title: Chk1

value: Santa-Cruz sc-8408 (G-4)

value: Mouse


title: P-Stat3-ser727

status: Public on Mar 07 2015

type: protein

city: Paris

first: Leanne

last: de Koning

address: 26 rue d'Ulm

department: Department of translational research

country: France

institute: Institut Curie

hyb_protocol: After washes with TBST, arrays were probed with horseradish peroxidase-coupled secondary antibodies (Jackson ImmunoResearch Laboratories, Newmarket, UK) diluted in TBST-BSA for 1 h at RT. To amplify the signal, slides were incubated with Bio-Rad Amplification Reagent for 15 min at RT. The arrays were washed with TBST, probed with Cy5-Streptavidin (Jackson ImmunoResearch Laboratories) diluted in TBST-BSA for 1 h at RT and washed again in TBST. For staining of total protein, arrays were incubated 15 min in 7% acetic acid and 10% methanol, rinsed twice in water, incubated 5 min in Sypro Ruby (Invitrogen) and rinsed again. The processed slides were dried by centrifugation

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner (Molecular Devices)

data_processing: Spot intensity was determined with MicroVigene software (VigeneTech Inc).  Raw data were subjected to quality control and all aberrent values, samples or antibodies were removed for further processing. For each sample, one relative protein expression level was determined from the technical replicates and the dilution series, using Normacurve software (Troncale et al., 2012). Bias due to the origin of the samples (NKI vs CAM) was removed using a median regression approach. In brief, data were scaled by array and the median for each sample across all arrays was computed. Then, linear regression was performed of scaled data on the median of proteins and residues were set as the final processed data. The entire normalisation process was done using all samples on the arrays, including cell lines and Triple-nagative breast cancer samples. Normalised data represent ILC samples only.

molecule: protein

organism: Homo sapiens

source_name: Invasive lobular carcinoma (ILC)

label_protocol: Arrays were labeled with commercially available antibodies using an Autostainer Plus robot (Dako). Briefly, slides were incubated with avidin, biotin and peroxydase blocking reagents (Dako) before saturation with TBS containing 0.1% Tween-20 and 5% BSA (TBST-BSA). Slides were then probed overnight at 4°C with primary antibodies diluted in TBST-BSA.

extract_protocol: Three sections of fresh frozen tissue were lysed in hot Laemmli buffer (50 mM Tris pH =6.8, 2% SDS, 5% glycerol, 2 mM DTT, 2.5 mM EDTA, 2.5 mM EGTA, 1x HALT Phosphatase inhibitor (Perbio 78420), Protease inhibitor cocktail complete MINI EDTA-free (Roche 1836170, 1 tablet/10 mL), 2 mM Na3VO4 and 10 mM NaF) and boiled for 10 min at 100°C. Samples were sonicated in a waterbath for 1-2min to break the DNA and spinned for 10 min at 13000 rpm.  Supernatant was snapfrozen and protein concentration was measured (BCA reducing agents compatible kit, Pierce, Ref 23252).

tag: antibody vendor/catalog#

tag: source of antibody

value: Rabbit

tag: clonality

value: Polyclonal


title: Smad1


title: Cofilin


title: Phospho-Chk2-Thr68

value: Monoclonal


title: topoisomeraseIIalpha

value: Epitomics 1826-1


title: Phospho-Chk1-ser280


title: ROCK-I-ROK-beta


title: P-c-jun-ser73


title: P-PTEN-ser380-thr382-383


title: c-jun

value: Epitomics 1696-1


title: alpha1-catenin

value: Abcam ab51032


title: cirrhosis [B166_placa96-3_G07]

type: RNA

city: New York

first: Augusto

last: Villanueva

address: 1425 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Array quality in mice studies was assessed with the arrayQualityMetrics package of Bioconductor (http://www.bioconductor.org). Data were normalized and logged-2 transformed using the RMA algorithm.

label: Biotin

molecule: total RNA

source_name: cirrhosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Samples collected within 1 hour of surgical resection and fresh-frozen. Stored at -80ºC.

extract_protocol: Trizol according to manufacturer

treatment_protocol: Samples didn't receive any treatment

tag: subject

value: hepatocellular carcinoma patient

tag: gender

tag: age (yrs)

tag: tumor stage

tag: tissue

value: liver

tag: tissue subtype

value: non-tumor cirrhosis

tag: sample type

value: fresh frozen tissue


title: cirrhosis [B168_placa96-3_G09]


title: hepatocellular carcinoma [B169_placa96-3_G10]

source_name: hepatocellular carcinoma

value: female

value: primary hepatocellular carcinoma


title: hepatocellular carcinoma [B161_placa96-3_G06]

value: male


title: PTEN


title: hepatocellular carcinoma [B159_placa96-3_G04]

value: bclcA


title: SEK1-MKK4


title: JnB

value: non-commercial


title: hepatocellular carcinoma [B167_placa96-3_G08]


title: cirrhosis [B158_placa96-3_G03]


title: cirrhosis [B160_placa96-3_G05]


title: hepatocellular carcinoma [B157_placa96-3_G02]


title: hepatocellular carcinoma [B153_placa96-3_F12]


title: P-p70-S6 kinase-Thr389

value: Upstate M04-392


title: P-p44-42-MAPK-Thr-202-Tyr204

value: Mouse


title: AMPK-alpha

value: Rabbit


title: MEKK3

value: Epitomics 1673-1


title: p70-S6-Kinase

value: Monoclonal


title: P-JnB


title: p53


title: 4E-BP1

value: Polyclonal


title: P-AMPK-beta1-Ser181

value: Epitomics 2271-1


title: FoxO3a-FKHRL1

value: Upstate (M07-702)


title: P-c-Abl-Tyr204


title: MELK

value: Chemicon MAB4331


title: NF-kB-p65


title: GATA3


title: JNK-SAPK1-pan


title: P-S6-Ribosomal-protein-Ser241


title: P-JNK-SAPK-Thr183-185


title: LKB1


title: cirrhosis [B152_placa96-3_F11]

value: hepatocellular carcinoma patient

value: liver


title: cirrhosis [B150_placa96-3_F09]

value: non-tumor cirrhosis

value: fresh frozen tissue


title: P-NFkB-p65-ser536


title: P-p38-MAPK-Thr180-182


title: cirrhosis [B110_placa96-3_F03]


title: hepatocellular carcinoma [B147_placa96-3_F08]

value: primary hepatocellular carcinoma


title: P-p53-Ser15


title: cirrhosis [B134_placa96-3_F05]


title: hepatocellular carcinoma [B131_plate4_H06]

value: male


title: cirrhosis [B156_placa96-3_G01]


title: p38-MAPK


title: p42-44-MAPK


title: hepatocellular carcinoma [B135_placa96-3_F06]

value: female


title: hepatocellular carcinoma [B111_placa96-3_F04]

value: bclcA


title: cirrhosis [B146_placa96-3_F07]


title: PTEN-XP

value: CST 9188S


title: Akt


title: E-cadherin

value: Mouse


title: Patient 8, before CC treatment

city: Lodz

first: Ida

last: Franiak-Pietryga

address: Pabianicka 62

country: Poland

institute: Copernicus Memorial Hospital in Lodz

description: control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://appliedbiosystems.com
For the normalization it uses the average of housekeeping gene: 18S
Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping gene).
Fold Change worksheet reports test/control (i.e., after CC treatment/before CC treatment) ratios.

label: FAM

source_name: B-CLL cells

label_protocol: PCR assays were performed using the 384 TaqMan Low Density Array (Human Apoptosis Panel) (Applied Biosystems, USA).

extract_protocol: Total RNA was extracted with the RiboPure Blood Kit (Ambion, USA). RNA was reversed transcribed to cDNA using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, USA).

treatment_protocol: All the patients received CC treatment by intravenous infusion according to the schedule: cladribine 0.12mg/kg-days 1-3, cyclophosphamide 600mg/m2- days 1-3. The regimen was repeated every 4 weeks until 6 courses.

value: Male

tag: cell type

value: lymphocytes B

tag: time

value: 0 days

tag: rai stage before treatment

tag: zap70 status

value: negative

tag: ighv mutation status

value: Mutated

tag: treatment response

value: CR

tag: cytogenetic abnormalities


title: PI3kinase-p110-beta

tag: antibody vendor/catalog#

value: Epitomics 1596-1

value: Rabbit

value: Monoclonal


title: Patient 8, after 2 weeks of CC treatment

description: test

tag: activation agent

value: cladribine, cyclophosphamide

value: 14 days


title: hepatocellular carcinoma [B109_placa96-3_F02]

value: hepatocellular carcinoma patient

value: liver

value: primary hepatocellular carcinoma

value: fresh frozen tissue


title: PI3kinase-class-III

tag: source of antibody

tag: clonality


title: c-abl

value: Polyclonal


title: S6-Ribosomal-protein


title: cirrhosis [B108_placa96-3_F01]

tag: subject

tag: gender

value: non-tumor cirrhosis


title: MEK1-2


title: Patient 7, before CC treatment

description: control

value: Female

value: Unmutated

value: No response (NR), died


title: Patient 7, after 2 weeks of CC treatment

description: test

value: lymphocytes B


title: hepatocellular carcinoma [B151_placa96-3_F10]

value: male

tag: age (yrs)

tag: tumor stage

value: bclcA


title: P-MEK1-2-Ser217


title: MW76-72C-high-agit - Slide 4

city: Raleigh

first: Aaron

last: Hawkins

state: NC

address: 840 Main Campus Dr

department: Chemical Engineering

institute: North Carolina State University

description:
Slide 4 - Four slide comparison of MW76 at high agitation before and after 3HP production at 72C under H2 and N2 environments. NB only the N2 comparison was presented in the paper.
04 h2loop_normdata.xlsx
04 MW76-1000E_MW76-1000_L.xlsx

hyb_protocol: Labeled cDNA was re-purified using Qiagen spin column and Cy3/Cy5 samples were combined according to experimental design. Combined cDNA was dried using a vacuum centrifuge and resuspended in 29 ul dH2O. Corning microarray slides were incubated in pre-hyb buffer for 90 minutes (1X SSC, 0.1% SDS, 1g/L BSA), after which labeled cDNA was mixed with 1 ul COT1 DNA, 30 uL of 2X hybridization buffer (2X SSC, 2X Denhardts solution, 0.1% SDS, 30% formamide), applied to slide and incubated at 42C for 18-20 hours.

scan_protocol: Images were aquired with a GenePix 4000B with automatic calculation of PMT gain. Scatterplots of signal intensities are reviewed to check for balance between channels.

data_processing: Signals for each channel were obtained using GenePix Pro v6.0 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once all slides are quantitated, data from all slides in loop were analyzed with JMP Genomics 5 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

organism: Pyrococcus furiosus

label_protocol: 20 µg of total RNA (10 ug of each biological repeast) were primed with random DNA primers at 70°C for 10 min, then reversed transcribed at 46°C for 16 h with SuperScript III RTase (Invitrogen), and 50 µM each dATP, dCTP, dGTP, with 28 µM dTTP, 22 µM amino-allyl-labelled dUTP. After RT, cDNA was purified using a Qiagen spin column, dried down in a vacuum centrifuge, and resuspended in 4.5 ul 0.1M sodium carbonate buffer (pH 9.0) with 4.5 ul Cy3 or Cy5 dye and incubated in darkness for 2 hours at room temperature for dye incorporation

growth_protocol: Pyrococcus furiosus (DMSZ 3638) and COM1 strains were routinely grown anaerobically under N2 at 95°C in a shaking oil bath (90 rpm) in seawater medium containing 1 × base salts, 1 × trace minerals, 10 μM sodium tungstate, 0.25 μg/ml resazurin, with added cysteine at 0.5 g/L, sodium sulfide at 0.5 g/L, and 1 mM potassium phosphate buffer (pH 6.8). For growth in serum bottles, sodium bicarbonate was also added at 1 g/L. However, when grown in bioreactors using gas feeds containing CO2, bicarbonate was omitted from the medium. Various complex media formulations were used that extended the seawater medium base. Routine medium for growth in serum bottles contained 5 g/L yeast extract and 5 g/L maltose (YM5) unless otherwise noted; 250 μg/L biotin was added to the medium when growing the engineered strains in the bioreactor.

extract_protocol: Cells were harvested from bottles or bioreactors and chilled to 4°C using dry ice and ethanol. Cells were pelleted by centrifugation at 4°C, 6000g, 15min, then stored at -80°C until RNA extraction. Cells were lysed using 1 mL Trizol and total RNA was extracted and purified using Qiagen RNeasy kits.

tag: strain

tag: genotype/variation

value: Pfu strain containing 3 M. sedula genes for production of 3HP plus genes for accessory proteins CA and BPL

tag: timepoint

value: Harvested 30-40 hours after temp shift (late)

tag: growth condition

value: Temp switched to 72C after cells reached 1x10^8, 1000 rpm, N2 headspace

value: Harvested after temp shift (early)


title: MW76-72C-high-agit - Slide 3

description:
Slide 3 - Four slide comparison of MW76 at high agitation before and after 3HP production at 72C under H2 and N2 environments. NB only the N2 comparison was presented in the paper.
04 h2loop_normdata.xlsx
04 MW76-1000E_MW76-1000_L.xlsx

value: Temp switched to 72C after cells reached 1x10^8, 1000 rpm, H2 headspace


title: P-Akt-Thr308

value: Rabbit

value: Monoclonal


title: MW76-72C-high-agit - Slide 2

description:
Slide 2 - Four slide comparison of MW76 at high agitation before and after 3HP production at 72C under H2 and N2 environments. NB only the N2 comparison was presented in the paper.
04 h2loop_normdata.xlsx
04 MW76-1000E_MW76-1000_L.xlsx


title: P-Akt-Ser473


title: Patient 6, before CC treatment

description: control

value: Male

tag: cell type

tag: time

value: 0 days

tag: rai stage before treatment

value: negative

value: NR


title: Patient 5, after 2 weeks of CC treatment

description: test

value: Female

value: cladribine, cyclophosphamide

value: 14 days

tag: ighv mutation status

value: Mutated

tag: treatment response

value: CR


title: MW76-72C-high-agit - Slide 1

description:
Slide 1 - Four slide comparison of MW76 at high agitation before and after 3HP production at 72C under H2 and N2 environments. NB only the N2 comparison was presented in the paper.
04 h2loop_normdata.xlsx
04 MW76-1000E_MW76-1000_L.xlsx


title: COM1-MW76-- Slide 6

description:
Slide 6 - Six slide comparison of MW56, MW76, and COM1 at 72C immediately after termperature shift (early) and later after 3HP production in MW76 (late) NB only MW76 and COM1 comparisons were discussed in manuscript
03 COM1_MW76-400.xlsx
03 COM1_MW56_MW76_normdata.xlsx

value: Pfu strain containing 3 M. sedula genes for production of 3HP

value: Temp switched to 72C after cells reached 1x10^8, 400 rpm


title: Patient 5, before CC treatment

description: control

value: lymphocytes B

tag: zap70 status

tag: cytogenetic abnormalities


title: P-mTor-Ser2448

tag: antibody vendor/catalog#

value: Abcam ab109268

tag: source of antibody


title: COM1-MW76 - Slide 5

description:
Slide 5 - Six slide comparison of MW56, MW76, and COM1 at 72C immediately after termperature shift (early) and later after 3HP production in MW76 (late) NB only MW76 and COM1 comparisons were discussed in manuscript
03 COM1_MW76-400.xlsx
03 COM1_MW56_MW76_normdata.xlsx

organism: Pyrococcus furiosus COM1

value: Competent Pfu strain COM1

value: Harvested after temp shift (early)


title: COM1-MW76 - Slide 4

description:
Slide 4 - Six slide comparison of MW56, MW76, and COM1 at 72C immediately after termperature shift (early) and later after 3HP production in MW76 (late) NB only MW76 and COM1 comparisons were discussed in manuscript
03 COM1_MW76-400.xlsx
03 COM1_MW56_MW76_normdata.xlsx

value: Harvested 30-40 hours after temp shift (late)


title: COM1-MW76 - Slide 2

description:
Slide 2 - Six slide comparison of MW56, MW76, and COM1 at 72C immediately after termperature shift (early) and later after 3HP production in MW76 (late) NB only MW76 and COM1 comparisons were discussed in manuscript
03 COM1_MW76-400.xlsx
03 COM1_MW56_MW76_normdata.xlsx

value: Pfu strain containing 3 M. sedula genes for production of 3HP plus genes for accessory proteins CA and BPL


title: COM1-MW76 - Slide 3

description:
Slide 3 - Six slide comparison of MW56, MW76, and COM1 at 72C immediately after termperature shift (early) and later after 3HP production in MW76 (late) NB only MW76 and COM1 comparisons were discussed in manuscript
03 COM1_MW76-400.xlsx
03 COM1_MW56_MW76_normdata.xlsx


title: mTor

value: Abcam ab51089

value: Rabbit

tag: clonality

value: Polyclonal


title: COM1 vs MW56 - Slide 2

description:
Slide 2 - dye flip comparing strain MW56 containing three heterologous Msed genes to parent strain COM1 at 95C
02 COM1_MW56.xlsx
02 com1vsmw56_normdata.xlsx

value: Harvested at 3-4x10^8 cell density

value: Grown at 95C

source_name: Pfu COM1


title: Patient 4, after 2 weeks of CC treatment

description: test

tag: gender

value: Male

tag: activation agent

value: cladribine, cyclophosphamide

value: Unmutated

value: Partial remission (PR)


title: Patient 4, before CC treatment

description: control

value: 0 days

value: negative


title: Patient 6, after 2 weeks of CC treatment

description: test

value: lymphocytes B

value: 14 days

value: NR


title: COM1-MW76 - Slide 1

description:
Slide 1 - Six slide comparison of MW56, MW76, and COM1 at 72C immediately after termperature shift (early) and later after 3HP production in MW76 (late) NB only MW76 and COM1 comparisons were discussed in manuscript
03 COM1_MW76-400.xlsx
03 COM1_MW56_MW76_normdata.xlsx

value: Harvested after temp shift (early)

value: Temp switched to 72C after cells reached 1x10^8, 400 rpm


title: Patient 3, after 2 weeks of CC treatment

description: test

value: Female

value: No response (NR), died

value: not done


title: COM1 vs MW56 - Slide 1

description:
Slide 1 - dye flip comparing strain MW56 containing three heterologous Msed genes to parent strain COM1 at 95C
02 COM1_MW56.xlsx
02 com1vsmw56_normdata.xlsx

value: Competent Pfu strain COM1

value: Pfu strain containing 3 M. sedula genes for production of 3HP


title: Patient 3, before CC treatment

description: control


title: WT vs COM1 - Slide 2

description:
Slide 2 - dye flip comparing WT Pfu to competent strain Pfu COM1 at 95C
01 COM1_WT.xlsx
01 com1vswt_normdata.xlsx

value: Harvested at 3-4x10^8 cell density

value: Grown at 95C

organism: Pyrococcus furiosus DSM 3638

source_name: Pfu WT

value: Wild-type P.furiosus


title: Patient 2, after 2 weeks of CC treatment

description: test

value: Male

value: cladribine, cyclophosphamide

value: Unmutated

value: Complete remission (CR)


title: Patient 2, before CC treatment

description: control

value: lymphocytes B

value: 0 days

value: negative


title: WT vs COM1 - Slide 1

description:
Slide 1 - dye flip comparing WT Pfu to competent strain Pfu COM1 at 95C
01 COM1_WT.xlsx
01 com1vswt_normdata.xlsx


title: Patient 1, after 2 weeks of CC treatment

description: test

value: 14 days


title: Patient 1, before CC treatment

description: control


title: cirrhosis [B174_placa96-3_G11]

tag: subject

value: hepatocellular carcinoma patient

tag: age (yrs)

tag: tumor stage

tag: tissue

value: liver

tag: tissue subtype

value: non-tumor cirrhosis

tag: sample type

value: fresh frozen tissue


title: Taxifol

status: Public on Mar 06 2015

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneChip 3000 scanner with G7 update.

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: HT1080 human fibrosarcoma cells were maintained in modified Eagle's medium (MEM) and NEAA (non-essential amino acids) + 10% FBS (foetal bovine serum) supplemented with 1% penicillin (100 U/ml) and streptomycin (100 μg/ ml), 1% sodium pyruvate and 1% L-glutamine. The cells were cultured in a humidified atmosphere with 5% CO2 at 37°C .

extract_protocol: RNA isolation from cell lines was performed using standard acid guanidinium thiocyanate-phenolchloroform extraction procedure. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: For every drug experiment, 80 µl of 3.125 × 106 cells/ml were placed in 6-well plates containing the medium. After 24 hours, the medium was replaced and the drugs or serum of patients treated with pycogenol were added to each well. The cultivated soft tissue sarcoma cells were incubated for 2 hours with the compounds or patient-serum.

tag: cell line

tag: treatment

value: taxifolin, 2h, 6.25 ng/ml


title: Resveratrol

value: resveratrol, 2h, 2195 ng/ml


title: pDC_IL3-Series_Medium_6h_R2

city: London

first: Raphael

last: Zollinger

state: London

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute (QMUL)

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: Data normalised in R using default settinsg of GCRMA package

label: biotin

source_name: Sorted pDC from healthy human buffy coats

label_protocol: Affymetrix double amplification

growth_protocol: After purification, cells where cultered for 6 or 24 hours in RPMI (Gibco) medium containing 10% FBS (Hyclone) at 37 degree Celsius and 5% CO2 containing environment.

extract_protocol: Qiagen Rneasy microkit with on-column DNAse digestion.

treatment_protocol: Treatment stimuli were given from the start of culture. Flu: Heat inactivated Inluenza virus at a concentration of 10E6 PFU/mL  GMCSF: Colony stimulating factor 2 (granulocyte-macrophage) recombinant cytokine at a concentration of 20ng/mL. LL37-DNA: Cathelicidin antimicrobial peptide LL-37 at 10 M mixed with purified DNA at 3 g/mL. Medium: Control, no stimulus.

tag: experiment series

tag: stimulus

value: medium

tag: time


title: pDC_IL3-Series_Medium_6h_R1


title: pDC_GMCSF-Series_Medium_6h_R3

value: GMCSF


title: pDC_GMCSF-Series_Medium_6h_R1


title: pDC_GMCSF-Series_Medium_24h_R3


title: pDC_GMCSF-Series_Medium_24h_R1


title: pDC_IL3-Series_IL3_and_Flu_6h_R2

value: LL37 and Flu


title: Control


title: pDC_GMCSF-Series_Medium_24h_R2


title: pDC_IL3-Series_IL3_and_Flu_6h_R1


title: pDC_IL3-Series_IL3_6h_R1


title: pDC_GMCSF-Series_LL37-DNA_6h_R3


title: Pycogenol

value: 5% pycnogenol-positive serum, 2h


title: Catechin

value: catechin, 2h, 11.25 ng/ml


title: Epicatechin

value: epicatechin, 2h, 6.25 ng/ml


title: pDC_IL3-Series_IL3_6h_R2


title: pDC_IL3-Series_Medium_6h_R3


title: pDC_IL3-Series_IL3_6h_R3


title: pDC_GMCSF-Series_LL37-DNA_6h_R1


title: pDC_GMCSF-Series_LL37-DNA_6h_R2


title: Pycnogenol control

value: 5% control serum, 2h


title: pDC_IL3-Series_Flu_6h_R1

value: Flu


title: pDC_IL3-Series_Flu_6h_R2


title: pDC_GMCSF-Series_LL37-DNA_24h_R2


title: pDC_GMCSF-Series_LL37-DNA_24h_R1


title: pDC_GMCSF-Series_LL37-DNA_24h_R3


title: CD3-CD56dimCD57brightNKG2A-NKG2C-, biological replicate4

city: Stockholm

first: Yenan

last: Bryceson

state: Sweden

address: Karolinska University Hospital Huddinge

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Following labeling, 500 ng of cDNA were hybridized at 45°C for 16 hr

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G

data_processing:
Analyses were performed with Affymetrix® Transcriptome Analysis Console (TAC) Software, using a gene-level normalization and signal summarization protocol
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.na33.1.hg19.transcript.csv
RMA normalized gene level expression values from Affymetrix® Transcriptome Analysis Console (TAC) Software

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

extract_protocol: Total RNA was isolate with Rneasy Kit (Qiagen).

tag: donor id

value: donor 4

value: PBMC

tag: cell subset


title: pDC_GMCSF-Series_GMCSF_and_LL37-DNA_6h_R2

value: GMCSF and LL37


title: pDC_GMCSF-Series_GMCSF_and_LL37-DNA_6h_R1


title: CD3-CD56dimCD57-NKG2A-NKG2C-, biological replicate4


title: pDC_IL3-Series_Flu_6h_R3


title: CD3-CD56dimCD57-NKG2A+, biological replicate4


title: pDC_GMCSF-Series_Medium_6h_R2


title: CD3-CD56dimCD57-NKG2A+, biological replicate3

value: donor 3


title: pDC_GMCSF-Series_GMCSF_and_LL37-DNA_6h_R3


title: pDC_GMCSF-Series_GMCSF_and_LL37-DNA_24h_R2


title: CD3-CD56dimCD57brightNKG2A-NKG2C-, biological replicate2

value: donor 2


title: pDC_GMCSF-Series_GMCSF_and_LL37-DNA_24h_R3


title: pDC_GMCSF-Series_GMCSF_and_Flu_6h_R3

value: GMCSF and flu


title: CD3-CD56dimCD57-NKG2A+, biological replicate2


title: pDC_GMCSF-Series_GMCSF_and_Flu_24h_R3


title: CD3-CD56dimCD57brightNKG2A-NKG2C+, biological replicate3


title: CD3-CD56dimCD57brightNKG2A-NKG2C+, biological replicate1

value: donor 1


title: CD3-CD56dimCD3-CD56dimCD57-NKG2A-NKG2C-, biological replicate2


title: pDC_GMCSF-Series_GMCSF_and_Flu_6h_R2


title: CD3-CD56dimCD57brightNKG2A-NKG2C+, biological replicate2


title: CD3-CD56dimCD57-NKG2A+, biological replicate1


title: pDC_GMCSF-Series_GMCSF_and_Flu_6h_R1


title: pDC_GMCSF-Series_GMCSF_and_LL37-DNA_24h_R1


title: CD3-CD56dimCD57-NKG2A-NKG2C-, biological replicate3


title: pDC_GMCSF-Series_GMCSF_6h_R3


title: CD3-CD56dimCD57brightNKG2A-NKG2C-, biological replicate3


title: pDC_GMCSF-Series_GMCSF_6h_R2


title: pDC_GMCSF-Series_GMCSF_and_Flu_24h_R1


title: pDC_GMCSF-Series_GMCSF_and_Flu_24h_R2


title: CD3-CD56dimCD57-NKG2A-NKG2C-, biological replicate1


title: pDC_GMCSF-Series_GMCSF_24h_R2


title: UIII_expression_rep2

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
UIII cell line under 0.1 nM R5020 treatment during 45 min, biological replicate 2
UIII_r2

hyb_protocol: Hybridization mix was laid onto each sector of subarray gasket slide and sandwiched against a 22K format oligonucleotide microarray (Rat Sureprint GE 22k Microarray, Agilent design ID 011868) inside a hybridization chamber which was hybridized overnight at 65ºC in a rotisserie oven rotating at 10 rpm for a total of 17 hours. Subsequently array chambers were disassembled submerged in Agilent Gene Expression Buffer 1 and washed 1 minute in another dish with the same solution with a magnetic stirrer at 200 rpm at room temperature, followed by 1 minute in gilent Gene Expression Buffer 2 with a magnetic stirrer at 200 rpm at 37ºC and immediate withdrawal from the solution and air drying.

scan_protocol: Fluorescent signal was captured into TIF images with an Agilent scanner using recommended settings (16 bit, 10 um resolution, 100% PMT and 100% laser power) with Scan Control software (Agilent).

data_processing: Signal intensities were extracted into a tabulated text file using GenPix software (Agilent) using the appropriate array configuration and annotation files. The normalized log2intensities were obtained using the lowess method with normexp background correction,  and chips were made comparable by quantile scaling of the log2ratios using the Bioconductor Limma package in R.

organism: Rattus norvegicus

source_name: uterine endometrial stromal cells UIII

label_protocol: For each sample 500 ng of total RNA were reversed transcribed into cDNA with a T7 promoter and the cDNA was in vitro transcribed into cRNA in the presence of Cy3-CTP using the Low RNA input labeling kit (Agilent). Labelled samples were purified using RNeasy mini spin columns (Qiagen) and yield and specific activity were assessed by spectrophotometry (Nanodrop) and confirmed to be within specifications (>825 ng and >6 pmol Cy3/ug cRNA). 600 ng of cRNA were preblocked and fragmented in Agilent fragmentation buffer and mixed with  Agilent GEx Hybridization mix.

growth_protocol: UIII rat normal uterine stromal cells were maintained in M199 medium supplemented with 10% fetal bovine serum (FBS) and gentamycin (100 ug/ml) at 37°C in humidified 95% air with 5% CO. Culture media were changed every 2 days.

extract_protocol: Total RNA was extracted using High Pure RNA isolation kit (Roche) according to the manufacturer's instructions. cDNA was obtained from 100 ng of total RNA using SuperScript VILO cDNA synthesis (Invitrogen). High RNA integrity was assessed by Bioanalyzer nano 6000 assay with RIN numbers >8

treatment_protocol: Cells were cultured in media supplemented with FBS and, 48 h later, media were replaced by fresh M199 without serum. After three days in serum-free conditions, media were replaced by either vehicle or hormones.

value: female

value: non-transformed uterine endometrial stroma

tag: agent

value: progestin R5020

value: control


title: pDC_IL3-Series_IL3_and_Flu_6h_R3

value: LL37 and Flu


title: pDC_GMCSF-Series_GMCSF_24h_R1

value: GMCSF


title: pDC_GMCSF-Series_GMCSF_24h_R3


title: CD3-CD56dimCD57brightNKG2A-NKG2C-, biological replicate1


title: pDC_GMCSF-Series_GMCSF_6h_R1


title: H3-HA(pInv)_2h_A

type: genomic

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

description:
H3-HA(pInv), 2h
Results reported in:
H3HA_2h_0h_2004_dup_signal.bar
H3HA_2h_0h_2004_A_signal.bar

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL.files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. Two sample comparisons of immunoprecipitated (strain 1) vs. immunoprecipitated (strain 2), quantile normalization (separate) and linear scaling to 100 was applied. Probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2004) and reported in BAR files.
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for relative enrichment (WT vs. set9, or 2h vs. 0h) for each probe.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: H3-HA(pInv), 2h

label_protocol: A specific sequence tag was attached to immunoprecipitated DNA fragments by PCR using sequenase and random primers (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'). This DNA was amplified using Taq polymerase and a primer recognizing the specific sequence tag (5'-GTTTCCCAGTCACGATC-3') in the precence of 5 mM dUTP. PCR products were purified using Qiaquick PCR purification kit. DNA was fragmented by UDG and APE nuclease treatment and labelled with biotin by Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols. Immunoprecipitation Assay Protocol

growth_protocol: Liquid cultures were grown in YES media shaking at 180 rpm at 30 °C (or 25°C for Hu2549).

extract_protocol: Immunoprecipitation was done using indicated antibody from chromatin extracts prepared from mid-logarithmic phase cells. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine, and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 600 bp were collected. Chromatin was immunoprecipitated with indicated antibody for 2 hours and incubated with protein A agarose beads for 1 hour. The beads were washed, chromatin eluted at with TES at 65C and crosslinks reversed at 65C over night, together with input samples. Proteins were digested with proteinase K and immunoprecipitated DNA recovered using QIAquick PCR Purification kit.

tag: strain

tag: genotype

tag: chip antibody

value: HA (abcam ab9110, lot GR98618-1)

value: ChIP DNA

value: 4h 8% glucose + 2h 4% sucrose


title: H3-HA(pInv)_2h_B

description:
H3-HA(pInv), 2h
Results reported in:
H3HA_2h_0h_2004_dup_signal.bar
H3HA_2h_0h_2004_B_signal.bar


title: pDC_GMCSF-Series_Flu_6h_R3

value: Flu


title: H3-HA(pInv)_0h_A

description:
H3-HA(pInv), 0h
Results reported in:
H3HA_2h_0h_2004_dup_signal.bar
H3HA_2h_0h_2004_A_signal.bar

source_name: H3-HA(pInv), 0h

value: 4h 8% glucose


title: pDC_GMCSF-Series_Flu_6h_R2


title: UIII_expression_rep3

description:
UIII cell line under 0.1 nM R5020 treatment during 45 min, biological replicate 3
UIII_r3

tag: gender


title: pDC_GMCSF-Series_Flu_24h_R2


title: Hypoth_vehicle_8weeks_rep1

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: 5.5 μg of each fragmented cDNA was end-labeled with biotin and hybridized to a Mouse 430.2.0 Microarray (Affymetrix, Santa Clara, CA, USA) according to manufacturer’s instructions.

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

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

organism: Mus musculus

source_name: Hypothalamus from vehicle treated mouse

label_protocol: Total RNA (100 ng) was used to perform target preparation using WT Expression Kit (Ambion).

growth_protocol: Dicer cKO (Cre+/Dicerlox/lox) were obtained by crossing hemizygotes Camk2a-CreERT2 (Cre+) animals with homozygote Dicer floxed (Dicerlox/lox) mice. Both lines were created on a mixed 129/SvxC57BL/6 and maintained on a C57BL/6J background by backcrossing to C57BL/6J animals for at least 9 generations. Camk2a-CreERT2 mice were purchased from Jackson laboratory (Bar Habor, USA; Stock Number 012362) and Dicerlox/lox (Jackson stock number 006366) were provided by Pr. David Gatfield, University of Lausanne, Switzerland. All experiments were approved by the Ethical Committee of the State of Vaud Veterinary Office, Switzerland.

extract_protocol: Immediately after sacrifice, cortex, hypothalamus, and hippocampus were extracted, flash frozen and kept at -80°C until tissue processing. Brain tissues were homogenized in QIAzol Lysis Reagent (Qiagen, Hombrechtikon, Switzerland). Total RNA was extracted and purified using the RNeasy Lipid Tissue Mini Kit 50 (Qiagen, Hombrechtikon, Switzerland) according to manufacturer’s instructions. All RNA sample amounts were measured with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, USA) and the quality of RNA samples was verified on Agilent 2100 bioanalyzer chips (Agilent technologies, Basel, Switzerland.

treatment_protocol: After crossing the above mentioned mouse lines and selecting Cre+;Dicerlox/lox offspring mice, recombination was induced in the adult by treatment with the exogenous oestrogen receptor ligand Tamoxifen, according to Metzger and Chambon, 2011. 8 weeks old animals were injected intraperitoneally with 1mg of tamoxifen (100µl) twice a day during five consecutive days. At the end of the five days, each mouse received a total dose of 10mg of tamoxifen. Control animals were injected with 100µl of sunflower seed oil/ethanol mixture (vehicle) at the same frequency.

value: vehicle

value: 8 weeks

value: Hypothalamus


title: UIII_expression_rep2_DyeSwap

description:
UIII cell line under 0.1 nM R5020 treatment during 45 min, biological replicate 2, Dye swap.
UIII_r2_DS


title: Hypoth_vehicle_8weeks_rep2


title: pDC_GMCSF-Series_Flu_24h_R3


title: Hypoth_tamox_8weeks_rep2

source_name: Hypothalamus from tamoxifen treated mouse

value: tamoxifen


title: pDC_GMCSF-Series_Flu_6h_R1


title: Hypoth_vehicle_8weeks_rep3


title: Hypoth_tamox_8weeks_rep3


title: Hypoth_vehicle_4weeks_rep3

value: 4 weeks


title: Hypoth_tamox_8weeks_rep1


title: Hypoth_vehicle_4weeks_rep1


title: UIII_expression_rep4

description:
UIII cell line under 0.1 nM R5020 treatment during 45 min, biological replicate 4
UIII_r4


title: H3-T7(RITE)_2h_A

description:
H3-T7(RITE), 2h
Results reported in:
T7_2_0h_signal.bar
T7_2_0h_A_2004_signal.bar

source_name: H3-T7(RITE), 2h

value: H3.2-lox-HA-hygR-Lox-T7, cdc25-22 (ts)

value: T7 (EMD chemicals 69522, lot D00137263

value: 36°C (5h) + estradiol (2h)


title: H3-T7(RITE)_0h_B

description:
H3-T7(RITE), 0h
Results reported in:
T7_2_0h_signal.bar
T7_2_0h_B_2004_signal.bar

source_name: H3-T7(RITE), 0h


title: H3-HA(RITE)_2h_B

description:
H3-HA(RITE), 2h
Results reported in:
HA_2_0h_signal.bar
HA_2_0h_B_2004_signal.bar

source_name: H3-HA(RITE), 2h


title: H3-HA(pInv)_0h_B

description:
H3-HA(pInv), 0h
Results reported in:
H3HA_2h_0h_2004_dup_signal.bar
H3HA_2h_0h_2004_B_signal.bar


title: pDC_GMCSF-Series_Flu_24h_R1


title: Hypoth_vehicle_4weeks_rep2


title: H3-HA(RITE)_2h_A

description:
H3-HA(RITE), 2h
Results reported in:
HA_2_0h_signal.bar
HA_2_0h_A_2004_signal.bar


title: Hypoth_tamox_4weeks_rep3


title: H3-HA(RITE)_0h_B

description:
H3-HA(RITE), 0h
Results reported in:
HA_2_0h_signal.bar
HA_2_0h_B_2004_signal.bar

source_name: H3-HA(RITE), 0h


title: Hippo_vehicle_8weeks_rep3

source_name: Hippocampus  from vehicle treated mouse

value: Hippocampus


title: Hypoth_tamox_4weeks_rep1


title: input_set9D

description:
input DNA, WT
Input files not used for comparisons, and therefore only provided as CEL files for reference.

source_name: input DNA, WT

value: input DNA


title: H4K20me3_set9D_B

description:
ChIP DNA, set9D, H4K20me3
Results reported in:
H4K20me3WT_set9_signal.bar

source_name: ChIP DNA, set9D, H4K20me3


title: Hippo_tamox_8weeks_rep3

source_name: Hippocampus  from tamoxifen treated mouse


title: H3-T7(RITE)_2h_B

description:
H3-T7(RITE), 2h
Results reported in:
T7_2_0h_signal.bar
T7_2_0h_B_2004_signal.bar


title: H4K20me1_set9D_A

description:
ChIP DNA, set9D, H4K20me1
Results reported in:
H4K20me1WT_set9_signal.bar

source_name: ChIP DNA, set9D, H4K20me1


title: input_WT

value: WT


title: H4K20me2_WT_B

description:
ChIP DNA, WT, H4K20me2
Results reported in:
H4K20me2WT_set9_signal.bar
H4K20me2WT_set9_B_signal.bar

source_name: ChIP DNA, WT, H4K20me2


title: Hippo_tamox_8weeks_rep2


title: H4K20me3_WT_A

description:
ChIP DNA, WT, H4K20me3
Results reported in:
H4K20me3WT_set9_signal.bar
H4K20me3WT_set9_A_signal.bar

source_name: ChIP DNA, WT, H4K20me3


title: Hippo_vehicle_4weeks_rep3


title: Hippo_vehicle_4weeks_rep2


title: Hippo_tamox_8weeks_rep1


title: H3-HA(RITE)_0h_A

description:
H3-HA(RITE), 0h
Results reported in:
HA_2_0h_signal.bar
HA_2_0h_A_2004_signal.bar


title: Hippo_tamox_4weeks_rep3


title: H4K20me1_WT_B

description:
ChIP DNA, WT, H4K20me1
Results reported in:
H4K20me1WT_set9_signal.bar
H4K20me1WT_set9_B_signal.bar

source_name: ChIP DNA, WT, H4K20me1


title: H4K20me2_WT_A

description:
ChIP DNA, WT, H4K20me2
Results reported in:
H4K20me2WT_set9_signal.bar
H4K20me2WT_set9_A_signal.bar


title: Hippo_tamox_4weeks_rep1


title: H4K20me1_WT_A

description:
ChIP DNA, WT, H4K20me1
Results reported in:
H4K20me1WT_set9_signal.bar
H4K20me1WT_set9_A_signal.bar


title: H4K20me2_set9D_B

description:
ChIP DNA, set9D, H4K20me2
Results reported in:
H4K20me2WT_set9_signal.bar

source_name: ChIP DNA, set9D, H4K20me2


title: Hippo_tamox_4weeks_rep2


title: Cortex_vehicle_8weeks_rep3

source_name: Cortex from vehicle treated mouse

value: Cortex


title: Hippo_vehicle_8weeks_rep1


title: Hippo_vehicle_8weeks_rep2


title: H4K20me3_WT_B

description:
ChIP DNA, WT, H4K20me3
Results reported in:
H4K20me3WT_set9_signal.bar
H4K20me3WT_set9_B_signal.bar


title: Slide 347284

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

description: Sample 1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the GenePix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with GenePix 6. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background-subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: wild type grown in SM17

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown in SM17 or M17 medium and harvested at OD600 of 0.15.

extract_protocol: RNA was isolated and purified using the High Pure RNA Isolation kit (Roche Diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche Diagnostics). RNA was isolated from three replicate cultures.

tag: strain/background

tag: genotype/variation

value: wild type

tag: medium

value: M17 + 0.5% sialic acid (SM17)

source_name: wild type grown in M17


title: Slide 347286

description: Sample 2


title: Slide 347334

description: Sample 2

data_processing: Dual-channel array images were analyzed with GenePix 6. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background-subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of ccpA mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

source_name: ccpA mutant grown in SM17

growth_protocol: Cells were grown in SM17 medium and harvested at OD600 of 0.15.

value: ccpA mutant


title: Cortex_vehicle_8weeks_rep1

tag: tissue


title: Slide 345310

description: Sample 1


title: Slide 345223

description: Sample 2

source_name: ccpA mutant grown in GM17

growth_protocol: Cells were grown in GM17 medium and harvested at OD600 of 0.15.

source_name: wild type grown in GM17


title: Cortex_vehicle_4weeks_rep3


title: Cortex_tamox_8weeks_rep2

source_name: Cortex from tamoxifen treated mouse


title: Cortex_tamox_8weeks_rep1


title: Slide 346913

description: Sample 1


title: Cortex_vehicle_4weeks_rep2


title: Cortex_tamox_4weeks_rep3


title: Cortex_vehicle_4weeks_rep1


title: Cortex_tamox_8weeks_rep3


title: Hypoth_tamox_4weeks_rep2

source_name: Hypothalamus from tamoxifen treated mouse


title: Cortex_vehicle_8weeks_rep2


title: Slide 347298

description: Sample 2

data_processing: Dual-channel array images were analyzed with GenePix 6. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background-subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of nanR mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

source_name: nanR mutant grown in SM17

value: nanR mutant


title: Slide 347281

description: Sample 1


title: Hu_12Opcw_INPUT_rep2

type: SRA

city: New Haven

first: Steven

middle: K

last: Reilly

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

library_source: genomic

data_processing:
Bowtie (v0.12.9), cd /panfs/sequencers/sequencerP/runs/131130_SN356_0279_BC30AWACXX/Data/Intensities/BaseCalls/Unaligned-Skr2/Project_Skr2/Sample_SR_40_Index5; zcat *.gz > ~/Scratch/Steve/Hu_12Fpcw_INPUT_rep1.fastq; source ~/.bashrc; cd ~/Scratch/Steve/; bowtie -q -n 2 -l 28 -m 1 -p 8 -5 1 -3 5 -t /home/jl56/GENOME/hg19/dna/hg19_nh ./Hu_12Fpcw_INPUT_rep1.fastq ./Hu_12Fpcw_INPUT_rep1.bowtie
Custom perl script , Cotney et al, Cell 2013.
RSEQTools (0.6.0), cat Hu_12Fpcw_INPUT_rep1.bowtie | bowtie2mrf genomic > ../mrf/Hu_12Fpcw_INPUT_rep1.mrf
RSEQTools (0.6.0) and wigToBigWig, cat Hu_12Fpcw_INPUT_rep1.mrf | mrf2wig Hu_12Fpcw_INPUT_rep1; cat Hu_12Fpcw_INPUT_rep1_chr*.wig | grep -v track > Hu_12Fpcw_INPUT_rep1.wig;  wigToBigWig -clip Hu_12Fpcw_INPUT_rep1 /home/jl56/GENOME/hg19/dna/hg19_nh.chrom.sizes Hu_12Fpcw_INPUT_rep1.bw
Genome_build: hg19 for human samples,  Gencode V10 gene annotation
Supplementary_files_format_and_content: bigWig (signal tracks)
Supplementary_files_format_and_content: bed (peak calls)

source_name: Human 12 p.c.w. Embryonic Occipital Cortex

growth_protocol: Human brain tissue and rhesus brain tissue were thawed and micro dissected.

extract_protocol:
Nuclei were extracted in six pellet volumes of lysis buffer I (50 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubating on ice for 15 minutes.  Tissue was homogenized with a dounce homogenizer and nuclei were harvested by centrifugation at 2000g for 10 minutes at 4°C.  Nuclei were resuspended in five pellet volumes of nuclear lysis buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubated on ice for 20 minutes.  300 mL nuclear lysates in 1.5 mL tubes were sonicated using a Misonix S4000 with 431A cup horn (10 second pulses, 10 second rest, 20 minutes total, 2°C maintained by circulating chiller).  Following sonication insoluble material was pelleted by centrifugation at 16000g for 10 minutes at 4°C.  A small sample of soluble crosslinked chromatin was purified, checked for correct sonication size range and DNA concentration was measured. For H3K27ac, 10-25 ug of chromatin was diluted to 450 mL with dilution buffer (16.7 mM Tris pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and added to 50 uL of Protein G Dynabeads (Invitrogen) prebound with 2 mg of H3K27ac antibody.For H3K4me2, 10-25 ug of chromatin was diluted to 450 mL with dilution buffer (16.7 mM Tris pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 1x Roche Complete Protease inhibitor) and added to 50 uL of Protein G Dynabeads (Invitrogen) prebound with 10 mg of H3K4me2 antibody.  Samples were incubated overnight at 4°C with rotation.  Beads were precipitated on magnet stand and washed eight times with 1 mL of wash buffer (100 mM Tris pH8.0, 500 mM LiCl, 1% NP-40, 1% deoxycholic acid, 1x Roche Complete protease inhibitor) and once with TE.  Immunoprecipiated chromatin was eluted from beads with 50 mL of elution buffer (TE + 1% SDS) at 65°C for 10 minutes.  Crosslinks were reversed overnight at 65°C.  Chromatin was treated with RNAseA and proteinase K then purified with Qiagen PCR cleanup kit.  Concentration of eluted chromatin was measured with PicoGreen (Invitrogen).
Standard Illumina Multiplexed Paired-End Library Prep

treatment_protocol: All tissues  were briefly homogenized and crosslinked with 1% formaldehyde at room temperature with rotation for 15 minutes.  Crosslinking was quenched with 150 mM glycine. Tissue were harvested by centrifugation at 1500g for 5 min at 4C.   Pelleted tissue was washed twice with cold PBS, flash frozen and stored at -80°C.

tag: developmental stage

value: 12 post conception weeks

value: Embryonic Occipital Cortex

tag: experiment type

value: ChIP-seq


title: Hu_12Opcw_INPUT_rep1


title: Hu_12Opcw_H3K4me2_rep2

value: H3K4me2 (Millipore 07-030)


title: Cortex_tamox_4weeks_rep1

value: tamoxifen


title: DAPT-treated mammospheres, biological rep2

city: Berlin

first: Linxiang

last: Lan

address: Robert-Roessle-Str. 10

department: Cancer Research Program

institute: Max-Delbrueck-Center for Molecular Medicine

description:
JJQ--11-DAPT2-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with DAPT.

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The chips were scanned on an Affymetrix GeneChip Scanner.

data_processing: Array data were analyzed using Expression Console and were normalized with MAS5.0. Normalized data were used for calculating fold changes of deregulated genes using Student's test. Only genes with a false discovery rate (FDR) adjusted p-value <0.05 and at least 1.5 fold differential expression were included in the analysis.

source_name: mammospheres, DAPT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit, Affymetrix).

growth_protocol: Primary mammary tumor cells were cultured as mammospheres under the serum-free, non-attached conditions containing EGF, FGF and B27.

extract_protocol: Trizol extraction of total RNA and subsequent purification by QIAGEN RNeasy Kits was performed according to the manufacturer's instructions.

treatment_protocol: Mammospheres were cultured for 10 days, treated with various inhibitors for 2 days and collected for RNA isolation.

value: FVB/N

value: MMTV-PyMT

tag: cell type

value: primary mammary tumor cells

tag: treatment

value: DAPT (Notch inhibitor)


title: TAE226-treated mammospheres, biological rep3

description:
JJQ--24-TAE2263-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with TAE226.

source_name: mammospheres, TAE226

value: TAE226 (Fak inhibitor)


title: PP2-treated mammospheres, biological rep2

description:
JJQ--26-PP22-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with PP2.

source_name: mammospheres, PP2

value: PP2 (Src inhibitor)


title: Cortex_tamox_4weeks_rep2

value: 4 weeks


title: U0126-treated mammospheres, biological rep3

description:
JJQ--15-U01263-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with U0126.

source_name: mammospheres, U0126

value: U0126 (Mek1 inhibitor)


title: Control mammospheres, biological rep3

description:
JJQ--09-DMSO3-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with vehicle.

source_name: mammospheres, vehicle

value: vehicle


title: Hu_12Opcw_H3K4me2_rep1


title: DAPT-treated mammospheres, biological rep3

description:
JJQ--12-DAPT3-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with DAPT.


title: DAPT-treated mammospheres, biological rep1

description:
JJQ--10-DAPT1-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with DAPT.


title: Control mammospheres, biological rep2

description:
JJQ--08-DMSO2-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with vehicle.


title: TAE226-treated mammospheres, biological rep2

description:
JJQ--23-TAE2262-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with TAE226.


title: TAE226-treated mammospheres, biological rep1

description:
JJQ--22-TAE2261-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with TAE226.


title: PP2-treated mammospheres, biological rep3

description:
JJQ--27-PP23-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with PP2.


title: U0126-treated mammospheres, biological rep1

description:
JJQ--13-U01261-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with U0126.


title: Hu_12Opcw_H3K27ac_rep2

value: H3K27ac (Abcam ab4729)


title: U0126-treated mammospheres, biological rep2

description:
JJQ--14-U01262-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with U0126.


title: PP2-treated mammospheres, biological rep1

description:
JJQ--25-PP21-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with PP2.


title: Hu_12Fpcw_INPUT_rep2

source_name: Human 12 p.c.w. Embryonic Frontal Cortex

value: Embryonic Frontal Cortex


title: Hu_12Opcw_H3K27ac_rep1


title: Hu_12Fpcw_INPUT_rep1


title: Hu_12Fpcw_H3K4me2_rep2


title: Data 206 Area 3

city: Quebec

first: Annie

last: Girard

state: Quebec

address: 2440, boul. Hochelaga

department: Sciences animales

country: Canada

institute: Université Laval

hyb_protocol: Samples were prepared with Gene Expression Hybridization Kit (Agilent, Santa Clara, CA) then hybridized onto Agilent-manufactured EmbryoGENE bovine microarray slides, using Agilent hybridization chambers.

scan_protocol: Microarray slides were read by the Tecan’s PowerScanner with the Autogain procedure on each individual array.

data_processing: Images were processed with Array-Pro Analyzer 6.4 (Media Cybernetics, Rockville, MD) and the FlexArray software (1.6.1) was used for normalization and correction of the background.

organism: Bos taurus

label_protocol: 825 ng of total RNA from each sample was labelled with ULS Fluorescent Labelling Kit for Agilent arrays (Kreatech Inc., Durham, NC).

growth_protocol: Dominant follicles were collected from slaughterhouse ovaries. Diameter was measured on ovary surface and follicles >9mm were collected.

extract_protocol:
Total RNA was extracted using PicoPure RNA Isolation kit (Life Technologies Inc., Burlington, ON).
[amp protocol] Linear amplification was done using RiboAmp HSPlus RNA Amplification Kit (Life Technologies Inc., Burlington, ON) .

treatment_protocol: Flow cytometry (FlowJo software) was used to classifiy the follicles among the three growth stages (growing, plateau and atresia).

tag: breed (cattle)

value: Holstein

value: ovary

tag: follicular size

value: > 9 mm

tag: cell collection method

value: dissection

tag: follicular status

value: plateau phase

value: granulosa cell

value: atretic phase


title: Data 206 Area 2


title: Data 206 Area 4


title: Control mammospheres, biological rep1

description:
JJQ--07-DMSO1-260712-430-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with vehicle.

value: FVB/N

value: MMTV-PyMT


title: Hu_12Fpcw_H3K27ac_rep2

value: 12 post conception weeks

value: ChIP-seq


title: Data 205 Area 3


title: Hu_8_5pcw_INPUT_rep2

source_name: Human 8.5 p.c.w. Embryonic Cortex

value: 8.5 post conception weeks


title: Hu_12Fpcw_H3K27ac_rep1


title: Hu_8_5pcw_H3K4me2_rep2

value: Embryonic Cortex

value: H3K4me2 (Millipore 07-030)


title: Hu_8_5pcw_H3K4me2_rep1


title: Hu_8_5pcw_INPUT_rep1


title: Hu_8_5pcw_H3K27ac_rep2


title: Hu_7pcw_INPUT_rep2

source_name: Human 7 p.c.w. Embryonic Cortex

value: 7 post conception weeks


title: Hu_8_5pcw_H3K27ac_rep1

value: H3K27ac (Abcam ab4729)


title: Hu_12Fpcw_H3K4me2_rep1

value: Embryonic Frontal Cortex


title: Data 206 Area 1

value: Holstein


title: Data 205 Area 1

value: ovary


title: Data  204 Area 2

value: > 9 mm

value: growing phase


title: Hu_7pcw_INPUT_rep1


title: Data  203 Area 1

value: dissection


title: Data 205 Area 2

value: granulosa cell

value: plateau phase


title: Data  204 Area 3

value: atretic phase


title: Data 205 Area 4


title: Data  203 Area 3


title: Data  203 Area 2


title: Hu_7pcw_H3K4me2_rep1


title: Data  203 Area 4


title: Data 248 Area 1 Cvs A4.2


title: Data  204 Area 1


title: Hu_7pcw_H3K4me2_rep2


title: Hu_7pcw_H3K27ac_rep2


title: Hu_7pcw_H3K27ac_rep1


title: Data 198 Area4


title: Data 198 Area3


title: Replicate 2, Unlabeled, Baseline, LysN Peptide Library Protocol

city: Boston

first: Catherine

middle: J

last: Wu

state: MA

address: 450 Brookline Ave.

institute: Dana Farber Cancer Institute

hyb_protocol: Light- standard and heavy/medium-labeled sample lysates were then combined in a 1:1 protein ratio (20µg each and therefore 40µg total). Protein disulfide bonds of the combined lysates were reduced for 45 min with 5 mM dithiothreitol (Thermo Scientific, 20291) and alkylated for 45 min with 10 mM iodoacetamide. Samples were then diluted 1:4 with 50 mM Tris HCl, pH 8.0, to reduce the urea concentration to <2 M. Lysates were digested overnight at room temperature with trypsin, or AspN, or LysN (depending on the experiment) in a 1:50 enzyme-to-substrate ratio (Promega, V511X) on a shaker. Peptide mixtures were acidified to a final volumetric concentration of 1% formic acid (Fluka, 56302) and centrifuged at 10,000g for 5 min to pellet urea that had precipitated out of solution. The peptide mixtures were fractionated by Strong Cation Exchange (SCX) using StageTips as previously described (8) with slight modifications. Briefly, one StageTip was prepared per sample by 3 SCX discs (3M, #2251) topped with 2 C18 discs (3M, #2215). The packed StageTips were first washed with 100µl methanol and then with 100 µl 80% acetonitrile and 0.5% acetic acid. Afterwards they were equilibrated by 100µl 0.5% acetic acid and the sample was loaded onto the discs. The sample was transeluted from the C18 discs to the SCX discs by applying 100µl 80% acetonitrile; 0.5% acetic acid, which was followed by 6 stepwise elutions and collections of the peptide mix from the SCX discs. The first fraction was eluted with 50µl 50mM NH4AcO; 20% MeCN (pH 4.1, adjusted with acetic acid), the second with 50µl 50mM NH4AcO; 20% MeCN (pH 5 4.8, adjusted with acetic acid), the third with 50µl 50mM NH4AcO; 20% MeCN (pH 6.2, adjusted with acetic acid), the fourth with 50µl 50mM NH4AcO; 20% MeCN (pH 7.2), the fifth with 50µl 50mM NH4HCO3; 20% MeCN (pH 8.5) and the sixth with 50µ l 0.1% NH4OH; 20% MeCN (pH 9.5). 200µl of 0.5% acetic acid was added to each of the 6 fractions and they were subsequently desalted on C18 StageTips as previously described (8) and evaporated to dryness in a vacuum concentrator. Peptides were reconstituted in 7µl 3% MeCN/0.1% formic acid (at an estimated concentration of 1µg/µl).

scan_protocol: LC-MS/MS

data_processing:
All mass spectra were analyzed with MaxQuant software version 1.3.5 using the mouse UniProt database (March 2013). MS/MS searches for the proteome data sets were performed with the following parameters: Oxidation of methionine and protein Nterminal acetylation as variable modifications; carbamidomethylation as fixed modification. Trypsin/P was selected as the digestion enzyme for the pulsed-SILAC experiments and either LysN or AspN was selected as the digestion enzyme for the additional protein quantification experiments for time 0h, and a maximum of 3 labeled amino acids and 2 missed cleavages per peptide were allowed. The mass tolerance for precursor ions was set to 20 p.p.m. for the first search (used for nonlinear mass recalibration) and 6 p.p.m. for the main search. Fragment ion mass tolerance was set to 20 p.p.m. The IBAQ feature was enabled in order to estimate relative proteins levels. For identification we applied a maximum FDR of 1% separately on the protein and peptide level. We required 2 or more unique/razor peptides for protein identification and a ratio count of 2 or more for protein quantification per replicate measurement.
We constructed “analysis groups” using the following rules:   1. All transcripts in the same transcript group are in the same analysis group, where transcript groups are defined by the UCSC Table Browser (query settings: assembly=”July 2007 (NCBI37/mm9)”, group=”Gene and Gene Predictions”, track=”UCSC Genes”, table=”knownIsoforms”; see the fields “clusterID” and “transcript”) and represent groups of transcripts (isoforms) that are derived from the same genic locus and cannot easily be resolved.   2. All proteins in the same MaxQuant protein group are in the same analysis group, where MaxQuant determines protein groups on the basis of the peptide library supplied. The groups represent the level of ambiguity MaxQuant can confidently resolve.   3. If a protein and a transcript are associated with one another, then they are in the same analysis group, where we associate (one or more) Uniprot protein ID with (one or more) UCSC transcript ID based on ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_ organism/MOUSE_10090_idmapping.dat
Expression estimates were based on MaxQuant’s un-normalized M/L and H/L ratios per protein group. For each protein and replicate, we scaled the ratio by the mean IBAQ L channel intensity observed for that protein across all conditions and time points (treating missing values as zeroes). Analysis groups were named according to the concatenation of all unique gene symbols associated with the UCSC transcripts in the analysis group.
Analysis groups (henceforth referred to as genes for simplicity) were excluded if they were not MS2-identified in at least 6 of the 10 time points in all conditions (time courses for LPS and MOCK stimulation), channels, and replicates. After applying this filter, we also excluded genes that did not have positive RNA-Seq values for at least 6 out of the 10 time points in all conditions and channels. These filters were not applied to the AspN or LysN data. We renormalized such that at each condition/time point the RNA-Seq expression values added up to exactly 1,000,000. Meanwhile, we normalized the protein data such that at each condition/time point protein (M+H) IBAQ values added up to exactly 1,000,000 (missing values were treated as zeroes).

label: Unlabeled

source_name: bone marrow-derived primary dendritic cells

label_protocol: See growth protocol

growth_protocol: GM-CSF-derived BMDCs were grown and selected in media containing medium- heavy L-arginine 13C6 (Arg6) and L-lysine 2H4 (Lys4) (Sigma). Just prior to LPS or MOCK stimulation, all cells were pooled, pelleted and re-suspended in media containing heavy L-arginine 13C6-15N4 (Arg10) and heavy L-lysine 13C6-15N2 (Lys8) (Sigma) and plated at 106 cells/ml on non-tissue culture treated Petri dishes. In parallel, GM-CSF derived BMDCs were grown in light L-arginine (Arg) and L-lysine (Lys) (Sigma) containing media. Concentrations for L-arginine and L-lysine were 42 mg/l and 40 mg/l, respectively. The cell culture media, RPMI-1640 deficient in L-arginine and L-lysine, was a custom media preparation from Caisson Laboratories (North Logan, UT) and dialyzed serum was obtained from SAFC-Sigma. We followed all standard SILAC media preparation and labeling steps as previously described (Ong and Mann, Nature Protocols, 2006).

extract_protocol: After stimulation (LPS or MOCK) and the appropriate time points, cells were washed twice with PBS and lysed for 30 min in ice-cold lysis urea buffer (8 M urea; 75 mM NaCl, 50 mM Tris HCl pH 8.0, 1 mM EDTA, 2 µg/mL aprotinin (Sigma, A6103), 10 µg/mL leupeptin (Roche, #11017101001), 1 mM PMSF (Sigma, 78830)). Lysates were centrifuged at 20,000g for 10 min, and protein concentrations of the clarified lysates were measured via BCA assay (Pierce). From this procedure, DC lysates produced ~100µg of protein per 1 million cells.

treatment_protocol: At day 9, cells were stimulated for various time points with LPS (100ng/ml, rough, ultrapure E. coli K12 strain, Invitrogen) or MOCK (= no stimulation).

value: female

value: mock-stimulated

tag: enzyme

value: LysN


title: H3-T7(RITE)_0h_A

description:
H3-T7(RITE), 0h
Results reported in:
T7_2_0h_signal.bar
T7_2_0h_A_2004_signal.bar

source_name: H3-T7(RITE), 0h

tag: strain

value: H3.2-lox-HA-hygR-Lox-T7, cdc25-22 (ts)

value: T7 (EMD chemicals 69522, lot D00137263

tag: sample type

value: ChIP DNA


title: Replicate 1, Unlabeled, Baseline, LysN Peptide Library Protocol


title: Replicate 1, Unlabeled, Baseline, AspN Peptide Library Protocol

value: AspN


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 24h

label: SILAC H

value: LPS-stimulated

value: Trypsin


title: Replicate 2, Unlabeled, Baseline, AspN Peptide Library Protocol


title: Data 198 Area2

value: Holstein


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 12h


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 9h


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 6h


title: Data 197 Area4

value: ovary


title: Data 198 Area1

value: > 9 mm


title: Hippo_vehicle_4weeks_rep1

source_name: Hippocampus  from vehicle treated mouse

tag: agent

value: vehicle

tag: time

value: 4 weeks

value: Hippocampus


title: Data 197 Arrea1

value: dissection

value: plateau phase

value: granulosa cell

value: growing phase


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 5h

tag: gender

value: female


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 4h


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 2h


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 3h


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 0.5h


title: Replicate 2, Heavy channel SILAC, LPS-stimulus, time 1h


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 9h

value: mock-stimulated


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 24h


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 6h


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 5h


title: Data 197 Area3


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 4h


title: Data 197 Area2


title: microRNA profile of case N9

city: Guangzhou

first: Mei-Yin

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log2 transformation of expression levels using EXPression Analyzer and DisplayER (EXPANDER, v.4.1)

source_name: Normal intrahepatic bile duct

label_protocol: 2.5 μg of total RNA of intrahepatic cholangiocarcinoma/normal intrahepatic bile duct tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: age

value: 41 years

value: Male

value: Normal intrahepatic bile duct


title: microRNA profile of case N7

value: 33 years


title: microRNA profile of case N8

value: 57 years


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 2h

value: Trypsin


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 0.5h


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 1h


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 12h


title: microRNA profile of case N6

value: 29 years

value: Female


title: Replicate 2, Heavy channel SILAC, time 0


title: microRNA profile of case N5

value: 48 years


title: Replicate 2, Heavy channel SILAC, Mock-stimulus, time 3h


title: microRNA profile of case N3

value: 40 years


title: microRNA profile of case N2

value: 55 years


title: microRNA profile of case N1

value: 54 years


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 24h

value: LPS-stimulated


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 6h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 5h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 12h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 9h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 4h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 3h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 1h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 2h


title: Replicate 1, Heavy channel SILAC, LPS-stimulus, time 0.5h


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 24h


title: microRNA profile of case ICC103

source_name: Intrahepatic cholangiocarcinoma

value: 65 years

tag: survival status

value: Dead

tag: survival time

value: 18.3 months

value: Intrahepatic cholangiocarcinoma


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 9h

value: female

value: mock-stimulated


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 6h


title: microRNA profile of case ICC101

value: 60 years

value: Male

value: Alive

value: 19.4 months

tag: tissue


title: microRNA profile of case N4

value: 59 years

value: Normal intrahepatic bile duct


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 5h

value: Trypsin


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 3h


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 2h


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 4h


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 12h


title: microRNA profile of case ICC100

value: 51 years

value: Female

value: 24.3 months


title: microRNA profile of case ICC106

value: 40 years

value: 12.8 months


title: Replicate 1, Heavy channel SILAC, time 0


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 1h


title: microRNA profile of case ICC99

value: 53 years

value: Dead

value: 15.1 months


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 24h

label: SILAC M

value: female

value: LPS-stimulated


title: Replicate 1, Heavy channel SILAC, Mock-stimulus, time 0.5h

value: mock-stimulated


title: microRNA profile of case ICC96

value: 43 years

value: Male

value: 10.1 months

value: Intrahepatic cholangiocarcinoma


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 9h


title: microRNA profile of case ICC92

value: 57 years

value: Alive

value: 28.5 months


title: microRNA profile of case ICC87

value: 42 years

value: Female

value: 25.3 months


title: microRNA profile of case ICC86

value: 72 years

value: 29.3 months


title: microRNA profile of case ICC85

value: 59 years

value: 31 months


title: microRNA profile of case ICC83

value: 71 years

value: 30.5 months


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 6h

value: female

value: LPS-stimulated

value: Trypsin


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 0.5h


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 4h


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 3h


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 5h


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 1h


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 2h


title: microRNA profile of case ICC80

value: 60 years

value: Dead

value: 14 months


title: microRNA profile of case ICC74

value: Male

value: 14.4 months

value: Intrahepatic cholangiocarcinoma


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 24h

value: mock-stimulated


title: microRNA profile of case ICC77

value: 76 years

value: Female

value: Alive

value: 29.5 months


title: Replicate 2, Medium channel SILAC, LPS-stimulus, time 12h


title: microRNA profile of case ICC72

value: 38 years

value: 16.2 months


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 12h


title: microRNA profile of case ICC70

value: 57 years

value: 37.7 months


title: microRNA profile of case ICC69

value: 75 years

value: 10.2 months


title: microRNA profile of case ICC66

value: 43 years

value: 27 months


title: microRNA profile of case ICC68

value: 66 years

value: Dead

value: 9.7 months


title: microRNA profile of case ICC65

value: 70 years

value: Male

value: 5.4 months

value: Intrahepatic cholangiocarcinoma


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 3h

value: female

value: mock-stimulated

value: Trypsin


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 5h


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 6h


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 2h


title: microRNA profile of case ICC61

value: 51 years

value: 28.8 months


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 0.5h


title: Replicate 2, Medium channel SILAC, time 0


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 4h


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 9h

value: LPS-stimulated


title: microRNA profile of case ICC59

value: 45 years

value: Alive

value: 18.6 months


title: microRNA profile of case ICC57

value: 48 years

value: Female

value: 5.3 months


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 24h


title: microRNA profile of case ICC56

value: 86 years

value: 2.7 months


title: microRNA profile of case ICC55

value: 53 years

value: Male

value: Dead

value: 9.9 months


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 9h

value: female

value: mock-stimulated


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 12h

value: Trypsin


title: microRNA profile of case ICC62

value: 62 years

value: 41.2 months

value: Intrahepatic cholangiocarcinoma


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 5h

value: LPS-stimulated


title: microRNA profile of case ICC52

value: 63 years

value: 14.9 months


title: microRNA profile of case ICC54

value: 55 years

value: 3.7 months


title: Replicate 2, Medium channel SILAC, Mock-stimulus, time 1h


title: microRNA profile of case ICC46

value: 51 years

value: 29.2 months


title: microRNA profile of case ICC49

value: Female

value: Alive

value: 50.3 months


title: microRNA profile of case ICC50

value: 68 years

value: Male

value: Dead

value: 19.8 months


title: microRNA profile of case ICC60

value: 43 years

value: 7.2 months


title: microRNA profile of case ICC48

value: 58 years

value: 3.9 months

value: Intrahepatic cholangiocarcinoma


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 3h

value: female

value: LPS-stimulated

value: Trypsin


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 2h


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 1h


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 24h

value: mock-stimulated


title: microRNA profile of case ICC43

value: 36 years

value: 14.9 months


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 0.5h


title: microRNA profile of case ICC42

value: 55 years

value: 4.4 months


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 6h


title: Replicate 1, Medium channel SILAC, LPS-stimulus, time 4h


title: microRNA profile of case ICC41

value: Alive

value: 56.3 months


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 12h


title: microRNA profile of case ICC40

value: 41 years

value: Male

value: Dead

value: 23.6 months


title: microRNA profile of case ICC38

value: 57 years

value: 57.4 months


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 4h


title: microRNA profile of case ICC36

value: 64.7 months

value: Intrahepatic cholangiocarcinoma


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 6h

value: female


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 5h

value: Trypsin


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 3h

value: mock-stimulated


title: microRNA profile of case ICC34

value: 36 years

value: 57.8 months


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 2h


title: microRNA profile of case ICC31

value: 49 years

value: 67.9 months


title: microRNA profile of case ICC33

value: 53 years

value: 12.2 months


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 1h


title: microRNA profile of case ICC29

value: 68 years

value: Female

value: 8.2 months


title: microRNA profile of case ICC28

value: 74 years

value: Male

value: Alive

value: 0.6 months


title: microRNA profile of case ICC26

value: 55 years

value: Dead

value: 3 months

value: Intrahepatic cholangiocarcinoma


title: microRNA profile of case ICC27

value: 13.8 months


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 0.5h

value: female

value: mock-stimulated

value: Trypsin


title: Replicate 1, Medium channel SILAC, Mock-stimulus, time 9h


title: Replicate 1, Medium channel SILAC, time 0


title: microRNA profile of case ICC23

value: 44 years

value: 2.8 months


title: microRNA profile of case ICC24

value: 52 years

value: 4.2 months


title: microRNA profile of case ICC20

value: 75 years

value: 75.3 months


title: microRNA profile of case ICC22

value: 33 years

value: Male

value: 34.2 months


title: microRNA profile of case ICC19

value: 43.7 months


title: microRNA profile of case ICC17

value: 68 years

value: Female

value: Dead

value: 30.6 months


title: microRNA profile of case ICC14

value: 34 years

value: 8 months

value: Intrahepatic cholangiocarcinoma


title: microRNA profile of case ICC11

value: 50 years

value: 15.2 months


title: microRNA profile of case ICC8

value: 53 years

value: 1.2 months


title: microRNA profile of case ICC9

value: 45 years

value: Alive

value: 29.9 months


title: microRNA profile of case ICC13

value: Male

value: 60 months


title: microRNA profile of case ICC10

value: 56 years

value: 27.7 months


title: P4-013M

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: Gene expression data from human knee meniscus

hyb_protocol: cDNA hybridized into the GeneChip Hybridization Oven 640 for 18 hours on Gene 2.0 ST array. Then Affymetrix Gene 2.0 microarrays were washed and processed in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized using quantile normalization with Partek Genomic Suite.

source_name: Meniscus from patient undergoing partial meniscectomy

label_protocol: Total RNA was amplified by Ovation Pico WTA Amplification System (NuGen, Inc., San Carlos, CA) and biotinylated cDNA synthesis was undertaken according to the standard NuGen Ovation Pico WTA System Amplification system using 50 ng total RNA. NuGen Encore Biotin Module kits were then used to fragment and label 5 μg of cDNA.

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

tag: patient id

tag: bmi

tag: procedure

value: knee undergoing partial meniscectomy

value: injured meniscus


title: P4-012M


title: microRNA profile of case ICC5

value: 60 years

value: Dead

value: 14.4 months


title: P4-009M

value: Female


title: microRNA profile of case ICC4

value: 49 years

value: 2.2 months

value: Intrahepatic cholangiocarcinoma


title: P4-011M


title: P4-010M


title: P4-008M


title: microRNA profile of case ICC3

value: 48 years

value: 40.4 months


title: 4h_LPS_donor3

city: Muenster

first: Nadine

last: Nippe

address: Roentgenstr. 21

department: Institute of Immunology

institute: University of Muenster

description: Human monocytes_4h_6

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16h at 45°C on to Affymetrix Human Genome 133 A Gene Chip arrays. Gene Chip Arrays were washed and stained using the Gene Chip Fluidics Station 400.

scan_protocol: Fluorescent signals were detected by the HP G2500A Gene Array Scanner.

data_processing: The data were analyzed with MicroArray Suite (MAS) Software 5.0 (Affymetrix). Signals were scaled to a target intensity of each array was arbitrarily set to 100 and log transformed. The algorithm applied in the MAS 5.0 software assigned individual average background values to each cell intensity and subtracted it from single raw cell intensities.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Manual Target Preparation for GeneChip® 3' Expression Arrays, Affymetrix).

growth_protocol: Human monocytes were obtained from buffy coats from healthy individual donors.

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

treatment_protocol: Human monocytes were exposed for 4 and 16 hours with 100 ng/ml E.coli O111:B4 LPS (Sigma-Aldrich) or solvent as control.

tag: donor status/id

value: healthy donor 3

value: blood monocytes

tag: stimulated with

value: 100 ng/ml E.coli O111:B4 LPS for 4hrs


title: microRNA profile of case ICC2

value: Male

value: Alive

value: 14.3 months


title: 4h_LPS_donor1

description: Human monocytes_4h_4

value: healthy donor 1


title: microRNA profile of case ICC1

value: 24 years

value: 28.3 months


title: 4h_LPS_donor2

description: Human monocytes_4h_5

value: healthy donor 2


title: P4-005M

value: knee undergoing partial meniscectomy

value: injured meniscus


title: 4h_control_donor3

description: Human monocytes_4h_3

value: solvent (control) for 4hrs


title: P4-004M

value: Female


title: P4-003M


title: P4-002M


title: 4h_control_donor1

description: Human monocytes_4h_1


title: 4h_control_donor2

description: Human monocytes_4h_2


title: genomic DNA from Donor 4 CD3+CD8+CD45RA+CD57- naïve T cells

description:
Healthy blood donor
SAMPLE_112

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2; the non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: CD3+CD8+CD45RA+CD57- naïve T cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from sorted lymphocytes using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: No treatments were tested - genomic DNA was extracted directly from sorted cells

tag: donor status

value: CMV seropositive donor

tag: donor id

value: donor 4

value: Peripheral Blood

tag: cell type

value: CD3+CD8+CD45RA+CD57- naïve T cells


title: P4-001M


title: 16h_LPS_donor3

description: Human monocytes_16h_6

value: healthy donor 3

value: blood monocytes

value: 100 ng/ml E.coli O111:B4 LPS for 16hrs


title: genomic DNA from Donor 4 CD3-CD56+CD57- canonical NK cells

description:
Healthy blood donor
SAMPLE_111

source_name: CD3-CD56+CD57- canonical NK cells

value: CD3-CD56+CD57- canonical NK cells


title: genomic DNA from Donor 4 CD3+CD8+CD45RA+CD57+ effector T cells

description:
Healthy blood donor
SAMPLE_107

source_name: CD3+CD8+CD45RA+CD57+ effector T cells

value: CD3+CD8+CD45RA+CD57+ effector T cells


title: P4-007M

value: Male


title: genomic DNA from Donor 3 CD3-CD56+CD57+EAT-2int adaptive NK cells

description:
Healthy blood donor
SAMPLE_106

value: donor 3


title: genomic DNA from Donor 4 CD3-CD56+CD57dim canonical NK cells

description:
Healthy blood donor
SAMPLE_109

source_name: CD3-CD56+CD57dim canonical NK cells

value: CD3-CD56+CD57dim canonical NK cells


title: genomic DNA from Donor 3 CD3-CD56+CD57- canonical NK cells

description:
Healthy blood donor
SAMPLE_103


title: genomic DNA from Donor 3 CD3-CD56+CD57+EAT-2+ canonical NK cells

description:
Healthy blood donor
SAMPLE_105

source_name: CD3-CD56+CD57+EAT-2+ canonical NK cells

value: CD3-CD56+CD57+EAT-2+ canonical NK cells


title: 3rd mammary gland at E13.5

city: Seoul

first: Eun-Jung

last: Kim

address: 50 Yonsei-ro

department: Department of Oral Biology

country: South Korea

institute: Yonsei Universiry

description:
miRNA
M

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: 3rd mammary gland at E13.5

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: Emrbyos were collected from pregnant mice at E13.5.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And then, extracted total RNA was purified using Rneasy min elute kit manufacturer's instructions.

treatment_protocol: no treatment

tag: strain

value: ICR

tag: developmental stage

value: 3rd mammary gland


title: genomic DNA from Donor 2 CD3-CD56+CD57+EAT-2- adaptive NK cells

description:
Healthy blood donor
SAMPLE_21

source_name: CD3-CD56+CD57+EAT-2- adaptive NK cells

value: donor 2

value: CD3-CD56+CD57+EAT-2- adaptive NK cells


title: genomic DNA from Donor 2 CD3+CD8+CD45RA+CD57- naïve T cells

description:
Healthy blood donor
SAMPLE_18

value: CMV seropositive donor


title: genomic DNA from Donor 2 CD3-CD56+CD57+EAT-2+ canonical NK cells

description:
Healthy blood donor
SAMPLE_19


title: mammary flank region between 3rd and 4th mammary gland at E13.5

description:
miRNA
MG control


title: P4-013A

description: Gene expression data from human knee artcular cartilage

source_name: Articular cartilage from patient undergoing partial meniscectomy

value: knee undergoing partial meniscectomy

value: normal articular cartilage


title: genomic DNA from Donor 2 CD3-CD56+CD57dim canonical NK cells

description:
Healthy blood donor
SAMPLE_24

value: Peripheral Blood


title: genomic DNA from Donor 2 CD3-CD56+CD57- canonical NK cells

description:
Healthy blood donor
SAMPLE_15


title: genomic DNA from Donor 4 CD3-CD56+CD57+EAT-2- adaptive NK cells

description:
Healthy blood donor
SAMPLE_110

value: donor 4


title: genomic DNA from Donor 2 CD3+CD8+CD45RA+ effector T cells

description:
Healthy blood donor
SAMPLE_13

source_name: CD3+CD8+CD45RA+ effector T cells

value: CD3+CD8+CD45RA+ effector T cells


title: genomic DNA from Donor 3 CD3+CD8+CD45RA+CD57+ effector T cells

description:
Healthy blood donor
SAMPLE_101


title: genomic DNA from Donor 3 CD3+CD8+CD45RA+CD57- naïve T cells

description:
Healthy blood donor
SAMPLE_104

value: CD3+CD8+CD45RA+CD57- naïve T cells


title: genomic DNA from Donor 3 CD3-CD56+CD57+EAT-2- adaptive NK cells

description:
Healthy blood donor
SAMPLE_102


title: genomic DNA from Donor 1 CD3-CD56+CD57+EAT-2- adaptive NK cells

description:
Healthy blood donor
SAMPLE_11

value: donor 1


title: P4-012A


title: 16h_control_donor3

description: Human monocytes_16h_3

value: healthy donor 3

value: blood monocytes

value: solvent (control) for 16hrs


title: genomic DNA from Donor 1 CD3-CD56+CD57+EAT-2+ canonical NK cells

description:
Healthy blood donor
SAMPLE_5


title: genomic DNA from Donor 1 CD3+CD8+CD45RA+CD57- naïve T cells

description:
Healthy blood donor
SAMPLE_9


title: Shp2 inhibition mammospheres, biological rep2

description:
LLX--08-GS493-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with Shp2 inhibitor.

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: mammospheres, Shp2 inhibition

treatment_protocol: Mammospheres were treated with Shp2 inhibitor GS493 for 2 days and collected for RNA isolation.

tag: strain/background

value: FVB/N

tag: genotype/variation

value: primary mammary tumor cells

tag: treatment

value: Shp2 inhibitor


title: P4-010A

tag: age

tag: gender

value: Male


title: 16h_control_donor1

description: Human monocytes_16h_1

value: healthy donor 1


title: Shp2 knockout mammospheres, biological rep2

description:
LLX--05-CreERT2-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres infected with CreERT2 retrovirus.

source_name: mammospheres, Shp2 knockout

treatment_protocol: Mammospheres were treated with 50 nM 4-OHT for 2 hours and collected for RNA isolation 5 days later.

value: CreERT2 retrovirus infection


title: Shp2 inhibition mammospheres, biological rep1

description:
LLX--07-GS493-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with Shp2 inhibitor.


title: P4-007A


title: Shp2 knockout mammospheres, biological rep3

description:
LLX--06-CreERT2-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres infected with CreERT2 retrovirus.


title: Shp2 inhibition mammospheres, biological rep3

description:
LLX--09-GS493-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres treated with Shp2 inhibitor.


title: Mouse NAPE knocked out fed with high fat diet

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Gene expression data from NAPE PLD cKO mice subcutaneous adipose tissue

hyb_protocol: Affymetrix hybridization control and hybridization wash and stain kit.

scan_protocol: The wash and stain protocols were runned on an Affy 450 station. The chips were scanned according to the Affymetrix standard procedure.

data_processing: Affymetrix Gene Expression Console and APT suite tool. Normalization: RMA-sketch procedure; signal detection p-values: DABG procedure.

source_name: Mouse (C57Bl6) subcutaneous adipose tissue

label_protocol: Biotinylated cRNAs were prepared according to the standard Ambion WT expression kit from 100ng of total RNA  followed by Affymetrix WT terminal labeling kit.

growth_protocol: two groups of mice:  NAPE PLD WT and NAPE PLD cKO were recruited for this experiment

extract_protocol: For the subcutaneous adipose tissue of each mice, RNA extraction was done using Tripure (Roche). After extraction RNAs from 4 to 5 mice per group were pooled, mice were selected based on their RNA quality.

treatment_protocol: each group of mice were fed either with control diet (composition: AIN93M, Research Diets) or high fat containing diet (composition: D12492, Research Diets)

value: subcutaneous adipose tissue

tag: genotype

value: AP2 Cre NAPE PLD lox/lox

value: 16 weeks


title: P4-009A

value: Female

value: knee undergoing partial meniscectomy

tag: tissue

value: normal articular cartilage


title: genomic DNA from Donor 1 CD3-CD56+CD57- canonical NK cells

description:
Healthy blood donor
SAMPLE_7

value: CMV seropositive donor

value: Peripheral Blood

value: CD3-CD56+CD57- canonical NK cells


title: 16h_control_donor2

description: Human monocytes_16h_2

value: healthy donor 2

value: blood monocytes


title: Shp2 knockout mammospheres, biological rep1

description:
LLX--04-CreERT2-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres infected with CreERT2 retrovirus.

value: FVB/N


title: Mouse NAPE knocked out fed with control diet


title: P4-002A

tag: patient id


title: Mouse NAPE wild-type fed with high fat diet

description: Gene expression data from NAPE PLD WT mice subcutaneous adipose tissue

value: NAPE PLD lox/lox


title: P4-001A

tag: bmi


title: P4-003A

tag: procedure


title: genomic DNA from Donor 1 CD3+CD8+CD45RA+CD57+ effector T cells

description:
Healthy blood donor
SAMPLE_3

value: donor 1

value: CD3+CD8+CD45RA+CD57+ effector T cells


title: P4-005A


title: Mouse NAPE wild-type fed with control diet


title: P4-008A

value: Male


title: Control mammospheres, biological rep1

description:
LLX--01-Control-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres infected with control retrovirus.

source_name: mammospheres, control

value: primary mammary tumor cells

value: control retrovirus infection


title: Anti-BPTF B16 cells Replicate 4

status: Public on Mar 05 2015

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

description:
M-IMCH-P4-233
The Universal Mouse Reference RNA is composed of total RNA from 11 mouse cell lines, to compensate for differential abundance of RNA species between cell lines.

hyb_protocol: Labeled cDNA was hybridized to a microarray slide at 63° C for 12-16 h.

scan_protocol: Slides were then washed and immediately scanned with Axon Imager 4000b (Axon Instruments, Foster City, Ca), using GenePixPro3 software.

data_processing: printTipLoess normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. SAM (Significance Analysis of Microarrays) was used to determine differntially expressed genes.

source_name: B16 murine melanoma cell line transfected with anti-BPTF shRNA-10

label_protocol: 10 microgram of total target RNA, side by side with 1 µg of universal mouse reference RNA (Stratagene #740100), was linearly amplified through two rounds of modified in vitro transcription. Randomized amplified RNAs were converted to aminoallyl-modified cDNA and coupled to N-hydroxysuccinimidyl esters of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ),

growth_protocol: Cells were cultured in RPMI medium 1640 with 5% FBS and 800 g/ml Geneticin (37°C, 5% CO2) at less than 80% confluency.

extract_protocol: Cells were trypsinized and were spun down to form a pellet. Cell pellets were then homogenized [Polytron 1200C, Brinkmann, Westbury, NY, at setting 4 for 30 sec] with 600µl of RNA lysis buffer plus 1% 2-mercaptoethanol, and RNA was isolated using RNEasy columns (Qiagen, Valencia, Ca).

tag: cell line

value: B16 murine melanoma cell line

tag: transfection

value: anti-BPTF shRNA-10

source_name: Stratagene Universal Mouse Reference RNA

tag: reference composition

value: embryo, fibroblast, kidney, liver, lung, B-lymphocyte, T-lymphocyte, mammary gland, muscle myoblast, skin, testis