title: RNAP_DdksA_SHX_rep1

description: RNAP ChIP-chip starved DdksA cells


title: Xray.4h repl. 4

status: Public on Apr 20 2014

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

country: Germany

institute: Uniklinikum Giessen

hyb_protocol: Cy3- and Cy5-labeled RNAs were hybridized overnight to Agilent Human Whole Genome 4x44K arrays (G4112F) and further processed following the Agilent protocol.

scan_protocol: Slides were scanned using the GenePix 4100A scanner (Axon Instruments, Downingtown, PA) at 5 µm resolution.

data_processing: Data were evaluated using the R software and the limma package from BioConductor. Pathway analyzes were done using the ranks of the test statistics  based on the KEGG.db annotation package.

molecule: total RNA

organism: Homo sapiens

source_name: A549 cells, Xray control, 4h

label_protocol: 1µg per pool was labeled by fluorescent dye Cy3 and Cy5 using dual-color QuickAmp kit (Agilent) according to the instructions matching a balanced dye-swap design.

growth_protocol: Human NSCLC adenocarcinoma cell lines A549 (ATCC-No.: CCL-185) were obtained from the American Type Culture Collection and maintained in RPMI 1640 (E15-840, PAA Laboratories GmbH) supplemented with 10% fetal bovine serum (Greiner BioOne), at 37 C in humidified atmosphere containing 5% CO2 in air. The cell lines were authenticated by microsatellite profiling (DSMZ, Germany).

extract_protocol: RNA was purified using RNeasy Mini Kit following the company’s instructions (Qiagen). Total RNA from two independent experiments was pooled.

treatment_protocol: For photon irradiation (X-ray) a 6 MV X-ray beam generated by a clinical linear accelerator (dose rate of 3 Gy/min) was used. Carbon-ion irradiations (12C) using the intensity controlled raster scanning system (25) were performed with a homogeneous 10 mm (for cells) or 40 mm (for tumor) spread-out Bragg peak (SOBP) with an energy of 120.45-135.16 MeV/u (cells) and 122.36-183.74 MeV/u (tumor) on target obtained from the SIS accelerator (GSI Helmholtzzentrum für Schwerionenforschung). Mean dose average of LET was 50 70 keV/µm.

tag: treatment

value: Xray control

tag: time

tag: cell line

source_name: A549 cells, Xray irradiated, 4h

value: Xray irradiated


title: wild-type 1

city: Boston

first: David

last: Weinstock

state: MA

address: 450 Brookline Ave

country: USA

institute: DFCI

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) per the standard Affymetrix protocol in the Dana-Farber microarray core (http://chip.dfci.harvard.edu/).

scan_protocol: After staining, the genechip arrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Gene Pattern (http://www.broadinstitute.org/cancer/software/genepattern) package was used for RMA normalization using the ExpressionFileCreator module.

label: biotin allonamide triphosphat

organism: Mus musculus

source_name: proB cell colonies

label_protocol: following the Affymetrix standard protocol

growth_protocol: bone marrow harvested and placed in B cell methylcellulose medium to generate proB cell colonies

extract_protocol: For total RNA, 10e6 cells were harvested in Trizol according to the manufacturers instructions.

treatment_protocol: proB cell colonies were harvested at 1 week

tag: b cell stage

value: proB

tag: genotype/variation

value: wild-type


title: Xray.1h repl. 4

source_name: A549 cells, Xray control, 1h

source_name: A549 cells, Xray irradiated, 1h


title: C12.4h repl. 4

source_name: A549 cells, C12 control, 4h

value: C12 control

source_name: A549 cells, C12 irradiated, 4h

value: C12 irradiated


title: Xray.4h repl. 2


title: C12.1h repl. 4

source_name: A549 cells, C12 control, 1h

source_name: A549 cells, C12 irradiated, 1h


title: RNAP_wt_untreated_rep1

status: Public on Apr 21 2014

type: genomic

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 600 16th Street

department: Microbiology and Immunology

institute: UC San Francisco

description: RNAP ChIP-chip wt cells

hyb_protocol: The labeled IP DNA and input DNA samples were hybridized to a NimbleGen high-density 2.1M promoter tiling array using a Maui hybridization apparatus (BioMicro Systems) by following the protocol from NimbleGen.

scan_protocol: The arrays were scanned by using the Axon 4000B scanner.

data_processing: The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

molecule: genomic DNA

organism: Escherichia coli

source_name: RNAP ChIP DNA from wt cells

label_protocol: The IP DNA samples and input DNA samples (recovered after similar treatment but without immunoprecipitation) were amplified by linker-mediated PCR as described in the protocol from NimbleGen. The amplified DNA was then labeled with Cy3 (input DNA) or Cy5 (IP DNA) dye by following the protocol from NimbleGen.

growth_protocol: Wild-types cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase at 37°C with vigorous shaking.

extract_protocol: Cells were fixed with 1% formaldehyde for 5min before quenching with ice-cold glycine (100mM). Cells were harvested, washed with ice-cold PBS and flash-frozen in liquid nitrogen. Cell pellets were resuspended in 500 ml of IP buffer (100 mM Tris pH 8, 300mM NaCl, 2% TritonX-100) and sonicated using a Misonix sonicator (S-4000) with a cup horn (431C) set at 60% output, 10 sec ON and 10 sec OFF, for a total sonication time of 16 min. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml; USB, Inc.) and the samples were centrifuged at 20,000 x g for 10 min at 4 °C to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads (Upstate; now Millipore) and protein G beads (GE Healthcare) in IP buffer for 3 hours at 4 °C. The beads were removed by centrifugation (1000 x g for 2 min at 4 °C) and antibodies were added to the pre-cleared lysate for an overnight incubation. For ChIP, we used anti-RNAP b subunit NT63 monoclonal antibodies (Neoclone W0002), anti-RNAP s70 subunit monoclonal antibodies (Neoclone W0004), or anti-DksA rabbit polyclonal antisera (a kind gift from Diana Downs). The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in 250 μl IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% Triton X-100), twice with 1 ml 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% SDS), twice with 1 ml 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% SDS), and twice with 1 ml TE (10 mM Tris pH 8, 1 mM EDTA). Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation (1000 x g for 2 min at 25 °C) to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted in a final volume of 65 μl with 10 mM Tris pH 8.

tag: genotype

tag: antibody

source_name: Input DNA from wt cells

value: None, input DNA


title: wild-type 2


title: Xray.1h repl. 1


title: Xray.4h repl. 3


title: C12.4h repl. 3


title: Xray.4h repl. 1


title: Xray.1h repl. 3


title: Xray.1h repl. 2


title: C12.1h repl. 3


title: Father of Lis_04_Twist [Paternal from Lis04_Twist]

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Standard Illumina protocol (GenomeStudio). All the cnvi probes were removed from the analysis

label: biotin and dinitrophenyl

source_name: Father of Lis_04_Twist

label_protocol: C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled

growth_protocol: Lis Cell Lines: Intact ICM clumps were placed on a feeder cell layer of mitomycin C-inactivated treated mouse embryo fibroblasts (MEFs), and cultured in hESC media; Following 5-7 passages,  cell lines were propagated by collagenase type IV. UCSFB Cell Lines: Quinn’s Cleavage medium for 24 h; transferred onto irradiated human foreskin fibroblasts (HFF) Quinn’s Blastocyst medium and cultured for 4 days; transferred to hESC medium at day 5

extract_protocol: genomic DNA was extracted using Quiagen DNeasy Blood & Tissue Kit

tag: hesc line

value: Paternal from Lis04_Twist

tag: gender

value: male


title: C12.4h repl. 2


title: RNAP_wt_SHX_rep1

description: RNAP ChIP-chip starved wt cells

source_name: RNAP ChIP DNA from starved wt cells

growth_protocol: Wild-types cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase and treated with 0.5mg/ml serine hydroxamate (SHX) for 20min at 37°C with vigorous shaking.

treatment_protocol: 0.5mg/ml SHX for 20min

value: 0.5mg/ml serine hydroxamate for 20min

value: anti-RNAP b subunit NT63 monoclonal antibodies

source_name: Input DNA from starved wt cells


title: RNAP_wt_SHX_rep2

description: RNAP ChIP-chip starved wt cells


title: RNAP_DdksA_untreated_rep1

description: RNAP ChIP-chip DdksA cells

source_name: RNAP ChIP DNA from DdksA cells

growth_protocol: DdksA cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase at 37°C with vigorous shaking.

value: MG1655 DdksA

source_name: Input DNA from DdksA cells


title: s70_wt_untreated_rep1

description: s70 ChIP-chip wt cells

source_name: s70 ChIP DNA from wt cells

value: anti-s70 monoclonal antibodies


title: UCC2003-lacI2 grown in ribose as sole carbohydrate vs. UCC2003 grown on ribose as sole carbohydrate

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: Sample 4

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: UCC2003-lacI2  grown on ribose as the sole carbohydrate source

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003, UCC2003-lacI1, UCC2003-lacI2 or UCC2003-rafR were grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), , supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing  ribose  as the sole carbohydrate source. The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: strain

value: UCC2003-lacI2 insertion mutant

tag: carbohydrate source

value: ribose

source_name: UCC2003 grown on ribose as the sole carbohydrate source


title: UCC2003 grown in ribose as sole carbohydrate vs. UCC2003-laci2 on ribose as sole carbohydrate

description: Sample 3

source_name: UCC2003 grown onribose as the sole carbohydrate source

source_name: UCC2003-lacI1 grown on ribose as the sole carbohydrate source


title: UCC2003 grown in ribose as sole carbohydrate vs. UCC2003-laci1 on ribose as sole carbohydrate

description: Sample 1

value: UCC2003-lacI1 insertion mutant


title: C12.1h repl. 2


title: C12.1h repl. 1


title: C12.4h repl. 1


title: RNAP_DdksA_untreated_rep2

description: RNAP ChIP-chip DdksA cells


title: 5326915002_L

status: Public on Apr 19 2014

city: Philadelphia

first: Wissam

last: Chatila

state: PA

address: 3500 N. Broad St.

institute: Temple University

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the protocols provided by the manufacturer

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). The data were normalised using quantile normalisation.

label: biotin

source_name: Teff cells from Healthy patients

label_protocol: Labeling was performed according to the protocol in the Illumina MicroRNA Expression Profiling kit

extract_protocol: We used mirVana miRNA Detection kit (Applied Biosystems, Life Technologies, Carlsbad CA) to extract total and low molecular weight (LMW) RNA from the purified nTreg and Teff cells.

treatment_protocol: We obtained peripheral blood from our participants and isolated peripheral blood mononuclear cells (PBMC) by Ficoll-Paque gradient centrifugation. We collected blood in EDTA tubes.  From the PBMC population we obtained CD4+ CD127- cells using magnetic cell separation following manufacturer’s protocol (MACS; Miltenyi Biotech, UK) then used these purified cells in another Treg kit, the CD25+CD49- T Cell Isolation Kit (Miltenyi Biotech), resulting in CD4+CD25+CD127-CD49- cells.  T effector (Teff) cells were purified from a different CD4+CD25+ Treg kit (Miltenyi Biotech) isolating the CD4+CD25- cells as our Teff cells of interest.  We confirmed the phenotype of the cells by flow cytometry (CD4-PerCP5.5, Foxp3-PE, eBioscience).  To test the function of the isolated Treg cells, we tested their suppressive activity by suspending 50×103 cells along with 50×103 Teff cells in culture medium in 96-well plates, serially diluting the nTreg cell population, giving Treg/Teff ratios of 1/1, 1/2, 1/4, 1/8 and 1/16. Wells without nTreg cells and without stimulation beads were included as controls in preparation of suppression curves. Each well was stimulated with Treg Suppression Inspector beads (Miltenyi) at a cell to bead ratio of 1:1.  After 4 days of incubation, we determined CD4+ cell divisions by carboxyfluorescein (CFSE) dilution (2).

tag: tissue

value: blood

tag: cell type

value: Effector T cells

tag: patient group

value: Healthy


title: 5326915002_K

source_name: Treg cells from Healthy patients

value: Regulatory T cells


title: 5326915002_J


title: 5326915002_I


title: Granuloma Comparison 16

city: Covington

first: Deepak

last: Kaushal

state: LA

address: 18703 Three Rivers Rd

department: Microbiology & Immunology

institute: Tulane National Primate Research Center

description: HG80 vs EL04

hyb_protocol: Hybridization buffer (Agilent) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed and scanned.

scan_protocol: Scanned using the GenePix 4000B Scanner

data_processing: Raw files were imported into R.  Normalization within arrrays was performed using the OLIN package for optimised local intensity-dependent normalisation and between array normalization was performed using the LIMMA package.

organism: Macaca mulatta

source_name: Granuloma

label_protocol: 1-2ug of total RNA were primed with 1.2ul T7 primer at 65°C for 10 min, then a cDNA master mix at 40°C for 2 h in the presence of 5X First Strand Buffer, 0.1M DTT, 10 mM dNTP mix, MMLV-RT, RnaseOut. Then transcribed at 40 40°C for 2 h in the presence of Nuclease-free water, 4X Transcription Buffer, 0.1M DTT, NTP mix, 50% Peg, RNaseOut, Inorganix pyrophosphatase, T7 RNA Polymerase, Cyanine 3-CTP or cyanine 5-CTP

extract_protocol: Total RNA extracted from individual lung samples using Trizol and the Rneasy mini kits (Qiagen) following manufacturer's instructions

tag: animal id

tag: days post-exposure


title: Control Granuloma 3

description: HA46 vs CG32

source_name: Control Lung


title: Granuloma Comparison 15

description: FR67 vs HH06


title: Granuloma Control 1

description: CT16 vs CA75


title: Granuloma Comparison 18

description: HC20 vs HB74


title: Granuloma Comparison 14

description: HJ91 vs HG80


title: Granuloma Comparison 17

description: HA77 vs HC90


title: Granuloma Comparison 12

description: HJ01 vs BV21


title: 5326915002_H


title: 5326915002_G


title: Granuloma Control 3

description: DV08 vs HJ01


title: Granuloma Comparison 13

description: FJ05 vs HA90


title: Granuloma Comparison 11

description: CA75 vs HC38


title: Control Granuloma 2

description: HC38 vs CT16


title: 5326915002_F


title: Granuloma Comparison 9

description: HJ93 vs HC20


title: UCC2003-rafR grown in ribose as sole carbohydrate vs. UCC2003 grown on ribose as sole carbohydrate

description: Sample 6

source_name: UCC2003-rafR grown on raffinose as the sole carbohydrate source

value: UCC2003-rafR insertion mutant

value: raffinose


title: Granuloma Comparison 8

description: BV21 vs HA46


title: 5326915002_E


title: 5326915002_D

source_name: Teff cells from Smoker patients

value: Smoker


title: 5326915002_C

source_name: Treg cells from Smoker patients


title: Granuloma Comparison 7

description: HH06 vs HA77


title: 5326915002_B


title: UCC2003 grown in ribose as sole carbohydrate vs. UCC2003-rafR on ribose as sole carbohydrate

description: Sample 5

source_name: UCC2003 grown on raffinose as the sole carbohydrate source


title: 5326915002_A


title: Granuloma Comparison 6

description: HJ93 vs HC90


title: 5326915001_H

source_name: Teff cells from COPD patients

value: COPD


title: 5326915001_K


title: 5326915001_L


title: Granuloma Comparison 5

description: HJ01 vs BV21


title: Granuloma Comparison 3

description: HC20 vs EL04


title: Granuloma Comparison 4

description: EL04 vs HJ91


title: 5326915001_J


title: 5326915001_I


title: Control Granuloma 1

description: HA90 vs DV08


title: wild-type 3

source_name: proB cell colonies

value: proB

value: wild-type


title: Granuloma Comparison 2

description: HB74 vs HJ93


title: Granuloma Comparison 1

description: HC90 vs FJ05


title: UCC2003-lacI1 grown in ribose as sole carbohydrate vs. UCC2003 grown on ribose as sole carbohydrate

description: Sample 2

source_name: UCC2003-lacI1  grown on ribose as the sole carbohydrate source


title: Granuloma Control 2

description: CG32 vs FE10


title: Granuloma Comparison 10

description: FE10 vs FR67


title: 5326915001_G

source_name: Treg cells from COPD patients


title: Epithelial WT5

city: Singapore

middle: Marc

last: Virshup

address: 8 College Road

department: Program in Cancer and Stem Cell Biology

country: Singapore

institute: Duke-NUS Graduate Medical School

description: sample id in raw file: Epi 31 (3)

hyb_protocol: Standard Illumina Hybridization protocol (The signal was developed using streptavidin-Cy3)

scan_protocol: Standard Illumina scanning protocol (BeadChips were scanned with an Illumina BeadArray Reader)

data_processing: The data was normalized by median centering

label: Biotin

source_name: small Intestine (Epithelial cells)

label_protocol: Biotinylated cRNA was prepared based on standar protocol

extract_protocol: RNA extraction was done using RNEasy mini (Qiagen, cat: 74106) and quality control was performed with Agilent Bioanalyzer.

value: Porcn(WT)/Villin-Cre(+,-)

value: Male

tag: age

value: 2-4 month-old

value: Small intestine

value: Epithelial


title: 5326915001_D


title: Epithelial WT1

description: sample id in raw file: 859 F3


title: Epithelial WT4

description: sample id in raw file: Epi 35 (3)


title: 5326915001_C


title: Epithelial KO5

description: sample id in raw file: Epi 50(3)

value: Porcn(flox)/Villin-Cre(+,-)


title: Epithelial WT3

description: sample id in raw file: 32 F3


title: 5326915001_B


title: 5326915001_E


title: 5326915001_F


title: Epithelial KO4

description: sample id in raw file: 33 F3


title: 5326915001_A


title: Epithelial KO3

description: sample id in raw file: Epi 49(3)


title: Epithelial WT2

description: sample id in raw file: 140 F3


title: Epithelial KO2

description: sample id in raw file: 145 F3


title: Epithelial KO1

description: sample id in raw file: 860 F3


title: Stromal WT1

description: sample id in raw file: Stromal 859 (3)

source_name: Small Intestine (Stromal cells)

value: Stromal


title: NPC H1 EtOH 20-2

city: Los Angeles

first: Yong

last: Kim

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

source_name: Neural progenitor cells from H1 hESC with 20mM EtOH

label_protocol: standard Affymetrix procedures

growth_protocol: H1 hESCs were grown in mTeSR1 medium and differentiated into neural stem cells by using STEMdiff neural differentiation system as instructed by manufacturer (StemCell Technologies Inc.)

extract_protocol: Total RNA was extracted by using Qiagen Rneasy kit

value: Neural progenitor cells from H1 hESC


title: Stromal WT4

description: sample id in raw file: Stromal 35


title: Stromal WT3

description: sample id in raw file: Stromal 32


title: NPC H1 EtOH 0-2

source_name: Neural progenitor cells from H1 hESC without EtOH


title: NPC H1 EtOH 0-1


title: Stromal KO4

description: sample id in raw file: Stromal 33


title: H1 p40 Und-2

source_name: Undifferentiated H1 hESC

value: Embryonic stem cell H1


title: Stromal KO3

description: sample id in raw file: Stromal 49


title: Stromal WT2

description: sample id in raw file: Stromal 140 (4)


title: Stromal KO2

description: sample id in raw file: Stromal 145 (4)


title: H1 EtOH 20 Rosett-1

source_name: Rosette from H1 hESC with 20mM EtOH

value: Neural stem cells from H1 hESC


title: H1 p40 Und-1


title: H1 EtOH 0 Rosett-2

source_name: Rosette from H1 hESC without EtOH


title: NPC H1 EtOH 20-1


title: H1 EtOH 0 Rosett-1


title: Stromal KO1

description: sample id in raw file: Stromal 860 (1)


title: rhHSA exp_decreased_rep3

status: Public on Apr 18 2014

city: Changchun

first: chongyang

last: Liang

state: Jilin

address: No.1266, Fujin Road

department: Pharmaceutical Sciences

country: China

institute: JiLin University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

organism: Komagataella pastoris

source_name: Sample from Fermentor #3, rhHSA expression amount is decreased to 220mg / L, fermentation ending.

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

extract_protocol: To maintain cells for further extractions, 9 ml of culture were mixed with 5 ml of freshly made chilled 5% (v/v) phenol (Sigma) solution in absolute ethanol, centrifuged at 4°C and 12, 000 rpm for 5 min; harvested cells were stored at -80°C until extraction.  RNA extractions were performed with RNeasy Mini Kit (Qiagen) following manufacturer’s protocol of enzymatic extraction using lyticase (Sigma). RNA samples were quantified and analysed for purity using Experion RNA StdSens Analysis Kit (Bio-Rad) with a RQI between 8.8 and 9.9.

treatment_protocol: The large-scale expression was done in a 40 L Bioflo-510 fermentor (NBS Co., USA). The fermentation preparation work can refer to the protocol that was reported by Richard HJ Begent&Kerry S Chester in the journal of Nature Protocol. Timing of fermentation process was described (Table 1) as below: 12h, 30h, 48h, 86h, 110h.

value: whole organism

tag: technological phase

value: fermentation ending


title: peak of rhHSA exp_rep2

source_name: Sample from Fermentor #2, Peak of rhHSA expression rate appearing.

value: Peak of rhHSA expression rate appearing


title: peak of rhHSA exp_rep3

source_name: Sample from Fermentor #3, Peak of rhHSA expression rate appearing.


title: BJ_Fibroblast_3

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description:
Gene expression data obtained from human fibroblasts
BJ1_Fibroblast_3

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: Data processed using AltAnalyze package

source_name: human fibroblast

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: Fibroblasts were grown in DMEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

value: human BJ fibroblast


title: rhHSA exp_decreased_rep1

source_name: Sample from Fermentor #1, rhHSA expression amount is decreased to 220mg / L, fermentation ending.


title: adapted methanol_rep1

source_name: Sample from Fermentor #1, Methanol-fed phase ending, cells has been completely adapted methanol as the sole carbon source.


title: rhHSA exp_decreased_rep2

source_name: Sample from Fermentor #2, rhHSA expression amount is decreased to 220mg / L, fermentation ending.


title: peak of rhHSA exp_rep1

source_name: Sample from Fermentor #1, Peak of rhHSA expression rate appearing.


title: adapted methanol_rep3

source_name: Sample from Fermentor #3, Methanol-fed phase ending, cells has been completely adapted methanol as the sole carbon source.


title: adapted methanol_rep2

source_name: Sample from Fermentor #2, Methanol-fed phase ending, cells has been completely adapted methanol as the sole carbon source.


title: case 60_4

city: Stockholm

first: Anna

last: Kwiecinska

address: CCK R8:00

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

hyb_protocol: The purified DNA from test and reference were pooled and mixed with 45μg of Cot1 DNA and 200 μg of Herring sperm DNA and precipitated. The precipitated DNA was dissolved in 30 μl hybridisation buffer, incubated at 37°C for 2 hours and applied to the prehybridised microarray. Hybridisation was performed in a humified Micro Array Hybridisation Chamber (Camlab, Cambridge, UK) at 37°C for 48 hours under a coverslip. The arrays then washed successively in 1xPBS/0.05% Tween20 at room temperature for 15 min twice, 50% formamide/2xSSC at 42°C for 30 min once, 1 x PBS/0.05% Tween 20 at room temperature for 15 min and 1 x PBS for 5 min twice. Dried by centrifugation.

scan_protocol: Scanned on an Axon GenePix 4100A personal scanner. Images were quantified using GenePix Pro version 5.1.

data_processing: The median of the ratio of test reference spot intensity, after subtraction of local background was used as the normalization factor. The chromosomal arm on which the most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was devided by normalization factor of each subarray, an avarage of the duplicate calculated and log2-transformed.

source_name: FL grade I

label_protocol: 400 ng of tumor and reference genomic DNA was labeled with Cy5dCTP or Cy3dCTP (Amersham Biosciences, Little Chalfont, UK) respectively using a BioPrime Kit (Invitrogen, Palsely, UK) with custom-made dNTP mix (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM).

extract_protocol: Proteinase K digestion followed by phenol_chloroform extraction

value: follicular lymphoma grade I

value: female

source_name: Mixed normal blood from 20 individuals (reference)

value: male

value: blood


title: case 60_3

source_name: FL grade II

value: follicular lymphoma grade II


title: case 60_2


title: case 60_5

source_name: transformed DLBCL (GC)

value: transformed DLBCL (GC)


title: Glycerol-fed phase ending_rep3

source_name: Sample From Fermentor #3, Glycerol-fed phase ending, carbon source starving for 40min.Methanol-fed phase starting.

value: carbon source starving for 40min. Methanol-fed phase starting


title: BJ_Fibroblast_2

description:
Gene expression data obtained from human fibroblasts
BJ1_Fibroblast_2


title: case 60_1


title: H1_ES_3

description:
Gene expression data obtained from human ES
H1_ES_3

source_name: human ES

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

value: H1 Human embryonic stem cells


title: BJ_Fibroblast_1

description:
Gene expression data obtained from human fibroblasts
BJ1_Fibroblast_1


title: H1_ES_2

description:
Gene expression data obtained from human ES
H1_ES_2


title: case 59_4


title: Glycerol-fed phase ending_rep1

source_name: Sample From Fermentor #1 Glycerol-fed phase ending, carbon source starving for 40min.Methanol-fed phase starting.


title: Glycerol-fed phase ending_rep2

source_name: Sample From Fermentor #2 Glycerol-fed phase ending, carbon source starving for 40min.Methanol-fed phase starting.


title: case 59_3


title: BG01_ES-2

description:
Gene expression data obtained from human ES
BG_ES_2

value: BG01 Human embryonic stem cells


title: case 59_2


title: case 59_1


title: H1_ES_1

description:
Gene expression data obtained from human ES
H1_ES_1


title: logarithmic growth phase_rep3

source_name: Sample from Fermentor #3, logarithmic growth phase

value: logarithmic growth phase


title: case 57_2


title: logarithmic growth phase_rep2

source_name: Sample from Fermentor #2, logarithmic growth phase


title: case 58_1


title: case 58_2


title: case 57_1


title: reverso2

city: São Paulo

first: Manuella

middle: Nóbrega

last: Dourado

state: São Paulo

address: Av. Prof. Lineu Prestes, 1374 - Ed. Biomédicas II

country: Brazil

institute: University of São Paulo

hyb_protocol: Labelled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardts solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS´and 50% formamide. Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: lides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 90% PMT gain

data_processing: Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with less than 50% of the pixels with values lower than the median local background plus two SD have been flagged and excluded from further analyses. Raw data were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array

organism: Xylella fastidiosa

source_name: X. fastidiosa (control)

label_protocol: Forty micrograms (40 ug) of total X. fastidiosa RNA were mixed with 1 ul of a 4 ug/ul random primer solution (9-mers) in 20 ul of water and heated to 65oC for 10 min. The tube was briefly chilled on ice and mixed with 4 ul of 5mM dNTPs, 4 ul of 0.1 M DTT, 8 ul of 5X first-strand buffer (Invitrogen) and 1.5 ul of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42oC for 1.5 h and terminated by a 15-min incubation at 65oC. The RNA was degraded by adding 1 ul of 10 mg/ml RNAse A and incubation at 37oC for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 ul. One microliter (1 ul) of 4 ug/ul random primer solution (9-mers) and 4 ul of 10X Klenow buffer were then added to the system. The tube was then heated at 65oC for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 ul of 10X low dNTP solution (5mM dATP, 5mM dTTP, 5mM dGTP and 2mM dCTP), 1 ul of Cy5-labeled dCTP (1mM) (Amersham Biosciences) and 1 ul of the Klenow fragment (50 units/ul) (Invitrogen). The reaction was then incubated at 37oC for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

growth_protocol: Both bacteria were grown, separately, in PW medium for 72 hours at 28°C (150 rpm), and 100 mL from each individual cell suspension (108 CFU mL-1) were mixed together (adding a total of 200 mL). The remains from each original culture (200 mL) were kept in separate flasks without interaction, to serve as controls. Afterwards, the interaction and control flasks were incubated at 28°C, in a rotatory shaker (150 rpm) for additional 24 hours.

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

treatment_protocol: The interaction between the phytopathogen X. fastidiosa 9a5c and the endophyte M. mesophilicum SR1.6/6 was evaluated in a co-cultivation experiment. For this analysis, both bacteria were grown, separately, in PW medium for 72 hours at 28°C (150 rpm), and 100 mL from each individual cell suspension (108 CFU mL-1) were mixed together (adding a total of 200 mL). The remains from each original culture (200 mL) were kept in separate flasks without interaction, to serve as controls. Afterwards, the interaction and control flasks were incubated at 28°C, in a rotatory shaker (150 rpm) for additional 24 hours.

source_name: X. fastidiosa+ M. mesophilicum

tag: treatment

value: SR1.6/6 co-culture


title: verso1


title: case 56_2


title: BG01_ES-3

description:
Gene expression data obtained from human ES
BG_ES_-3

tag: cell line


title: reverso1


title: case 56_1


title: logarithmic growth phase_rep1

source_name: Sample from Fermentor #1, logarithmic growth phase


title: case 55_2


title: BG01_ES-1

description:
Gene expression data obtained from human ES
BG_ES_1


title: WT_T8_2

city: Sydney

first: xiuquan

last: ma

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description:
XM_9.2
RNA from cells, vector

hyb_protocol: Labeled, fragmented RNA hybridized to Affymetrix Mouse Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

data_processing: Data was RMA normalised using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

source_name: 3T3-L1 cells, vector, 8hr

label_protocol: RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

growth_protocol: 3T3-L1 cells expressing ISL1 or not were grown in Dulbecco's Modified Eagle's Medium supplemented with 10% newborn calf serum or fetal calf serum, 2 mM L-glutamine, 100 units/liter penicillin, and 100 ug/liter streptomycin at 37 °C in 10% CO2.

extract_protocol: Total RNA was extracted with the RNeasy Mini kit (Qiagen) according to manufacturer's instructions. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: 3T3-L1 cells expressing ISL1 or not were grown to confluence at 37 °C in 10% CO2. Two days after reaching 100% confluence, 3T3-L1 fibroblast cells were treated by differentiation medium containing 10% fetal calf serum, 350 nmol/l insulin, 0.5 mmol/l isobutylmethylxanthine, 250 nmol/l dexamethasone, 400 nmol/l biotin for different times as indicated. 0h means just prior to the differentiation induction.

tag: construct

value: pMIG vector

value: differentiation medium

tag: time point


title: WT_T8_1

description:
XM_9.1
RNA from cells, vector


title: case 55_1


title: case 53_2


title: case 52_1


title: WT_T4_3

description:
XM_8.3
RNA from cells, vector

source_name: 3T3-L1 cells, vector, 4hr


title: case 51_2


title: case 51_1


title: case 54_2


title: case 53_1


title: WT_T4_2

description:
XM_8.2
RNA from cells, vector


title: WT_T2_2

description:
XM_7.2
RNA from cells, vector

source_name: 3T3-L1 cells, vector, 2hr


title: WT_T1_1

description:
XM_6.1
RNA from cells, vector

source_name: 3T3-L1 cells, vector, 1hr


title: WT_T1_3

description:
XM_6.3
RNA from cells, vector


title: case 50_2


title: WT_T4_1

description:
XM_8.1
RNA from cells, vector


title: WT_T1_2

description:
XM_6.2
RNA from cells, vector


title: WT_T2_3

description:
XM_7.3
RNA from cells, vector


title: WT_T0.5_3

description:
XM_5.3
RNA from cells, vector

source_name: 3T3-L1 cells, vector, 0.5hr


title: WT_T0.5_2

description:
XM_5.2
RNA from cells, vector


title: case 49_2

source_name: Mixed normal blood from 20 individuals (reference)


title: case 50_1

source_name: FL grade I


title: WT_T0.5_1

description:
XM_5.1
RNA from cells, vector


title: case 49_1

source_name: FL grade II


title: WT_T2_1

description:
XM_7.1
RNA from cells, vector


title: case 47_1


title: case 48_1


title: WT_T8_3

description:
XM_9.3
RNA from cells, vector


title: G/G-microglia, biological rep2

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-1_0-st-v1
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: Primary cultured microglia of fosB-null mouse

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol:
Primary microglial cells were prepared from the cerebral cortex of 2-day-old mice. After ten days of culture, microglia were isolated and collected.  The collected microglia were further plated at density of 1x106 cell/6cm dish, and culture d for 24 h.
Cultured microglia were washed twice with PBS, harvested and stored at -80˚C.

extract_protocol: Total RNA was isolated using a combination of Isogen and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

tag: background strain


title: case 48_2

source_name: transformed DLBCL (GC)


title: G/G-microglia, biological rep3


title: G/G-microglia, biological rep1


title: case 46_2


title: case 46_1

source_name: FL n.a.

value: follicular lymphoma n.a.


title: wt-microglia, biological rep3

source_name: Primary cultured microglia of wild type mouse


title: case 45_1

source_name: follicular lymphoma grade I


title: case 45_2


title: H1 EtOH 20 Rosett-2

source_name: Rosette from H1 hESC with 20mM EtOH

value: Neural stem cells from H1 hESC


title: case 44_1


title: case 47_2


title: case 58_3


title: subject 60 at Trimester 3

city: Stanford

first: Stephen

last: Quake

address: 318 Campus Drive, E300

department: Bioengineering Dept

institute: Stanford University

hyb_protocol: Fragmentation and hybridisation as per Affymetrix protocol

scan_protocol: Scan using genechip fluidics station

data_processing: Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method

source_name: plasma cell-free RNA

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol

extract_protocol: cell-free circulating RNA extraction performed as indicated in paper's protocol

value: cell-free plasma

tag: pregnancy stage

value: Trimester 3


title: Non-Pregnant Subject 3

value: Non-Pregnant


title: case 43_2

value: female


title: case 44_2

source_name: follicular lymphoma grade III

value: follicular lymphoma grade III

value: male


title: case 42

source_name: de novo DLBCL (GC)

value: de novo DLBCL (GC)

value: blood


title: Non-Pregnant Subject 2


title: Non-Pregnant Subject 1


title: case 39


title: subject 60 at Post Partum

value: Post Partum


title: wt-microglia, biological rep1


title: case 41

value: transformed DLBCL (GC)


title: case 40

source_name: de novo DLBCL (non GC)

value: de novo DLBCL (non GC)


title: case 37


title: Non-Pregnant Subject 4


title: case 38


title: wt-microglia, biological rep2


title: subject 60 at Trimester 1

value: Trimester 1


title: subject 60 at Trimester 2

value: Trimester 2


title: subject 54 at Post Partum


title: subject 58 at Trimester 1


title: subject 58 at Trimester 3


title: verso2

source_name: X. fastidiosa (control)

source_name: X. fastidiosa+ M. mesophilicum

value: SR1.6/6 co-culture


title: case 36


title: case 35


title: case 34


title: case 33


title: case 27


title: case 31


title: case 32


title: case 29


title: case 30


title: subject 58 at Trimester 2


title: subject 58 at Post Partum


title: case 28


title: case 25


title: subject 54 at Trimester 1


title: subject 54 at Trimester 3


title: case 26


title: subject 36 at Trimester 3


title: case 24

source_name: de novo DLBCL

value: de novo DLBCL


title: subject 53 at Trimester 3


title: subject 53 at Trimester 2


title: case 23


title: subject 36 at Trimester 2


title: subject 36 at Post Partum


title: case 21


title: subject 53 at Trimester 1


title: subject 32 at Trimester 2


title: subject 32 at Post Partum


title: subject 36 at Trimester 1


title: case 22


title: case 20


title: subject 32 at Trimester 1


title: subject 24 at Trimester 2


title: subject 54 at Trimester 2


title: subject 24 at Trimester 1


title: case 15


title: subject 32 at Trimester 3


title: case 18


title: subject 24 at Trimester 3


title: case 16


title: subject 16 at Trimester 1


title: case 17


title: case 12


title: case 19


title: case 9

source_name: relaps DLBCL (GC)

value: relaps DLBCL (GC)


title: case 14

source_name: Mixed normal blood from 20 individuals (reference)


title: case 11


title: case 13


title: subject 16 at Post Partum


title: subject 16 at Trimester 3


title: case 8


title: case 10


title: case 5


title: case 6


title: subject 16 at Trimester 2


title: subject 15 at Trimester 3


title: case 3


title: case 7


title: Sample 5

type: SRA

city: London

first: Michael

last: Lovett

state: London

address: Dovehouse St

department: NHLI

country: United Kingdom

institute: Imperial College

library_source: transcriptomic

data_processing:
Sequences were mapped to gga3 using Tophat v1.4.0 with default settings
Alignment files (.bam) were inputed to Partek Genomics Suite v6.6 to calculate RPKM
Genome_build: gga3
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values of individual samples

organism: Gallus gallus

source_name: Basal papilla

extract_protocol:
Chicken cochleae were dissected from E6.5 embryos.  Cochlea were divided into three approximately equal sized pieces to produce proximal, middle, and distal pieces.  Pieces from each region were pooled together and immediately transferred into three 1.5 mL eppendorf tubes containining 0.5 mL Tri Reagent RT (Molecular Research Center, Inc.).  Samples were then stored at -20C until further processing.  Samples from each section of the cochlea were then processed using Illumina mRNA-seq or TrueSeq preparation kits.  Separate biological replicates were also prepared and similarly analyzed.  mRNA was selected by oligo-dT magnetic beads and fragmented.  First-strand cDNA was then generated using random primers.  Second-strand synthesis, end repair and addition of a single A base and adaptor ligation were then performed.  Each RNA-seq library was DNA-sequenced the Illumina HiSeq 2000.
libraries were made using Illumina mRNA-seq or TrueSeq preparation kits.

value: cochlea

tag: cochlear region

value: Mid-BP

value: embryonic day 6.5


title: subject 15 at Post Partum

value: cell-free plasma


title: subject 12 at Trimester 2


title: subject 15 at Trimester 2


title: subject 12 at Post Partum


title: subject 12 at Trimester 3

value: Trimester 3


title: case 4

tag: gender

value: female


title: subject 15 at Trimester 1


title: subject 02 at Post Partum


title: case 2

value: male


title: subject 12 at Trimester 1


title: case 1


title: subject 02 at Trimester 1


title: subject 02 at Trimester 2


title: subject 02 at Trimester 3


title: MDA-MB-231 sh159-1_overnight

city: nashville

first: Miaojun

last: Han

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University

description: MDA-MB-231 shRNA 3

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

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix) at the Vanderbilt Microarray Core Facility (FGSR).

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

source_name: MDA-MB-231, TIP-1 shRNA 159 A1

label_protocol: GeneChip WT Sense Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Cell growth in RPMI 1640 + 10% FBS.

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

treatment_protocol: Fresh trypsinized cells seeding in RPMI 1640 and cultured cells overnight for RNA extraction.

tag: shRNA


title: Apc-mutated organoid, TGF-beta treated 4

city: Helsinki

first: Zoltan

last: Wiener

address: Haartmaninkatu 8

department: Molecular Cancer Biology Programme

country: Finland

institute: University of Helsinki

description: replicate 4

data_processing: The data were normalized with the default normalization method for Illumina arrays in Chipster

source_name: ex vivo intestinal organoid

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

growth_protocol: Intestinal organoids were grown according to Sato et al (Nature, 2009), but without adding growth factors

extract_protocol: Total RNA was extracted by the NucleoSpin RNA II isolation kit (Macherey-Nagel) according to the manufacturer, including DNase treatment. RNA quality was checked by Agilent Bioanalyzer

treatment_protocol: TGF-beta 3 ng/ml for 18h or untreated

tag: genetic background

value: 4-5 months

value: intestinal organoid

tag: genotype

value: Apc-mutated

value: TGF-beta treated


title: Apc-mutated organoid, tamoxifen, TGF-beta treated 2

description: replicate 2

growth_protocol: Intestinal organoids were grown according to Sato et al (Nature, 2009).  After the addition of Tamoxifen, the growth factors were removed from the medium.

value: 3-4 months

tag: tissue

value: tamoxifen + TGFbeta


title: Apc-mutated organoid, tamoxifen, untreated 3

description: replicate 3

value: tamoxifen


title: Apc-mutated organoid, TGF-beta treated 2

description: replicate 2


title: MDA-MB-231 sh159-2_overnight

description: MDA-MB-231 shRNA 4

source_name: MDA-MB-231, TIP-1 shRNA 159 A4


title: Apc-mutated organoid, tamoxifen, untreated 2

description: replicate 2


title: Apc-mutated organoid, tamoxifen, TGF-beta treated 1

description: replicate 1


title: Apc; Kras mutated organoid, TGF-beta treated 3

description: replicate 3

value: Apc; Kras mutated


title: MDA-MB-231 sh162-2_overnight

description: MDA-MB-231 shRNA 2

source_name: MDA-MB-231, TIP-1 shRNA 162 B4


title: Apc; Kras mutated organoid, TGF-beta treated 1

description: replicate 1


title: Apc-mutated organoid, tamoxifen, TGF-beta treated 4

description: replicate 4


title: MDA-MB-231 control 2_overnight

description: MDA-MB-231 control 2

source_name: MDA-MB-231, shRNA control

value: control


title: Apc-mutated organoid, tamoxifen, untreated 4

description: replicate 4


title: Apc-mutated organoid, tamoxifen, TGF-beta treated 3

description: replicate 3


title: Apc-mutated organoid, tamoxifen, untreated 1

description: replicate 1


title: Apc; Kras mutated organoid, TGF-beta treated 2

description: replicate 2


title: Apc; Kras mutated organoid, TGF-beta treated 4

description: replicate 4


title: Apc-mutated organoid, TGF-beta treated 3

description: replicate 3


title: MDA-MB-231 control 1_overnight

description: MDA-MB-231 control 1


title: Apc-mutated organoid, TGF-beta treated 1

description: replicate 1


title: AROM+Testis_5 month_rep2

city: Beijing

first: Wanpeng

last: Yu

address: Yuanmingyuan West Road No.2

institute: China Agricultrual University

description: gene expression in testis from 5 month old AROM+ mice.

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parametersto obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: AROM+ single whole testis_5 month_rep2

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: AROM+

value: whole testis

value: 5 month


title: MDA-MB-231 sh162-1_overnight

description: MDA-MB-231 shRNA 1

source_name: MDA-MB-231, TIP-1 shRNA 162 B1


title: AROM+Testis_5 month_rep3

source_name: AROM+ single whole testis_5 month_rep3


title: MKN1 Hypoxia

city: Daegu

first: You Mie

last: Lee

address: 80, Daehak-ro

country: South Korea

institute: Kyungpook National University

description: The updated miRNA sequences with mature and most precursor probes all on one array (miRBase v13), for human over 1300 miRNA probes. > 3 logs of dynamic range on most scanners. Positive control probes (U6)

hyb_protocol: According to for GenoExplorer Labeled miRNA Hybridization assay, we used 12-bay MAUI system for hybridization step.

scan_protocol: Consult the scanner (GenePix 4000B scanner) manufacturer instructions for laser and PMT settings. The SA-S dye stain signal can be detected using the scanner’s 635 nm wavelength (Cy5) channel.

data_processing: Differentially expressed miRNA were selected through Agilent GeneSpring GX software. Clustering and functional analysis were done by GeneSpring GX, Java-based Array to Kegg software.

source_name: Gastic cancer cell line

label_protocol: According to for GenoExplorer miRNA Labeling Kit, biotin labels are ligated to the 5’ ends of RNA molecules which do not contain a 5’-capped structure.

growth_protocol: MKN1 human gastric cancer cells were maintained in RPMI-1640 containing 10% fetal bovine serum and 1% antibiotics. For hypoxia, cells were incubated 5% CO2, 1% O2, 94% N2 in a hypoxic chamber at 37 °C.

extract_protocol: Total RNA from MKN1 cells treated with normoxia or hypoxia for 24 h was prepared using Trizol Reagent.

treatment_protocol: MKN1 cells treated with normoxia or hypoxia for 24 h.

tag: microenvironment

value: Hypoxia


title: Apc-mutated organoid, untreated 5

description: replicate 5

value: untreated


title: subject 53 at Post Partum

source_name: plasma cell-free RNA

value: cell-free plasma

value: Post Partum


title: AROM+Testis_5 month_rep1

source_name: AROM+ single whole testis_5 month_rep1

value: male


title: MKN1 Normoxia

value: Normoxia


title: Apc; Kras mutated organoid, untreated 5

description: replicate 5

value: 4-5 months

value: intestinal organoid


title: LacZ rep1

city: Barcelona

first: M Lluisa

last: Espinas

address: Baldiri Reixac 10

country: Spain

institute: IBMB-CSIC

description: 477 2012.CEL

hyb_protocol: 8 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

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

organism: Drosophila melanogaster

source_name: S2_LacZ RNAi as control.

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

extract_protocol: RNA was extracted with a combination of Trizol and RNeasy minikit (Qiagen)

tag: genotype/variation

value: LacZ RNAi as control.


title: WtTestis_5 month_rep3

description: gene expression in testis from 5 month old WT mice.

source_name: Wt single whole testis_5 month_rep3

value: wt


title: WtTestis_5 month_rep1

source_name: Wt single whole testis_5 month_rep1


title: Adult_rep4

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description:
C. elegans sample from young adult stage
X3149_12664_808r._C.elegans.CEL

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix GeneChip C. elegans Genome array (Catalog number 900384) . Array hybridization, washing, and staining were performed according to the Affymetrix recommended protocol EuKGE_Ws2v5

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm.

organism: Caenorhabditis elegans

source_name: animal pool 4, young adult stage

label_protocol: cDNA synthesis and preamplification were performed using Nugen Ovation RNA Amplification System V2 (Catalog #3100-60). The amplified cDNA was then fragmented and labeled for hybridization to Affymetrix GeneChip C. elegans Genome Array (Catalog #900384).

growth_protocol: C. elegans was cultured by standard methods on the surface of NGM 1.5% agar Petri dishes of 5.5 cm diameter. Animals were fed the OP50 derivative bacterial strain DA837 and cultivated at 20 degrees Celsius unless noted otherwise. The wild-type strain used was N2, variety Bristol, which was obtained from the C. elegans Genetics Center in 2007, and was freshly thawed every 6 months.

extract_protocol: To extract the RNA, 40 microliters chloroform was added to 200 microliters of Trizol worm suspension, then centrifuged at 13,000 RPM in an Eppendorf 5415C centrifuge for 15 minutes at 4 degree Celsius. The top aqueous phase was then transferred to a fresh microfuge tube, combined with equal volume of chilled 70% ethanol, and mixed. The RNA was then isolated using RNeasy MinElute columns (Qiagen) according to manufacturer’s instructions, eluted in 12 microliters of RNAse-free water and stored at -80 degrees Celcius until further processing. Experiments to assess the quality of the isolated RNA, cDNA synthesis, pre-amplification, and microarray hybridization were all performed at the University of Pennsylvania Molecular Profiling Facility. The A260/A280 ratio ranged 1.56-2.17 (average 1.95, standard deviation 0.16), and the A260/A230 ratio ranged 0.27-1.77 (average 0.97, standard deviation 0.43). The average±standard deviation totalf RNA in nanograms isolated per pooled sample was 22.3±7.0 (L4), 18.6±3.5 (L4 lethargus), and 75.3±10.3 (Young adults). The quality of RNA was further assessed using Agilent 2100 Bioanalyzer. RNA was accepted for further microarray processing if the RNA Integrity Number was >5. Based on this quality assurance analysis, one sample each from the L4, L4 lethargus, and Adult groups was eliminated from further processing.

treatment_protocol: Embryos were collected by the alkaline bleach method from populations of N2 hermaphrodite animals on the first day that the bacteria on the agar plate were depleted. The collected embryos were kept in M9 buffer without bacteria for 16 hours to permit hatching and developmental arrest at the L1 diapause stage. Developmentally arrested L1 animals were then transferred at a density of 3 animals per microliter in a 100 microliter volume onto NGM plates fully covered with DA837 bacteria and allowed to develop at 20 degrees Celsius. Staged animals were collected in batches of 20 animals into 50 microliters of ice-cold Trizol reagent (Invitrogen) in a 1.5 mL microfuge tube, vortexed for 30 seconds, and then flash-frozen by immersion in dry ice in ethanol. Staged animals were collected by hand at room temperature (22.5 degrees Celsius) under 50x (total magnification) stereomicroscopic (Zeiss Stemi 2000) visual guidance using a sterile platinum wire coated with bacteria. Late fourth larval stage (L4) animals were identified based on age (42 hours after feeding L1 arrested animals), size, and a mid body ventral clearance with a dark shadow in its center, which correspond to the developing reproductive structures. L4 animals were all moving and feeding. L4 lethargus animals were identified 45-50 hours after feeding arrested L1s based on quiescence of locomotion and pharyngeal pumping. By checking the cohorts of animals every 10 minutes and removing animals in lethargus, we insured that any newly identified lethargus animal was within 10 minutes of the start of L4 lethargus. These early L4 lethargus animals were transferred to a fresh NGM plate covered with a lawn of DA837 bacteria. A subset of these L4 lethargus animals were allowed to age for 30 minutes at room temperature before collection. Thus, the L4 lethargus animals were collected 30-40 minutes after cessation of pharyngeal pumping. Prior to collecting each animal, it was verified by visual inspection of its behavior to still be in lethargus. Another subset of these L4 lethargus animals were allowed to age for six hours at room temperature before collection during the early adult stage. These early adult animals, which were at an age of approximately four hours after the L4-adult molt, had not yet begun making embryos. Following collection in cohorts of 20 animals per tube, samples were pooled such that each sample of L4, L4 lethargus, and young adult animals had a total of 100 animals (5 tubes per pooled sample). A total of six samples, each with 100 animals, were collected for L4, L4 lethargus, and Adult stages. Based on the quality of RNA as assessed using an Agilent 2100 Bioanalyzer, one sample from each biological group was eliminated from further interrogation by microarray.

tag: group

value: Adult


title: Apc-mutated organoid, untreated 4

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

tag: age

value: Apc-mutated


title: CP190 rep2

description: 475 2012.CEL

source_name: S2_CP190 RNAi

value: CP190 RNAi


title: Adult_rep5

description:
C. elegans sample from young adult stage
X3149_12665_809r._C.elegans.CEL

source_name: animal pool 5, young adult stage


title: Apc; Kras mutated organoid, untreated 4

description: replicate 4

value: Apc; Kras mutated


title: Apc-mutated organoid, untreated 2

description: replicate 2


title: Apc; Kras mutated organoid, untreated 3

description: replicate 3


title: LacZ rep2

description: 478 2012.CEL


title: CG9740 rep2

description: 472 2012.CEL

source_name: S2_CG9740 RNAi

value: CG9740 RNAi


title: Apc; Kras mutated organoid, untreated 2

description: replicate 2

source_name: ex vivo intestinal organoid


title: WtTestis_5 month_rep2

source_name: Wt single whole testis_5 month_rep2

value: whole testis


title: CG9740 rep1

description: 471 2012.CEL


title: Apc-mutated organoid, untreated 3

description: replicate 3


title: Adult_rep2

description:
C. elegans sample from young adult stage
X3149_12662_806r._C.elegans.CEL

source_name: animal pool 2, young adult stage


title: Adult_rep1

description:
C. elegans sample from young adult stage
X3149_12661_805r._C.elegans.CEL

source_name: animal pool 1, young adult stage


title: CP190 rep1

description: 474 2012.CEL


title: L4-lethargus_rep5

description:
C. elegans sample from L4-lethargus stage
X3149_12660_804r._C.elegans.CEL

source_name: animal pool 5, fourth larval stage lethargus


title: Apc; Kras mutated organoid, untreated 1

description: replicate 1


title: subject 24 at Post Partum


title: Adult_rep3

description:
C. elegans sample from young adult stage
X3149_12663_807r._C.elegans.CEL

source_name: animal pool 3, young adult stage


title: HF_MSC_iPS_2

description:
Gene expression data obtained from PB CD34+ blood iPS
HF_MSC_iPS_2

data_processing: RMA (Bioconductor Affy Package)

source_name: iPS

tag: cell type

value: iPS cells derived from mesenchymal stem cells isolated from the dermal sheath/papilla of hair follicles


title: Rbpj_WT_rep1

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

description:
Gene expression from WT PyMT
Rbpj_WT_rep1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using GeneChip Affymetrix scanner 3000 7G

data_processing: The data was analyzed using the RMA and limma methods to assess differential expression. RMA normalized intensities were further processed for Principal Component Analysis

source_name: WT PyMT

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

extract_protocol: miRNeasy kit extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

tag: strain

value: Rbpj fl/fl MMTV-PyMT

tag: facs gating strategy

value: 20 weeks

value: tumor associated macrophages


title: L4-lethargus_rep4

description:
C. elegans sample from L4-lethargus stage
X3149_12659_803r._C.elegans.CEL

source_name: animal pool 4, fourth larval stage lethargus


title: HF_MSC_iPS_1

description:
Gene expression data obtained from PB CD34+ blood iPS
HF_MSC_iPS_1


title: Rbpj_KO_rep2

description:
Gene expression from CD11cCre Rbpj fl/fl PyMT
Rbpj_KO_rep2

source_name: CD11cCre Rbpj fl/fl PyMT

value: CD11cCre Rbpj fl/fl MMTV-PyMT

value: non-terminally differentiated tumor associated macrophages


title: Rbpj_WT_rep2

description:
Gene expression from WT PyMT
Rbpj_WT_rep2


title: BJ1_iPS_1

description:
Gene expression data obtained from fibroblasts iPS
BJ1_iPS_1

value: iPS cells derived from BJ fibroblast


title: H9_ES_1

source_name: human ES

growth_protocol: standard HESC growth conditions as described in Pick et al. (2009).

value: H9 Human embryonic stem cells


title: TAM_CD11blo_rep3

description:
Gene expression from tumor associated macrophages, CD11blo
TAM_CD11blo_rep3

source_name: tumor associated macrophages, CD11blo

value: MMTV-PyMT

value: 16 weeks

value: tumor associated macrophages, CD11blo


title: L4-lethargus_rep1

description:
C. elegans sample from L4-lethargus stage
X3149_12656_800r._C.elegans.CEL

source_name: animal pool 1, fourth larval stage lethargus


title: L4-lethargus_rep3

description:
C. elegans sample from L4-lethargus stage
X3149_12658_802r._C.elegans.CEL

source_name: animal pool 3, fourth larval stage lethargus


title: L4_rep5

description:
C. elegans sample from L4 stage
X3149_12655_799r._C.elegans.CEL

source_name: animal pool 5, fourth larval stage


title: TAM_CD11blo_rep2

description:
Gene expression from tumor associated macrophages, CD11blo
TAM_CD11blo_rep2


title: BJ1_iPS_2

description:
Gene expression data obtained from fibroblasts iPS
BJ1_iPS_2


title: Apc-mutated organoid, untreated 1

description: replicate 1

value: 4-5 months

value: intestinal organoid

tag: treatment

value: untreated


title: Rbpj_KO_rep1

description:
Gene expression from CD11cCre Rbpj fl/fl PyMT
Rbpj_KO_rep1


title: H9_ES_2


title: L4-lethargus_rep2

description:
C. elegans sample from L4-lethargus stage
X3149_12657_801r._C.elegans.CEL

source_name: animal pool 2, fourth larval stage lethargus


title: L4_rep3

description:
C. elegans sample from L4 stage
X3149_12653_797r._C.elegans.CEL

source_name: animal pool 3, fourth larval stage


title: TAM_CD11blo_rep1

description:
Gene expression from tumor associated macrophages, CD11blo
TAM_CD11blo_rep1


title: L4_rep2

description:
C. elegans sample from L4 stage
X3149_12652_796r._C.elegans.CEL

source_name: animal pool 2, fourth larval stage


title: H1_ES_2

value: H1 Human embryonic stem cells


title: MTM_CD11bhi_rep1

description:
Gene expression from mammary tissue macrophages, CD11bhi
MTM_CD11bhi_rep1

source_name: mammary tissue macrophages, CD11bhi

value: mammary tissue macrophages, CD11bhi


title: MTM_CD11bhi_rep2

description:
Gene expression from mammary tissue macrophages, CD11bhi
MTM_CD11bhi_rep2


title: L4_rep4

description:
C. elegans sample from L4 stage
X3149_12654_798r._C.elegans.CEL

source_name: animal pool 4, fourth larval stage


title: H1_ES_1


title: PBMC(GH)_iPS1_2

value: iPS cells derived from peripheral blood derived mononuclear cells (PBMCs)


title: TAM_PCA_rep2

description:
Gene expression from population I tumor associated macrophages
TAM_PCA_rep2


title: PBMC(GH)_iPS1_1


title: TAM_PCA_rep1

description:
Gene expression from population I tumor associated macrophages
TAM_PCA_rep1


title: L4_rep1

description:
C. elegans sample from L4 stage
X3149_12651_795r._C.elegans.CEL

source_name: animal pool 1, fourth larval stage


title: dH1F_iPS_1

value: iPS cells derived from dH1F fibroblast


title: L3-lethargus_rep3

description: C. elegans sample from L3 stage-lethargus stage

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix GeneChip C. elegans Genome array (Catalog number 900384). Array hybridization, washing, and staining were performed according to the Affymetrix recommended protocol EuKGE_Ws2v5

source_name: animal pool 3, third larval stage lethargus

growth_protocol: C. elegans was cultured by standard methods on the surface of NGM 1.5% agar Petri dishes of 5.5 cm diameter. Animals were fed the OP50 derivative bacterial strain DA837 and cultivated at 20 degrees Celsius  unless noted otherwise. The wild-type strain used was N2, variety Bristol, which was obtained from the C. elegans Genetics Center in 2007, and was freshly thawed every 6 months.

extract_protocol: To extract the RNA, 40 microliters chloroform was added to 200 microliters of Trizol worm suspension, then centrifuged at 13,000 RPM in an Eppendorf 5415C centrifuge for 15 minutes at 4 degree Celsius. The top aqueous phase was then transferred to a fresh microfuge tube, combined with equal volume of chilled 70% ethanol, and mixed. The RNA was then isolated using RNeasy MinElute columns (Qiagen) according to manufacturer’s instructions, eluted in 12 microliters of RNAse-free water and stored at -80 degrees Celcius until further processing.   Experiments to assess the quality of the isolated RNA, cDNA synthesis, pre-amplification, and microarray hybridization were all performed at the University of Pennsylvania Molecular Profiling Facility. The A260/A280 ratio ranged 1.56-2.17 (average 1.95, standard deviation 0.16), and the A260/A230 ratio ranged 0.27-1.77 (average 0.97, standard deviation 0.43). The average±standard deviation totalf RNA in nanograms isolated per pooled sample was 29.1±15.9 (L3) and 19.7±3.5 (L3 lethargus). The quality of RNA was further assessed using Agilent 2100 Bioanalyzer. RNA was accepted for further microarray processing if the RNA Integrity Number was >5.

treatment_protocol: Embryos were collected by the alkaline bleach method from populations of N2 hermaphrodite animals on the day that the bacteria on the agar plate was depleted. The collected embryos were kept in M9 buffer without bacteria for 16 hours to permit hatching and developmental arrest at the L1 diapause stage. Developmentally arrested L1 animals were then transferred at a density of 3 animals per microliter in a 100 microliter volume onto NGM plates fully covered with DA837 bacteria and allowed to develop at 20 degrees Celsius. Staged animals were collected in batches of 20 animals into 50 microliters of ice-cold Trizol reagent (Invitrogen) in a 1.5 mL microfuge tube, vortexed for 30 seconds, and then flash-frozen by immersion in dry ice in ethanol. Staged animals were collected by hand at room temperature (22.5 degrees Celsius) under 50x (total magnification) stereomicroscopic (Zeiss Stemi 2000) visual guidance using a sterile platinum wire coated with bacteria. Third larval stage (L3) animals were collected based on age (32 hours after feeding L1s) and active behavior. L3 lethargus animals were collected based on age (37 hours after feeding L1s) and quiescence of locomotion and feeding. Following collection in cohorts of 20 animals per tube, samples were pooled such that each sample of L3 and L3 lethargus animals had a total of 200 animals (10 tubes per pooled sample). A total of four samples, each with 200 animals, were collected for L3 and L3 lethargus stages. Based on the quality of RNA as assessed using a Agilent 2100 Bioanalyzer, one sample of each type was excluded from interrogation by microarray.


title: L3-lethargus_rep1

source_name: animal pool 1, third larval stage lethargus


title: BJ1_Fibroblast_1

source_name: human fibroblast

value: human BJ fibroblast


title: L3_rep2

description: C. elegans sample from L3 stage

source_name: animal pool 2, third larval stage


title: dH1F_iPS_2

source_name: iPS


title: dH1F_Fibro_1

value: human dH1F fibroblast


title: BJ1_Fibroblast_2


title: L3-lethargus_rep2

source_name: animal pool 2, third larval stage lethargus


title: dH1F_Fibro_2


title: L3_rep3

description: C. elegans sample from L3 stage

source_name: animal pool 3, third larval stage


title: islet graft from Akita mouse

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

description: The transplanted mouse islets into hyperglycemic  mouse (Akita mouse) at 6 hours post-transplantation

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

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

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

source_name: islet graft from Akita hyperglycemic mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Expression Kit User Manual, P/N 702646 Rev. 8, Affymetrix).

growth_protocol: Wild-type (WT) C57BL/6 mice were used as donors for islet transplantation, WT male mouse and heterozygous male Akita mouse were used as recipients. Islets were isolated by the collagenase digestion of the pancreas.

extract_protocol: Total RNA was extraced using RNeasy Micro Kit, according to the manufacturer's instructions.

treatment_protocol: Fifty islets were transplanted under the left kidney capsule of the recipient using a 24-gauge catheter on the day of isolation.

tag: islet donor strain

value: wild type C57BL/6

tag: recipient strain

value: heterozygous Akita

tag: recipient strain gender

value: male

tag: recipient mouse status

value: hyperglycemic

value: islets graft at 6 hours post-transplantation


title: Input1

status: Public on Apr 17 2014

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

library_source: genomic

data_processing:
Alignments: Sequences generated by the Illumina Genome Analyzer were processed by the Illumina analysis pipeline version 1.6.1, and aligned to the Human Reference Genome (assembly hg18, NCBI Build36.1, March 2008) using BWA version 0.5.523.
Reads were filtered by removing those with a BWA alignment quality score less than 15.
Peaks: Enriched regions of the genome were identified by comparing the ChIP samples to input samples using the MACS peak caller version 1.3.7.113.
Genome_build: hg18
Supplementary_files_format_and_content: wig files

source_name: LNCaP cells

growth_protocol: RPMI & 10% Foetal Bovine Serum

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: LNCaP

tag: sample type

value: Input

tag: antibody


title: IgGChIP

tag: chip anitbody

value: IgG


title: splenicDC_PCA_rep1

description:
Gene expression from CD11b+ splenic dendritic cells
splenicDC_PCA_rep1

source_name: CD11b+ splenic dendritic cells

value: MMTV-PyMT

value: 20 weeks

value: CD11b+ splenic dendritic cells


title: MycChIP

tag: chip antibody

value: c-Myc

tag: chip vendor

value: SantaCruz

tag: chip catalog#


title: 2-LNCaP-EV-Bic-E2F1-ChIP

growth_protocol: RPMI & 10% Foetal Bovine Serum & Puromycin

treatment_protocol: Bicalutamide 1uM or Vehicle (Ethanol)

tag: vendor

tag: catalog#

tag: condition

value: empty vector and Bicalutamide treated


title: 1-LNCaP-EV-Veh-E2F1-ChIP

value: empty vector and vehicle treated


title: 4-LNCaP-Hes6-Bic-E2F1-ChIP

value: overexpressing Hes6 and Bicalutamide treated


title: 3-LNCaP-Hes6-Veh-E2F1-ChIP

value: overexpressing Hes6 and vehicle treated


title: islet graft from WT mouse

description: The transplanted mouse islets into normoglycemic mouse at 6 hours post-transplantation

source_name: islet graft from Wt normoglycemic  mouse

value: wild type C57BL/6

value: normoglycemic

tag: tissue


title: Control_Castrated OWJ52

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: LNCaP-LM xenograft control

growth_protocol: LNCaP-LM xenografts were grown subcutaneously in NSG mice

extract_protocol: Total RNA was extracted using the QIAGEN AllPrep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Castration of host mice at 100mm3

value: LNCaP-LM NSG xenografts

tag: expression

value: vector control


title: Control_Castrated OWJ75


title: Hes6_Castrated OWJ42

source_name: LNCaP-LM xenograft with Hes6 overexpression

value: Hes6 overexpression


title: L3_rep1

description: C. elegans sample from L3 stage

source_name: animal pool 1, third larval stage

tag: group


title: input36-EV-Full (E2F1 )

value: LNCaP

value: INPUT

value: EV-Full


title: Hes6_Castrated OWJ64


title: Hes6_Castrated OWJ72


title: input1-Hes6-Castrated (E2F1 )


title: Control_Castrated OWJ5


title: Control_Castrated OWJ59


title: Hes6_Castrated OWJ40


title: Control_Castrated OWJ2


title: Hes6_Castrated OWJ39


title: MCF7vector_subpolysomal_nutlin_16h_rep3

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: MCF7vector,subpolysomal,nutlin,16h,replicate 3

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf)

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

growth_protocol: MCF7 vector were growth in RPMI supplemented with 10% FBS, antibiotics (100 units/ml penicillin plus 100 mg/ml streptomycin) and 2mM L-Glutamine. In order to maintain the selection, we added Puromycin at 0.5 μg/mL as final concentration.

extract_protocol: Cells were treated with cycloheximide (final concentration of 10 μg/ml) for 5 min at 37°C in order to stabilize the polysomes. Cells were then washed twice with PBS containing the same concentration of cycloheximide and lysed by adding directly on the plate 300 μl of lysis buffer [10 mM NaCl, 10 mM MgCl2, 10 mMTris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/ml RNase inhibitors, 1 mM dithiothreitol and 10 μg/ml cycloheximide]. Lysates were transferred to Eppendorf tubes using cell scrapers, incubated on ice for 5 min with occasional vortexing, and centrifuged for 10 min at 12 000 g at 4°C. The supernatant was frozen in liquid nitrogen and stored at −80°C or loaded directly onto a 15–50% linear sucrose gradient (15 ml total volume) containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged in a SW41 rotor for 110 min at 180 000 g. Using an automated fraction collector, fractions containing subpolysomal and polysomal RNA were identified based on the quantification of UV fluorescence. All the fractions identifying the subpolysomal RNA (free, 40S, 60S, 80S) were collected and then treated with proteinase K (100 μg/ml) in 1% SDS for 3 h at 37°C followed by extraction with 1 volume of phenol–chloroform and 10 mM NaCl and by precipitation in one volume of isopropanol overnight at -80°C followed by 30 min centrifugation at 10 000 rpm. A final wash of the RNA pellet in 70% v/v ethanol was performed in order to remove as much as possible traces of phenol contamination.

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and allowed to reach 70-80% of confluency before treatment with 10 μM of Nutlin for 16h.

tag: treatment

value: Nutlin

tag: rna fraction

value: subpolysomal RNA


title: MCF7vector_polysomal_nutlin_16h_rep2

description: MCF7vector,polysomal,nutlin,16h,replicate 2

extract_protocol: Cells were treated with cycloheximide (final concentration of 10 μg/ml) for 5 min at 37°C in order to stabilize the polysomes. Cells were then washed twice with PBS containing the same concentration of cycloheximide and lysed by adding directly on the plate 300 μl of lysis buffer [10 mM NaCl, 10 mM MgCl2, 10 mMTris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/ml RNase inhibitors, 1 mM dithiothreitol and 10 μg/ml cycloheximide]. Lysates were transferred to Eppendorf tubes using cell scrapers, incubated on ice for 5 min with occasional vortexing, and centrifuged for 10 min at 12 000 g at 4°C. The supernatant was frozen in liquid nitrogen and stored at −80°C or loaded directly onto a 15–50% linear sucrose gradient (15 ml total volume) containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged in a SW41 rotor for 110 min at 180 000 g. Using an automated fraction collector, fractions containing subpolysomal and polysomal RNA were identified based on the quantification of UV fluorescence. All the fractions identifying polysomal RNAs were collected and then treated with proteinase K (100 μg/ml) in 1% SDS for 3 h at 37°C followed by extraction with 1 volume of phenol–chloroform and 10 mM NaCl and by precipitation in one volume of isopropanol overnight at -80°C followed by 30 min centrifugation at 10 000 rpm. A final wash of the RNA pellet in 70% v/v ethanol was performed in order to remove as much as possible traces of phenol contamination.

value: polysomal RNA


title: MCF7vector_polysomal_dmso_16h_rep1

description: MCF7vector,polysomal,dmso,16h,replicate 1

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and allowed to reach 70-80% of confluency before treatment with DMSO for 16h.

value: DMSO


title: MCF7vector_polysomal_doxorubicin_16h_rep1

description: MCF7vector,polysomal,doxorubicin,16h,replicate 1

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and allowed to reach 70-80% of confluency before treatment with 1.5 μM of Doxorubicin for 16h.

value: Doxo


title: MCF7vector_polysomal_dmso_16h_rep3

description: MCF7vector,polysomal,dmso,16h,replicate 3


title: MCF7vector_subpolysomal_dmso_16h_rep1

description: MCF7vector,subpolysomal,dmso,16h,replicate 1


title: MCF7vector_polysomal_nutlin_16h_rep3

description: MCF7vector,polysomal,nutlin,16h,replicate 3


title: MCF7vector_polysomal_doxorubicin_16h_rep2

description: MCF7vector,polysomal,doxorubicin,16h,replicate 2


title: MCF7vector_subpolysomal_doxorubicin_16h_rep2

description: MCF7vector,subpolysomal,doxorubicin,16h,replicate 2


title: MCF7vector_polysomal_nutlin_16h_rep1

description: MCF7vector,polysomal,nutlin,16h,replicate 1


title: MCF7vector_subpolysomal_nutlin_16h_rep2

description: MCF7vector,subpolysomal,nutlin,16h,replicate 2


title: MCF7vector_subpolysomal_doxorubicin_16h_rep3

description: MCF7vector,subpolysomal,doxorubicin,16h,replicate 3


title: MCF7vector_subpolysomal_dmso_16h_rep2

description: MCF7vector,subpolysomal,dmso,16h,replicate 2


title: MCF7vector_total_doxorubicin_16h_rep3

description: MCF7vector,total RNA,doxorubicin,16h,replicate 3

extract_protocol: Total RNA was extracted using the Agilent Total RNA Isolation Mini kit according to the manufacturer’s protocol. RNA was quantified using a spectrophotometer and its quality was checked by Agilent 2100 Bioanalyzer platform, following the manufacturer’s guidelines for sample preparation and analysis of data (Agilent 2100 Bioanalyzer 2100 Expert User's Guide, http://www.agilent.com).

treatment_protocol: MCF7 vector were seeded into 6-well plates and allowed to reach 70-80% of confluency before treating with 1.5 μM of Doxorubicin for 16h.

value: total RNA


title: MCF7vector_subpolysomal_doxorubicin_16h_rep1

description: MCF7vector,subpolysomal,doxorubicin,16h,replicate 1


title: MCF7vector_total_nutlin_16h_rep3

description: MCF7vector,total RNA,nutlin,16h,replicate 3

treatment_protocol: MCF7 vector were seeded into 6-well plates and allowed to reach 70-80% of confluency before treating with 10 μM of Nutlin for 16h.


title: MCF7vector_total_nutlin_16h_rep1

description: MCF7vector,total RNA,nutlin,16h,replicate 1


title: MCF7vector_total_doxorubicin_16h_rep2

description: MCF7vector,total RNA,doxorubicin,16h,replicate 2


title: MCF7vector_total_dmso_16h_rep3

description: MCF7vector,total RNA,dmso,16h,rep3

treatment_protocol: MCF7 vector were seeded into 6-well plates and allowed to reach 70-80% of confluency before treating with DMSO for 16h.


title: MCF7vector_polysomal_dmso_16h_rep2

description: MCF7vector,polysomal,dmso,16h,replicate 2


title: MCF7vector_subpolysomal_nutlin_16h_rep1

description: MCF7vector,subpolysomal,nutlin,16h,replicate 1


title: MCF7vector_polysomal_doxorubicin_16h_rep3

description: MCF7vector,polysomal,doxorubicin,16h,replicate 3


title: MCF7vector_total_dmso_16h_rep1

description: MCF7vector,total RNA,dmso,16h,replicate 1


title: MCF7vector_total_dmso_16h_rep2

description: MCF7vector,total RNA,dmso,16h,replicate 2


title: Breast Cancer Sample BC5127

city: Frankfurt

first: Thomas

last: Karn

address: Theodor-Stern-Kai 7

description: Gene expression data from primary breast tumors

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturers instructions

extract_protocol: RNeasy kit, Qiagen. according to the manufacturer's instructions

treatment_protocol: samples were snap frozen and stored at -80°C

tag: gender

value: female

value: pretreatment surgical biopsy

tag: cohort

value: HH


title: MCF7vector_subpolysomal_dmso_16h_rep3

description: MCF7vector,subpolysomal,dmso,16h,replicate 3

tag: cell line


title: MCF7vector_total_nutlin_16h_rep2

description: MCF7vector,total RNA,nutlin,16h,replicate 2


title: Breast Cancer Sample BC5102


title: MCF7vector_total_doxorubicin_16h_rep1

description: MCF7vector,total RNA,doxorubicin,16h,replicate 1


title: Breast Cancer Sample BC5067


title: Breast Cancer Sample BC5133


title: Breast Cancer Sample BC5106


title: Breast Cancer Sample BC5012


title: Breast Cancer Sample BC5031


title: Breast Cancer Sample BC5108


title: Breast Cancer Sample BC1919


title: Breast Cancer Sample BC1918


title: Breast Cancer Sample BC5116


title: Breast Cancer Sample BC5114


title: Breast Cancer Sample BC1914


title: Breast Cancer Sample BC1917


title: Breast Cancer Sample BC5003


title: Breast Cancer Sample BC1916


title: Breast Cancer Sample BC1922


title: Breast Cancer Sample BC5056


title: Breast Cancer Sample BC1913


title: Breast Cancer Sample BC1833


title: Breast Cancer Sample BC1831


title: #2_undiff_5hr_deltaLeu

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: undifferentiated human ES_Leucine deprived_5hr

growth_protocol: Before the following assay, human ES cells (khES3) are grown in human ES media to 80% confluent.

extract_protocol: Total RNA was extraced using RNeasy Mini Kit, according to the manufacturer's instructions.

treatment_protocol: khES3 cells are cultured in the complete media for 5hr (#2_undiff_5hr_compl), or in the presence or abesence of  extracellular leucine or lysine for 5hr (#2_undiff_5hr_deltaLeu, #2_undiff_5hr_deltaLys).

tag: cell type

value: undifferentiated human ES cells

tag: culture medium

value: Leucine deprived medium

tag: culture duration

value: 5 hrs


title: #2_undiff_5hr_compl

source_name: undifferentiated human ES_complete medium for 5hr

value: complete medium


title: Breast Cancer Sample BC1830


title: #2_undiff_5hr_deltaLys

source_name: undifferentiated human ES_Lysine deprived_5hr

value: Lysine deprived medium


title: #1_Endoderm

source_name: human ES cell derived endoderm cells

growth_protocol: Before the following assay, human embryonic stem cells (khES3) are grown in human ES media to 70-80% confluent. Endoderm cells are prepared by directed-differentiation of khES3 with activinA (#1_Endoderm).

treatment_protocol: khES3 cells are cultured in the presence or abesence of  extracellular methionine for 5 or 24 hr (#1_undiff_5hr_compl, #1_undiff_5hr_deltaMet, #1_undiff_24hr_compl, #1_undiff_24hr_deltaMet). 0hr indicates khES3 cells just before these manipulations (#1_undiff_0hr).

value: human ES cell derived endoderm cells

value: Activin containing media

value: 5 days


title: Breast Cancer Sample BC1828


title: Breast Cancer Sample BC1827


title: Breast Cancer Sample BC1820


title: Breast Cancer Sample BC1824


title: splenicDC_PCA_rep2

description:
Gene expression from CD11b+ splenic dendritic cells
splenicDC_PCA_rep2

tag: strain

tag: genotype/variation

value: MMTV-PyMT

tag: facs gating strategy

tag: age

value: 20 weeks

value: CD11b+ splenic dendritic cells


title: #1_undiff_5hr_compl

source_name: undifferentiated human ES_complete medium_5hr


title: Breast Cancer Sample BC1823


title: #1_undiff_24hr_deltaMet

source_name: undifferentiated human ES_methionine deprived medium for 24hr

value: methionine deprived medium

value: 24 hrs


title: Breast Cancer Sample BC1815


title: #1_undiff_24hr_compl

source_name: undifferentiated human ES_complete medium for 24hr


title: Breast Cancer Sample BC1816


title: Breast Cancer Sample BC1819


title: Breast Cancer Sample BC1814


title: Breast Cancer Sample BC1826


title: #1_undiff_5hr_deltaMet

source_name: undifferentiated human ES_methionine deprived medium for 5hr


title: #1_undiff_0hr

source_name: undifferentiated human ES cells before treatment

value: 0 hr (untreated control)


title: Breast Cancer Sample BC1818

value: female


title: Breast Cancer Sample BC1810

value: pretreatment surgical biopsy


title: Breast Cancer Sample BC1812

value: HH


title: Breast Cancer Sample BC1813


title: swd2.2delta cells-replica 3-FW and RV strands

city: Lyon

first: Vincent

last: Vanoosthuyse

address: 46 allée d'Italie

department: Laboratoire de Biologie Moléculaire de la Cellule

country: France

institute: CNRS

description: strand-specific expression data from fission yeast cells lacking Swd2.2 grown for 3 hours at 34°C

hyb_protocol: 5 µg of cDNAs were then hybridized on a GeneChip S.pombe Tiling 1.0FR Array (Affymetrix), according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0
Series supplementary files contain RMA normalized data and UTR ratio
corresponds to the chromosome followed by the position on the given chromosome of the 1st nucleotide of the probe
Raw data were normalized with Partek Genomic Suite software 6.5 (Partek Inc., St. Louis, MO, US) using Robust Multiarray Average (RMA) statistical algorithm, which includes RMA background correction, quantile normalization and log2 transformation.
UTR ratios
Columns ABCDE:  Gene of interest (E) with its position on the chromosome (ABCD)
Columns FGHI: Genomic positions of the 5'UTR, the coding sequence (CDS) and the 3'UTR of the gene of interest
Columns JKL:  Average signal intensity recorded in swd2.2+ cells for the 5'UTR (column J), the CDS (column K) and the 3'UTR (column L) of the gene
Columns MNO:  Average signal intensity recorded in swd2.2delta cells for the 5'UTR (column M), the CDS (column N) and the 3'UTR (column O) of the gene
Column P UTR ratio swd2.2+: Ratio of the average signal intensity recorded in the 3'UTR versus the CDS in swd2.2+ cells
Column Q UTR ratio swd2.2delta: Ratio of the average signal intensity recorded in the 3'UTR versus the CDS in swd2.2delta cells
Column R UTR ratio swd2.2delta/UTR ratio swd2.2+

organism: Schizosaccharomyces pombe

source_name: swd2.2delta cells grown at 34°C for 3 hours, replica 3

label_protocol: Extracted RNA were purified using the miRNeasy mini kit (Qiagen), dosed using a nanodrop and their quality were assessed using a Bioanalyzer 2100 (Agilent). To prepare cDNAs, 250 ng of RNA were then amplified using the WT Expression Kit (Ambion). The resulting cDNAs were then dosed (nanodrop) and their quality assessed using a Bioanalyzer 2100 (Agilent). 5,5 µg of cDNAs were then fragmented and labelled using the GeneChIP WT Terminal Labelling Kit (Affymetrix)

growth_protocol: cells were grown in rich YES+ Adenine medium for one generation (3 hours) at 34°C

extract_protocol: RNA was extracted from 2.10^8 cells according to the procedure described in (Wilhelm et al., 2008; Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239-1243.).

tag: genotype

tag: genetic background


title: LNCaPEV_pre F

description: F

source_name: LNCaP cells with EV control

growth_protocol: LNCaP cells grown in RPMI & 10% FBS

treatment_protocol: No treatment

value: LNCaP

value: vector control