: P1-FL-Bulk Reprogrammed Cells

description: Individual sample

source_name: Fetal Liver CD34+ progenitors 3 weeks after transfection with  7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen)


title: Bone Marrow CD34+ progenitors

description: Individual sample

source_name: Bone Marrow CD34+ progenitors_Day 0

value: Bone Marrow CD34+ progenitors_Day 0

value: Obtained from ALLCELLS (Emeryville, CA), stimulated with Flt3L, TPO, SCF X 3 days


title: H19 drug sensitive tissue


title: H80 drug sensitive tissue


title: H32 drug sensitive tissue


title: Cord Blood CD34+ progenitors Sample 1

description: Individual sample

source_name: Cord Blood CD34+ progenitors_Day 0

value: Cord Blood CD34+ progenitors_Day 0


title: Adult keratinocytes

description: Individual sample

source_name: Adult keratinocytes

value: Adult keratinocytes

value: Isolated from hair folicle in Zambidis laboratory, as per Peters et al. Human Embryonic and Induced Pluripotent Stem Cells, Springer Protocols Handbooks, Part 2:202-227. 2011


title: Fetal Liver CD34+ progenitors

description: Individual sample

source_name: Fetal Liver CD34+ progenitors_Day 0

value: Fetal Liver CD34+ progenitors_Day 0


title: H8 drug sensitive tissue


title: H20 drug sensitive tissue


title: H15 drug sensitive tissue


title: C178 drug resistant tissue

value: drug resistant


description: Individual sample

source_name: mobilized peripheral blood CD34+ progenitors_Day 0


title: P1-mPB-Bulk Reprogrammed Cells

description: Individual sample

source_name: mobilized peripheral blood CD34+ progenitors 3 weeks after transfection with  7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen)


title: H31 drug sensitive tissue


title: M-MØ_5HT_donor1_rep1

value: healthy donor

value: Monocyte-derived M-CSF macrophages

value: 10 uM 5HT


title: C173 drug resistant tissue


title: C153 drug resistant tissue


title: C151 drug resistant tissue


title: C149 drug resistant tissue


title: B27+B28 T-cells CD3/28+RNase7M 10µg/ml

city: Hannover

first: Verena

last: Kopfnagel

address: Carl-Neuberg-Straße 1

department: Dermatology

institute: Hannover Medical School

description:
Feature Extraction file: M3371.txt
M3371g
Gene expression after 6h Rnase 7 stimulation

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: GE2_107_Sep09.xml.  For inter-array normalization, processed intensity values ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS) of microarray 2 were further transformed as follows: All PS values (gPS and rPS) of microarray 2 were multiplied with a specific scaling factor. This factor was calculated by dividing the 75th Percentile value of gPS of microarray 1 by the 75th Percentile value of the gPS values of microarray 2. Accordingly, normalized PS values for microarray 2 were calculated by the following formula:   normalized PS Array 2 = PS Array 2  x normalization factor. gPS and rPS values of microarray 1 were left unchanged.

source_name: Buffy coat

label_protocol: Total RNA was used to prepare C3- or C5-labeled cRNA (Quick Amp Labeling kit, two color, #5190-0444, Agilent Technologies) as directed by the company. Prior to the reverse transcription reaction, 1µl of a 1:3200 dilution of Agilent’s Two-Color spike-in mixes A (for Cy3-labeled samples) or B (for Cy5-labeled samples) (#5188-5282, Agilent Technologies) were added to 1000ng of total RNA of each analyzed sample.

extract_protocol: RNA was extracted from the cells using the Roche High Pure mRNA Isolation kit

treatment_protocol: CD3+ T-cells were isolatet from human blood (buffy coat). Cells were cultured in IAB medium; Iscove medium (Biochrom) supplemented with 4% human AB serum. Isolated CD3+ T-cells from four healthy donors were stimulated with activating anti-CD3 (1 µg ⁄ ml) and anti-CD28 (0.2 µg ⁄ ml) antibodies and RNase 7M 10µg/ml for 6h

value: CD3+ T-cells


title: C100 drug resistant tissue


title: C142 drug resistant tissue


title: SMR wing disc rep2

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The CEL files were processed with Biconductor Starr and Ringo packages, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
WD_Smr_EGS_r1.sm_quant-all_Ringo_hw300v8.sgr.gz file contains the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 10 minimum Probes in window with the Bioconductor Ringo package. The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

source_name: SMR wing disc replicate 2

label_protocol: Library was generated using GenomePlex® Complete Whole Genome Amplification (WGA) Kit #WGA2-50RXN. The amplification reaction was complemented by adding 0.75ul of 10mM dUTP. The amplification was performed for 14 cycles. Samples were then fragmented and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

growth_protocol: For each ChIP experiment we used 50 Drosophila wing imaginal discs harvested from L3 wanering larvae. 3 independent ChIP samples were pulled for each biological replicate

extract_protocol: 30 third instar wandering transgenic larvae carrying the target fusion protein transgene (SMRTER-YFP) were dissected in 1 x PBS (Phosphate-Buffered Saline). The dissected larval heads were inverted to expose the wing discs. Fat was removed from the larval heads when possible. The inverted larval heads were then transferred to a 1.5ml tube and were fixed with 1ml of 4% PFA (+1.5mM of EGS for the SMRTER-YFP genotype) at room temperature for 25 minutes. Following fixation, 200μl of 2M-glycine solution was added to quench the reaction. The larval heads were then rinsed 3 times with cold PBS, after which they were incubated in 1 x PBS + Roche cOmplete protease inhibitor cocktail.  Wing discs were then removed from the larval head carcasses and once 50 wing discs were collected they were centrifuged at 5000rpm at room temperature for 1 minute. After spinning down the discs, the supernatant was carefully removed and replaced with 50μl of nuclear lysis buffer (50 mM Tris-HCl pH 8; 10 mM EDTA; 1% SDS; 1x Roche cOmplete protease inhibitor). The sample was then incubated on ice for 10 minutes after which the wing discs were homogenised with a disposable plastic pestle.  250μl of IPDB (ImmunoPrecipitation Dilution Buffer) was then added to the mixture. The sample was sonicated for 7 minutes with a 30 second “ON/OFF” cycle setting in a pre-cooled bioruptor (Diagenode UCD-200).  After sonication, the sample was centrifuged at 13200rpm at 4oC for 10 minutes, after which the chromatin containing supernatant was transferred to a new 1.5ml tube and was further diluted with 200μl of IPDB.

value: L3 imaginal wing disc

tag: antibody

value: Abcam rabbit anti-GFP (ab290)


title: B46+B47 T-cells CD3/28+RNase7M 10µg/ml

description:
Feature Extraction file: M3370.txt
M3370r
Gene expression after 6h Rnase 7 stimulation


title: SMR wing disc input rep1

source_name: SMR wing disc input replicate 1


title: C28 drug resistant tissue


title: C29 drug resistant tissue


title: B46+B47 T-cells CD3/28

description:
Feature Extraction file: M3370.txt
M3370g
Gene expression after 6h Rnase 7 stimulation


title: B27+B28 T-cells CD3/28

description:
Feature Extraction file: M3371.txt
M3371r
Gene expression after 6h Rnase 7 stimulation


title: SMR wing disc rep1

source_name: SMR wing disc replicate 1


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 8

city: Rokkasho

first: Takashi

last: Sugihara

state: Aomori

address: 2-121 Hacchazawa

department: Radiobiology

country: Japan

institute: Institute for Environmental Sciences

hyb_protocol: Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 40°C for 120 minutes in a reaction volume of 100 ml containing 1x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides, (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 13.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quickamp lebeling kit (Agilent) according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: A piece of livers with adenomas or non-adenoma were homogenized in Trizol (Invitrogen, Carlsbad, CA, USA) reagent within 2 h after death.

treatment_protocol: Female B6C3F1 mice from 8 weeks of age were irradiated for 400 d at LDR at 0.02 Gy/22 h/d (0.00091 Gy/h) 137Cs-γ rays (74 GBq), in which the total doses was 8 Gy. And the chronically irradiated mice for 400 d (8 Gy) were bled in the SPF condition without irradiation for 100, 200 and 300 d, in which the total days were 500, 600, 700 d after beginning of irradiation, respectively.

value: Female

tag: disease state

value: HCA

tag: treatment

value: irradiated

value: liver (adenoma section)


title: C22 drug resistant tissue

tag: tissue

value: human breast cancer tissue


title: SMR wing disc input rep2

source_name: SMR wing disc input replicate 2


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 4

tag: gender


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 10


title: Su(H) Kc input rep3

data_processing:
The CEL files were processed with Biconductor Starr and Ringo packages, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
Sg290rep123_quant-all_Ringo_hw350v10.sgr.gz file contains the median of replicate ratios smoothed into window scores using a sliding window of 700bp and 10 minimum Probes in window with the Bioconductor Ringo package. The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

source_name: Su(H) Kc input replicate 3

extract_protocol: Chromatin extraction was performed from one 10cm of confluent Kc167 cell per conditions, cell were washed twice with PBS and crosslinked with 1%FA for 10 minutes at 25˚C. The cross liking reaction was stopped by adding glycine to a final concentration of 150mM. Crossliked cells were washed three times with PBS and were collected in 600µl of extraction buffer (50 mM Tris-HCl pH 8; 10 mM EDTA; 1% SDS; 1x complete proteinase inhibitor Roche). Sonication was performed using Bioruptor UCD-200 (Diagenode) for 7 minutes on setting ‘high’ at 4˚C (30’’ on 30’’ off). 150ul chromatin was diluted 1 in 10 on dilution buffer (20mM Tris-HCl pH 8.1; 150 mM NaCl; 2mM EDTA; 1% Triton X-100; 1x Roche complete inhibitor). Chromatin was pre-absorbed incubating the diluted chromatin with 50µl of protein A/G agarose (Santa Cruz) plus 0.5ug of rabbit IgG for 2-3 hours. Pre-absorbed chromatin was incubated overnight with 40µl of protein A/G agarose plus 1ul of rabbit anti-GFP (ab290). Agar-bead were washed twice in dilution buffer, twice in wash buffer I (20 mM Tris-HCl pH 8; 50 mM NaCl; 2 mM EDTA; 1% Triton X-100; 0.01% SDS), twice in wash buffer II (10 mM Tris-HCL pH 8; 250 mM LiCl; 1 mM EDTA; 1% NP-40; 0.25% deoxycholic acid) and once with TE buffer (10 mM Tris-HCL pH 8; 1 mM EDTA). Chromatin was eluted for the bead using elution buffer (100 mM NaHC03, 1% SDS) 10 min at 65˚C with agitation. Chromatin was decrosslinked adding NaCl to a final concentration of 300mM and incubated overnight at 65˚C. DNA was treated with 10ng/ul RNAse A for 30 min at 37˚C and 2 hous with proteinase K 20ng/µl before clean the DNA using Qiagen PCR cleaning columns.

treatment_protocol: Cell were grow in 100mm petri dish until reach 1x10^7 cells, cell where diluted 1 in 10 in KC media, cells were transfected with GFP-Su(H) plasmid containing  ~7kb of  Su(H) locus (~1.8kb of the upstream to ~2kb of downstream sequence from genomic region) using Fugene. Cells were incubated for 72 hours before harvesting.

tag: cell line

value: Kc167 cells transfected with GFP-Su(H)


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 6


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 7


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 2


title: Su(H) Kc rep3

source_name: Su(H) Kc replicate 3


title: Patient #1 Replicate 2

city: Tsukuba

first: Taro

last: Takemura

state: Ibaraki

address: 1-2-1 Sengen

department: Nanotechnology Innovation Station

institute: National Institute for Materials Science

description: Biological replicate 2 of 2. Patient #1, intact subscapularis muscle (Cy5) vs. torn supraspinatus muscle (Cy3).

hyb_protocol: Hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to the microarray slide enclosed in Agilent SureHyb-enabled hybridization chamber. After hybridization, the slide was washed.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and LOWESS normalization. Log2 ratio was calculated from Cy5/Cy3 for the Rep1 samples and from Cy3/Cy5 for the Rep2 samples.

source_name: Patient #1, intact subscapularis muscle

label_protocol: 200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions.

growth_protocol: Muscle biopsies (approximately 300 mg) were obtained from the middle of the supraspinatus and subscapularis muscles.

extract_protocol: Total RNA extracted from the satellite cells using ISOGEN following manufacturer's instructions.

treatment_protocol: Blood cells in the muscle biopsies were washed out. The tissue was minced and digested with collagenase and DNase I. The satellite cells were selected from the digested muscle tissues by FACS.

value: subscapularis muscle

source_name: Patient #1, torn supraspinatus muscle

value: supraspinatus muscle


title: Patient #7 Replicate 1

description: Biological replicate 1 of 2. Patient #7, torn supraspinatus muscle (Cy5) vs. intact subscapularis muscle (Cy3).

source_name: Patient #7, torn supraspinatus muscle

source_name: Patient #7, intact subscapularis muscle


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 9


title: Su(H) Kc input rep2

source_name: Su(H) Kc input replicate 2


title: Patient #1 Replicate 1

description: Biological replicate 1 of 2. Patient #1, torn supraspinatus muscle (Cy5) vs. intact subscapularis muscle (Cy3).


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 3


title: M-MØ_5HT_donor3_rep1

tag: cell type


title: Su(H) Kc rep2

source_name: Su(H) Kc replicate 2


title: Patient #7 Replicate 2

description: Biological replicate 2 of 2. Patient #7, intact subscapularis muscle (Cy5) vs. torn supraspinatus muscle (Cy3).


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 1


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 8

value: liver (non-adenoma section)


title: Su(H) Kc input rep1

source_name: Su(H) Kc input replicate 1


title: Su(H) Kc rep1

source_name: Su(H) Kc replicate 1


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 10


title: (c2) Liver from LDR(20mGy/d)-irradiated mice with HCA (adenoma sections) 5


title: Hairless wing disc rep3

data_processing:
The CEL files were processed with Biconductor Starr and Ringo packages, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
WDHg_123_quant-all_Ringo_hw350v10.sgr.gz file contains the median of replicate ratios smoothed into window scores using a sliding window of 700bp and 10 minimum Probes in window with the Bioconductor Ringo package. The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

source_name: Hairless wing disc replicate 3

extract_protocol: 30 third instar wandering transgenic larvae carrying the target fusion protein transgene (Hairless-GFP) were dissected in 1 x PBS (Phosphate-Buffered Saline). The dissected larval heads were inverted to expose the wing discs. Fat was removed from the larval heads when possible. The inverted larval heads were then transferred to a 1.5ml tube and were fixed with 1ml of 4% PFA (+1.5mM of EGS for the SMRTER-YFP genotype) at room temperature for 25 minutes. Following fixation, 200μl of 2M-glycine solution was added to quench the reaction. The larval heads were then rinsed 3 times with cold PBS, after which they were incubated in 1 x PBS + Roche cOmplete protease inhibitor cocktail.  Wing discs were then removed from the larval head carcasses and once 50 wing discs were collected they were centrifuged at 5000rpm at room temperature for 1 minute. After spinning down the discs, the supernatant was carefully removed and replaced with 50μl of nuclear lysis buffer (50 mM Tris-HCl pH 8; 10 mM EDTA; 1% SDS; 1x Roche cOmplete protease inhibitor). The sample was then incubated on ice for 10 minutes after which the wing discs were homogenised with a disposable plastic pestle.  250μl of IPDB (ImmunoPrecipitation Dilution Buffer) was then added to the mixture. The sample was sonicated for 7 minutes with a 30 second “ON/OFF” cycle setting in a pre-cooled bioruptor (Diagenode UCD-200).  After sonication, the sample was centrifuged at 13200rpm at 4oC for 10 minutes, after which the chromatin containing supernatant was transferred to a new 1.5ml tube and was further diluted with 200μl of IPDB.


title: Hairless wing disc input rep3

source_name: Hairless wing disc input replicate 3


title: Hairless wing disc input rep2

source_name: Hairless wing disc input replicate 2


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 9


title: Hairless wing disc rep2

source_name: Hairless wing disc replicate 2


title: Hairless wing disc input rep1

source_name: Hairless wing disc input replicate 1


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 7


title: Hairless wing disc rep1

source_name: Hairless wing disc replicate 1


title: Hairless Kc input rep3

data_processing:
The CEL files were processed with Biconductor Starr and Ringo packages, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
Hg290rep123_quant-all_Ringo_hw350v10.sgr.gz file contains the median of replicate ratios smoothed into window scores using a sliding window of 700bp and 10 minimum Probes in window with the Bioconductor Ringo package. The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

source_name: Hairless Kc input replicate 3

treatment_protocol: Cell were grow in 100mm petri dish until reach 1x10^7 cells, cell where diluted 1 in 10 in KC media, cells were transfected with Hairless-GFP plasmid containing  ~11kb of Hairless locus (~2kb of the upstream to ~2kb of downstream sequence from genomic region) using Fugene. Cells were incubated for 72 hours before harvesting.

value: Kc167 cells transfected with Hairless-GFP


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 4


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 6


title: Hairless Kc rep3

source_name: Hairless Kc replicate 3


title: Hairless Kc input rep2

source_name: Hairless Kc input replicate 2


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 5


title: Hairless Kc rep2

source_name: Hairless Kc replicate 2


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 3


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 9

value: control

value: liver


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 2


title: (c1) Liver from LDR(20mGy/d)-irradiated mice with HCA (normal sections) 1


title: Hairless Dam Kc rep3

data_processing:
The CEL files were processed with Biconductor Starr and Ringo packages, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
HDam123_quant-all_Ringo_hw350v10.sgr.gz file contains the median of replicate ratios smoothed into window scores using a sliding window of 700bp and 10 minimum Probes in window with the Bioconductor Ringo package. The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

source_name: Hairless Dam Kc replicate 3

extract_protocol: Cells were harvested by centrifugation 5min 700g at room temperature and washed twice in PBS. Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue Kit (#69504 or #69506), following manufacturer's instructions. 2.5µg of genomic DNA were digested in 10µl with DpnI at overnight at 37˚C. DpnI was inactivated at 80˚C for 20min. Genomic DNA fragments where ligated to Phosphorylated AdR adapters (AdRt  5' CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA, aligned to  AdRb  5' TCCTCGGCCG) in 20µl reaction for 2 hours at 22˚C using FERMENTAS (cat# EL0011), the reaction was complemented with PEG-4000.  The reaction was inactivated at 65˚C for 10 mim and subsequently digested with DpnII to destroy unmethylated GATC DNA fragments and subsequently the DNA fragments where cleaned using Qiagen PCR cleaning kit  (Cat#28104). DNA was amplified for 15 cycles by PCR using Expand DNA polymerase (Can#11732641001) and Adr-PCR primer (5' GGTCGCGGCCGAGGATC). After amplification, adapter were removed by DpnII digestion.

treatment_protocol: Cell were grow in 100mm petri dish until reach 1x10^7 cells, cell where diluted 1 in 10 in KC media, cells were transfected with Hairless-DAM plasmid containing  ~11kb of Hairless locus (~2kb of the upstream to ~2kb of downstream sequence from genomic region) using Fugene. Cells were incubated for 72 hours before harvesting.

value: Kc167 cells transfected with Hairless-DAM


title: Hairless Kc input rep1

source_name: Hairless Kc input replicate 1


title: Wt

city: Nagoya

first: Aya

last: Naiki-Ito

address: 1-Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Experimental Pathology and Tumor Biology

institute: Nagoya City University Graduate School of Medical Sciences

hyb_protocol: 1 µg of labeled probe was used for hybridization with TaKaRa Hybridization Chamber at 37°C for 16 hours. After hybridization, slides were washed sequential

scan_protocol: Scanned on 3D-gene Scanner 3000 (TORAY)

data_processing: Global normalized, background subtracted data obtained.

organism: Rattus norvegicus

source_name: Rat liver

label_protocol: １ µg of total RNA were amplified with Ambion Amino Allyl aRNA kit, then 10 µg of amlified RNA labelded with Amersham Cy5  Mono-Reactive Dye.

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

treatment_protocol: Cx32 dominant negative transgenic rats and wild-type rats at 10 weeks of age were given an intraperitoneal injection of diethylnitrosamine and fed methionine-choline deficient diet (MCDD) or MCDD with luteolin for 12 weeks.

tag: genotype

value: wild-type

value: Sprague-Dawley


title: Hairless Dam Kc input rep2

source_name: Hairless Dam Kc input replicate 2

value: Kc167 cells transfected pMT-DAM


title: Infected_2

city: Helsinki

first: Tommaso

last: Raffaello

address: Latokartanonkaari 7 PO Box 27

department: Forest Sciences

country: Finland

institute: University of Helsinki

hyb_protocol: Hybridization by NimbleGen Company.

scan_protocol: Scanning by NimbleGen Company.

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264.

organism: Pinus sylvestris

source_name: Tree stem, infection

label_protocol: Labelling by NimbleGen Company.

growth_protocol: The field experiment of Scots pine (Pinus sylvestris L.) was established at Layliainen- Finalnd. The samples were collected after three months. Trees were cut down and the areas closed to the inoculations sites were cut as disks. The sample disks were stored in -20ºC.

extract_protocol: Reference:  Chang SJ, Puryear J, Cairney J: A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 1993, 11(2):113-116.  Isolation of RNA from plant tissue    1. Grind plant tissue in liquid nitrogen with mortar and pestle. Transfer the ground sample to a sterile tube. Add 5 ml of Extraction buffer (preheated at 65ºC) and 50 μl DTT (1mol/L). Incubate for 15 min at 65ºC.   2. Add equal volume of chloroform:isoamyl alcohol (24:1). Shake well and centrifuge at 8000rpm for 30 min at 25ºC. Repeat this step.  3. Transfer aqueous phase to a new sterile tube. Add 1/4 volume of 10M LiCl and mix well. Precipitate RNA overnight at 4ºC. Centrifuge at 8000rpm for 40 min.  4. Pour out the supernatant carefully and dry the pellet briefly. Dissolve the pellet in 2 ml SSTE and transfer each 500 μl into a sterile 1.5 ml tube.  5. Add an equal volume of chloroform:isoamyl alcohol. Shake well and centrifuge at 13000rpm for 30 min at 25ºC.  6. Transfer aqueous phase to a new tube. Add 2 volume of cold absolute ethanol. Precipitate at -20ºC for at least 2 hours. Centrifuge at 13000rpm for 30 minutes.   7. Pour out the supernatant carefully. Wash the pellet by adding approximately 100 μl cold 70% ethanol at room temperature. Centrifuge at half speed for 5 min.  8. Pour out the supernatant and dry the pellet in the sterile hood. Re-suspend the pellet in DEPC-treated water.    Extraction buffer: 50 ml  2% CTAB CTAB 1 g  100 mM Tris-HCl 1 M Tris-HCl 5 ml  25 mM EDTA 0.5 M EDTA 2.5 ml  2 M NaCl 4 M NaCl 25 ml  DEPC-treated water  17.5 ml (up to 50 ml)          SSTE: 2 ml  1 M NaCl 4 M NaCl 0.5 ml  0.5% SDS 5% SDS (pre-heated at 65ºC) 0.2 ml  10 mM Tris-HCl 1 M Tris-HCl 20 μl  1 mM EDTA 0.5 M EDTA 4 μl  DEPC-treated water  1.276 ml (up to 2 ml)

treatment_protocol: Sterile dowels of Scots pine wood (diameter 5 mm) were placed on a one-month-old malt agar culture of H. annosum (isolate Dragstjard 05044, courtesy of K. Korhonen, LUKE, Finland). Plates were incubated at room temperature in darkness for three weeks. Two H. annosum artificial inoculations were done in the shoots and two in the roots of each replicate tree (three replicate trees in total) in July 2009. Stem first inoculation was done at breast height (approx. 1.3 m) and the second above the first inoculation with distance of 50 cm. Root inoculations were done for this clone in separate roots. Holes were made radially and the inoculated dowels were inserted through the holes, and then were sealed with parafilm. Wounding control trees were inoculated with sterile dowels of Scots pine wood incubated in malt agar plates. and mock inoculations were performed on stems and roots of each genotype. The samples were collected after three months. Trees were cut down and the areas close to the inoculation sites were cut as disks. The sample disks were stored in -20°C. Xylem and phloem of each inoculation were collected separately. The bark was removed, and the necrotic lesions formed in the phloem were measured; length was measured from each inoculation point, and the width was measured when the necrosis was wider than the dowel. After documentation, the infected phloem was removed gently and stored in -80°C. After the removal of phloem, same measurements were documented from the infected xylem. Finally, the xylem samples were cut in pieces with band saw and stored in -20°C. Tissues of phloem and xylem from unwounded tree served as a control.

tag: soil type

value: Agricultural

value: 97 Varkaus-8

value: stem (bulk of xylem and phloem)

tag: inoculation status

value: inoculated with Heterobasidion annosum


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 10

value: Female

value: irradiated


title: Wounded_2

source_name: Tree stem, wounding

value: 97 Varkaus-6

value: non-inoculated


title: Wounded_3


title: Tg + luteolin

value: connexin dominant negative transgenic

value: luteolin


title: Hairless Kc rep1

source_name: Hairless Kc replicate 1

value: Kc167 cells transfected with Hairless-GFP

value: Abcam rabbit anti-GFP (ab290)


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 6

value: control

value: liver


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 8


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 3


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 7


title: Infected_3


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 4


title: Tg


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 5


title: Infected_1


title: Wt+ luteolin

value: wild-type


title: M-MØ_Control_donor3_rep1

description: Gene expression in M-MØ

value: healthy donor

value: Monocyte-derived M-CSF macrophages

value: none (control)


title: Hairless Dam Kc input rep1

source_name: Hairless Dam Kc input replicate 1

value: Kc167 cells transfected pMT-DAM


title: HB3-36h (exon-level)

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 100 Galvin Life Science Building

department: Biological Science

institute: University of Notre Dame

description:
2 biological replicates: HB3-1-36h , HB3-2-36h
Raw data files:
2015-07-29_256178610013_HB3-1-36h_532_635_converted_GE1_Dec2014_MTF_EXP_1_3.txt
2015-07-29_256178610013_HB3-2-36h_532_635_converted_GE1_Dec2014_MTF_EXP_2_3.txt

hyb_protocol: 2.5ug of labeled cDNA was mixed with Agilent 10X Blocking Agent and 2X Hi-RPM Hybridization Buffer as directed by standard Agilent protocols to bring total volume of sample to 50.0uL. A total of 40uL was loaded into the gasket slides and hybridized to the Agilent Array.

scan_protocol: Microarrays were scanned with the Nimblegen scanner at 2.0uM resolution. Autogain for the entire array was set based on laser intensity for plex 1-1.

data_processing: Image file was processed using Agilent Feature Extraction. Samples were robust multiarray averaged simultaneously with all samples used in this study. Probes below background and those not meeting a 5% false discovery rate were removed before further analysis. Signal intensities for probes were then averaged by exon and by gene.

organism: Plasmodium falciparum

source_name: O+ blood culture of HB3 parasites, 36 hours post invasion

label_protocol: 300ng of RNA was used as starting material for cDNA synthesis using Sigma WTA2 kit. Then 1ug of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.

growth_protocol: Parasite cultures were grown in replicates at 37C and 5% hematocrit in O+ human erythrocytes using RPMI 1640 supplemented with 0.5% Albumax I, 0.25% sodium bicarbonate, and 0.01mg/mL genatmicin under an atmosphere of 90% nitrogen, 5% oxygen, and 5% carbon dioxide.

extract_protocol: Total RNA was extracted from 20mLs of culture using TriZol reagent.

treatment_protocol: Cultures were synchronized using 5% sorbitol prior to collection of specific time points.

tag: time

value: 36 hours post invasion

tag: host cell type

value: human erythrocyte


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 2

tag: strain

value: Female


title: HB3-48h (exon-level)

description:
2 biological replicates: HB3-1-48h , HB3-2-48h
Raw data files:
2015-07-29_256178610013_HB3-1-48h_532_635_converted_GE1_Dec2014_MTF_EXP_1_4.txt
2015-07-29_256178610013_HB3-2-48h_532_635_converted_GE1_Dec2014_MTF_EXP_2_4.txt

source_name: O+ blood culture of HB3 parasites, 48 hours post invasion

value: 48 hours post invasion


title: Wounded_1

value: Agricultural

value: 97 Varkaus-5

value: stem (bulk of xylem and phloem)


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 11


title: (b) Liver from LDR(20mGy/d)-irradiated mice without HCA 1

value: irradiated


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 10


title: Hairless Dam Kc rep2

city: Cambridge

last: Bray

address: Downing Street

institute: University  of Cambridge

source_name: Hairless Dam Kc replicate 2

value: Kc167 cells transfected with Hairless-DAM


title: Hairless Dam Kc rep1

source_name: Hairless Dam Kc replicate 1


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 9


title: HB3-12h (exon-level)

description:
2 biological replicates: HB3-1-12h , HB3-2-12h
Raw data files:
2015-07-29_256178610013_HB3-1-12h_532_635_converted_GE1_Dec2014_MTF_EXP_1_1.txt
2015-07-29_256178610013_HB3-2-12h_532_635_converted_GE1_Dec2014_MTF_EXP_2_1.txt

source_name: O+ blood culture of HB3 parasites, 12 hours post invasion

value: 12 hours post invasion


title: HB3-24h (exon-level)

description:
2 biological replicates: HB3-1-24h , HB3-2-24h
Raw data files:
2015-07-29_256178610013_HB3-1-24h_532_635_converted_GE1_Dec2014_MTF_EXP_1_2.txt
2015-07-29_256178610013_HB3-2-24h_532_635_converted_GE1_Dec2014_MTF_EXP_2_2.txt

source_name: O+ blood culture of HB3 parasites, 24 hours post invasion

value: 24 hours post invasion


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 8

value: control

value: liver


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 5


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 3


title: Ovarian_PrimarySurgery_LA543

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

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

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

data_processing: BeadStudio software v3.2.  The sample data table contains Average Beta and the non_normalized.txt file contains Unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: Epithelia ovarian cancer

extract_protocol: genomic DNA was extracted and purified from tumor tissue and scarpping cells using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Primary surgery

tag: age

tag: survival status

value: deceased

value: malignant ovarian tumor

tag: Stage

value: stage 3

tag: grading

tag: subtype

value: serous


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 2

tag: disease state


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 6

tag: treatment


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 7

tag: tissue


title: Ovarian_PrimarySurgery_LA600

value: mucinous


title: Ovarian_PrimarySurgery_LA243

value: stage 4


title: Ovarian_PrimarySurgery_LA347


title: Ovarian_PrimarySurgery_LA805


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 4

tag: gender

value: Female


title: (a)Liver from non-irradiated female B6C3F1 mice without HCA (Control) 1


title: Ovarian_PrimarySurgery_LB165


title: Ovarian_PrimarySurgery_L953


title: Ovarian_PrimarySurgery_LA97


title: Ovarian_PrimarySurgery_L822

value: clear cell


title: Ovarian_PrimarySurgery_LD048

value: alive


title: Ovarian_PrimarySurgery_LD108


title: Ovarian_PrimarySurgery_LD29


title: Ovarian_PrimarySurgery_LB699


title: Ovarian_PrimarySurgery_LB630


title: Ovarian_PrimarySurgery_LD037


title: Ovarian_PrimarySurgery_LD100


title: Ovarian_PrimarySurgery_LD085


title: Ovarian_PrimarySurgery_LD041


title: Ovarian_PrimarySurgery_LB797


title: Human Dermal Microvascular Endothelial Cells-3

city: Columbus

first: Chandan

last: Sen

state: Ohio

address: 473W. 12th Avenue,

department: Surgery

institute: Ohio State University Wexner Medical Center

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: Raw data were processed with GeneSpring GX (Agilent Technologies)  for background correction and normalization. Data analysis and statistical evaluations were performed with GeneSpring GX (Agilent Technologies) .

source_name: Immortalized primary cells, foreskin, CDC

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

growth_protocol: Primary human adult dermal fibroblast were grown in fibroblast basal medium supplemented with fibroblast growth kit-serum-free at 370C in humidified atmosphere with 5% CO2. The cells were first grown to full confluency overnight on the 3D Nanochannel electropoartion device. Human dermal microvascular endothelial cells (HMECs) were cultured in MCDB-131 medium.

extract_protocol: Total RNA from cells was extracted by using miRVana miRNA isolation kit (Thermo Fisher Scientific; cat.no. AM1560) according to the manufacturer’s instructions. All samples were treated with DNase I, amplification grade (Thermo Fisher Scientific; 18068015) to remove contaminating DNA from RNA. The RNA quantity was measured using a NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA quality was checked using RNA6000 NanoAssay on Agilent BioAnalyzer 2100 (AgilentTechnologies, Santa Clara, CA). A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: A pulsed electric field was used to deliver control or miR200b inhibitor (50nM) into the cells. The cells were then harvested and placed in EBM-2 basal medium supplemented with EGM-2 MV SingleQuot kit for 7 days. HMECs was used in our study as positive control.

value: endothelial

tag: Sex

value: female

tag: transfection

value: untransfected


title: Human Dermal Microvascular Endothelial Cells-2


title: Ovarian_PrimarySurgery_LB542


title: Ovarian_PrimarySurgery_LA590


title: Ovarian_PrimarySurgery_LA269


title: Ovarian_PrimarySurgery_LA731


title: Human Dermal Adult Fibroblasts, transfected with control inhibitor-3

source_name: primary cells, abdominal skin, ATCC

value: fibroblast

value: control inhibitor


title: Ovarian_PrimarySurgery_LA554


title: Human Dermal Adult Fibroblasts, transfected with miR-200b inhibitor-1

value: miR-200b inhibitor


title: Human Dermal Adult Fibroblasts, transfected with miR-200b inhibitor-3


title: Human Dermal Adult Fibroblasts, transfected with control inhibitor-1


title: Ovarian_PrimarySurgery_LA527


title: Human Dermal Adult Fibroblasts, transfected with miR-200b inhibitor-2


title: Ovarian_PrimarySurgery_LB44


title: Human Dermal Microvascular Endothelial Cells-1


title: Ovarian_PrimarySurgery_LA473


title: Ovarian_PrimarySurgery_L513


title: Human Dermal Adult Fibroblasts, transfected with control inhibitor-2


title: Ovarian_PrimarySurgery_LA73


title: Ovarian_PrimarySurgery_L991


title: Patient 29 recurrent tumour

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: minfi 1.18.1, SWAN Normalisation

source_name: FFPE primary tumour tissue

extract_protocol: Genomic DNA was extracted using Promega ReliaPrep™ FFPE gDNA Miniprep System.

tag: tissue type (primary=0, recurrent=1, recurrent2=2)

value: M

tag: survival (months)

tag: time to relapse (months)

tag: survival (months

tag: includepaired (0=no, 1=yes)

tag: replicate array (0=no, 1=yes)

tag: treatment prior to second surgery


title: Patient 26 recurrent tumour

tag: age

value: Stupp concurrent and standard adjuvant


title: Patient 29 recurrent tumour 2


title: Patient 29 primary tumour


title: Patient 26 primary tumour


title: Patient 28 recurrent tumour


title: Patient 22 recurrent tumour

value: Stupp concurrent and 4 cycles adjuvant


title: Patient 28 primary tumour


title: Patient 21 primary tumour

value: F


title: Ovarian_PrimarySurgery_LB364

tag: survival status

value: malignant ovarian tumor

tag: Stage

value: stage 3


title: Patient 20 recurrent tumour

value: Stupp concurrent and 9 cycles adjuvant AVAglio (+/-bev)


title: Patient 19 primary tumour

value: Stupp concurrent and standard adjuvant, then 2nd line bevacizumab 8 months


title: Patient 22 primary tumour


title: Patient 21 recurrent tumour


title: Patient 19 recurrent tumour


title: Patient 10 recurrent tumour

value: Stupp concurrent and 2 cycles adjuvant AVAglio (+/-bev)


title: Patient 12 recurrent tumour


title: Patient 14 recurrent tumour


title: Patient 9 primary tumour

value: Stupp concurrent and adjuvant AVAglio (+/-bev)


title: Patient 16 primary tumour


title: Patient 15 recurrent tumour

value: Stupp concurrent only


title: Patient 18 recurrent tumour


title: Patient 7 primary tumour


title: Patient 16 recurrent tumour


title: Patient 20 primary tumour


title: Patient 15 primary tumour


title: Patient 7 recurrent tumour


title: Patient 8 primary tumour


title: Patient 8 recurrent tumour


title: Patient 4 recurrent tumour


title: Non-grafted drought tolerant grapevine rootstock (110R) under well watered period (WWP) _rep2

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

description:
110R_WWP_non-grafted_2
Vitis berlandieri X Vitis rupestris
Gene expression data from well watered roots of nongrafted-drought tolerant grapevine rootstock (110R).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Vitis vinifera (grape) 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 Robust Multiarray Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Vitis cinerea var. helleri x Vitis rupestris

source_name: roots grown under well watered control condition at 90-100% field capacity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Drought tolerant 110R rootstock were firstly grafted with sultana seedless. After callusing and rooting, grafted and non-grafted plants were grown for two years in 20 L pots filled with soil (clay loam (pH 6.4) with 0.0062 dS/m EC, 1.9% organic carbon content) perlite mixture (4:1). All the experiments were carried out in semi-controlled greenhouse.

extract_protocol: Roots collected from control and drought treated plants were utilized for total RNA isolation as described in Chang et al. (1993) with minor modifications as described in Le-Provost et al. (2007).

treatment_protocol: Drought treatment applied to plants by completely withholding irrigation from the pots. Sampling was done when the soil water content of the pots decreased to 5-10% at the end of drought treatment. Control condition was created by well irrigation of the replicates at the field capacity.

value: root

tag: genotype/variation

value: non-grafted drought tolerant

value: two-year-old non-grafted and rooted cuttings

value: well watered


title: Patient 2 primary tumour

label_protocol: Standard Illumina Protocol


title: Non-grafted drought tolerant grapevine rootstock (110R) under drought stress (DS)_rep1

description:
110R_DS_non-grafted_1
Vitis berlandieri X Vitis rupestris
Gene expression data from drought treated roots of nongrafted-drought tolerant grapevine rootstock (110R).

source_name: drought treated roots at 5-10% field capacity

value: drought