title: ZFA107_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 107, HK design


title: ZFA160_HK_9mer

status: Public on Dec 02 2010

type: protein

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

country: USA

institute: Mount Sinai School of Medicine

description: platform design file: GPL11261

hyb_protocol: 12.5 μl of the in vitro translation mix was added to 137.5 μl of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween 20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween 20 and once with PBS/0.01% Triton X 100. After a one-hour incubation at room temperature, the array was washed once with PBS/0.5% Tween 20/50 μM zinc acetate and once with PBS/0.01% Triton X 100/50 μM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 μM zinc acetate. After a one-hour incubation at room temperature, the array was washed three times with PBS/0.05% Tween 20/50 μM zinc acetate and once with PBS/50 μM zinc acetate.

scan_protocol: Protein-bound microarrays were scanned using an Agilent microarray scanner at 2 μM resolution to detect Cy5-conjugated antibody.

data_processing:
Microarray TIF images were analyzed using ImaGene version 7.5 software (BioDiscovery)
We provide several scores for each 8-mer or 9-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.
Please see the supplementary files on the platform record (GPL11261) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: Artificial zinc finger array 160, HK design

label_protocol: T7-GST tagged proteins were not labelled after purification

extract_protocol: The zinc finger arrays were cloned as SacI-BamHI fragments into pTH5352, a modified T7-driven GST expression vector (see http://hugheslab.ccbr.utoronto.ca/supplementary-data/C2H2_modularity/ for a vector map). We expressed proteins using a PURExpress in vitro protein synthesis kit (New England BioLabs), supplemented with RNase inhibitor and 50 μM zinc acetate.

tag: zn finger

tag: platform_id design

value: HK


title: LM30__Q504E2

status: Public on Dec 03 2010

type: genomic

city: Hamburg

first: Simon

middle: A

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: According to the manufacturer's instructions (Kreatech Biotechnology, Amsterdam).

extract_protocol:
As decribed in:
Joosse SA, et al. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat. 2008 Aug 14

tag: tissue

value: colon

tag: disease state

value: carcinoma

tag: metastasis

value: liver

source_name: Women reference pool

tag: tag

value: A pool of DNA from peripheral blood lymphocytes, from 7 apperently healty women.


title: ZFA3_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 3, HK design


title: ZFA152_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 152, HK design


title: ZFA24_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 24, HK design


title: ZFA145_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 145, HK design


title: ZFA15_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 15, HK design


title: ZFA4_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 4, HK design


title: ZFA169_HK_8mer

description: platform design file: GPL11260

data_processing:
Microarray TIF images were analyzed using ImaGene version 7.5 software (BioDiscovery)
We provide several scores for each 8-mer or 9-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.
Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

source_name: Artificial zinc finger array 169, HK design


title: ZFA45_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 45, HK design


title: ZFA2_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 2, HK design


title: ZFA107_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 107, ME design

value: ME


title: ZFA57_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 57, ME design


title: ZFA1_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 1, HK design


title: ZFA7_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 7, HK design


title: ZFA5_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 5, HK design


title: ZFA10_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 10, HK design


title: ZFA160_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 160, ME design


title: ZFA75_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 75, HK design


title: ZFA93_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 93, HK design


title: ZFA188_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 188, ME design


title: ZFA57_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 57, HK design


title: ZFA160_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 160, HK design


title: ZFA145_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 145, ME design


title: ZFA75_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 75, ME design


title: ZFA8_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 8, HK design


title: ZFA169_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 169, ME design


title: MDA-MB-435-L1Mic (Poly-like) cell line [L1mic-7t2m]

type: RNA

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description:
L1mic-7t2m
Classifier: Polymets

data_processing: the qPCR data were processed and outputed by Sequence Dectection System (SDS) Software (Applied Biosystems); the undetermined data were set to the Ct value of 40. The raw Ct values were scrutinized to identify and remove technical sample outliers with exceptionally higher portion of undetermined miRNAs. The Ct values were then normalized by quantile normalization using R package HTqPCR.

label: syberGreen

molecule: total RNA

source_name: Injection of MDA-MB-435-GFP cancer cells into the mammary pat pad to develop oligo- or poly-metastasis in lung.

label_protocol: qPCR was performed using the 7900HT Fast Real-Time PCR System, TaqMan Universal PCR Master Mix and Taqman MiRNA Array A Card v2.0 (Applied Biosystems)

extract_protocol:
Total RNA extracted using Trizol (Gibco/BRL) according to manufacturer's instructions
cDNA were generated using 30ng of total RNA,  Megaplex RT Primers, Human Pool Set v2.0 and TaqMan MiRNA Reverse Transcription kit (Applied Biosystems)

tag: cell line

value: MDA-MB-435-L1Mic (Poly-like) cell line


title: CGXII 50mM L-lactate_vs_CGXII 50mM DL-lactate

city: Bielefeld

first: Jung-Won

last: Youn

address: Universitaetsstrasse 25

department: Genetics of Prokaryotes

institute: Bielefeld University

hyb_protocol: Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with applified PCR fragments, hybridisation and stringent washing of the microarrays were performed as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

scan_protocol: After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 6000 laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis.

organism: Corynebacterium glutamicum ATCC 13032

source_name: CGXII+50 mM L-lactate

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

growth_protocol: Bacterial strains, media and growth conditions. The C. glutamicum type strain ATCC 13032 was used as wild type. For growth experiments and DNA microarray experiments, cells from a fresh LB agar plate were inoculated into into 50 ml  LB medium in a 500 ml baffled shake flask and this first preculture was incubated at 30°C and 120 rpm. For DNA microarray experiments, cells were washed in 0.9 % saline solution and the second preculture and subsequently the main culture were inoculated to an optical density at 600 nm (OD600) of 0.1 and 0.5, respectively, in 50 ml either CgXII minimal medium with D- and L-lactate or without D-lactate and in LB with and without D-lactate. The cultures were incubated at 30°C and 120 rpm.

extract_protocol: Preparation of total RNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

treatment_protocol: see growth protocol

tag: growth conditions

value: CGXII+50 mM L-lactate

tag: growth phase

value: exponential

source_name: CGXII+50 mM DL-lactate

value: CGXII+50 mM DL-lactate


title: ZFA93_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 93, ME design


title: MDA-MB-435-L1Mic (Poly-like) cell line [L1mic-8t2m]

description:
L1mic-8t2m
Classifier: Polymets


title: LB_vs_LB+50mM D-lactate

source_name: LB

value: LB

source_name: LB+50mM D-lactate

value: LB+50mM D-lactate


title: CGXII 50mM DL-lactate_vs_CGXII 50mM L-lactate


title: LB+50mM D-lactate_vs_LB 2


title: MDA-MB-435-L1Mic (Poly-like) cell line [L1mic-3t2m]

description:
L1mic-3t2m
Classifier: Polymets


title: MDA-MB-435-L1Mic (Poly-like) cell line [L1mic-2t2m]

description:
L1mic-2t2m
Classifier: Polymets


title: ZFA152_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 152, ME design


title: LB+50mM D-lactate_vs_LB 1


title: ZFA45_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 45, ME design


title: ZFA152_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 152, HK design


title: ZFA24_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 24, ME design


title: ZFA188_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 188, HK design


title: MDA-MB-435-L1-GFP (Ol-like) cell line [L1-8T-2m]

description:
L1-8T-2m
Classifier: Oligomets

value: MDA-MB-435-L1-GFP (Ol-like) cell line


title: ZFA107_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 107, HK design


title: MDA-MB-435-L1-GFP (Ol-like) cell line [L1-3T-2m]

description:
L1-3T-2m
Classifier: Oligomets


title: ZFA75_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 75, HK design


title: ZFA57_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 57, HK design


title: ZFA145_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 145, HK design


title: ZFA93_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 93, HK design


title: ZFA15_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 15, ME design


title: ZFA10_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 10, ME design


title: ZFA8_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 8, ME design


title: MDA-MB-435-L1-GFP (Ol-like) cell line [L1-4T-2m]

description:
L1-4T-2m
Classifier: Oligomets

source_name: Injection of MDA-MB-435-GFP cancer cells into the mammary pat pad to develop oligo- or poly-metastasis in lung.


title: ZFA45_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 45, HK design


title: ZFA7_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 7, ME design


title: ZFA5_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 5, ME design


title: ZFA8_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 8, HK design


title: PP LD-Delay 1500, rep2

city: Kobe, Hyogo

first: Hiroki

middle: R

last: Ueda

address: 2-2-3, Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
Gene expression data from mice pars tuberalis at ZT8 in the long day delay condition.
Pooled samples from 25 mice.

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to the manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm using the R/Bioconductor package (R version 2.8.0, Bioconductor version 2.3).

label: biotin

organism: Mus musculus

source_name: long day delay, ZT8

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix).

growth_protocol: Male CBA/N mice (Japan SLC, Shizuoka, Japan) were purchased 3 weeks after birth. The mice were housed under short-day conditions (light: dark = 8 h:16 h, ZT0 = lights on, ZT8 = lights off, 400 lux), and were given food and water ad libitum and kept under these short-day conditions for 3 weeks. The mice were then separated into 2 groups. One group was maintained under the short-day conditions and the other was housed under long-day conditions (light:dark = 16 h:8 h, ZT0 = lights on, ZT16 = lights off, 400 lux) for 2 weeks. The PTs of the two groups were retrieved every 4 h for 1 day, starting at ZT0. For the experiments performed during the first day of the long-day conditions, we applied two different conditions, following 3 weeks under short-day conditions. In one, the light-onset was advanced by 8 hours (advance condition), and in the other, the dark period was delayed by 8 hours (delay condition). PTs from both groups were obtained every 4 h for 1 day, starting at the lights-on time. (Lights on for the advance condition was ZT16 as defined by the short-day condition. Lights on for the delay condition was ZT0).

extract_protocol: The total RNA was prepared from the pooled samples for each region taken at all time points using Trizol reagent (GIBCO BRL).

treatment_protocol: Slices (0.5-mm thick) of the brain of CBA/N mice were cut on a Mouse Brain Matrix (Neuroscience, Tokyo) and frozen. The PT was punched out with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope.

tag: strain

value: CBA/N

tag: gender

value: male

value: pars tuberalis

tag: age

value: 6 weeks

tag: condition

value: long day delay

tag: time point


title: 10 day schistosomula from Balb/C host v5

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

description: Parasite development depending on host environment

hyb_protocol: 1.4 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 55ul  containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x GEx HI-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent S.mansoni 44k oligoneucleotide microarray 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (B version) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 ) to obtain background

organism: Schistosoma japonicum

source_name: Isolated parasite

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from isolated parasites using TRIzol Reagent using the manufacturer’s protocol.

tag: Stage

value: 10 day post infection

tag: host

value: Balb/C mouse


title: ZFA10_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 10, HK design

value: HK


title: PP LD-Delay 1500, rep1


title: PP LD-Delay 1900, rep1

description:
Gene expression data from mice pars tuberalis at ZT12 in the long day delay condition.
Pooled samples from 25 mice.

source_name: long day delay, ZT12


title: ZFA24_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 24, HK design


title: PP LD-Delay 1100, rep2

description:
Gene expression data from mice pars tuberalis at ZT4 in the long day delay condition.
Pooled samples from 25 mice.

source_name: long day delay, ZT4


title: PP LD-Delay 300, rep1

description:
Gene expression data from mice pars tuberalis at ZT20 in the long day delay condition.
Pooled samples from 25 mice.

source_name: long day delay, ZT20


title: 10 day schistosomula from M. fortis host v5

value: Microtus fortis


title: ZFA7_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 7, HK design


title: ZFA15_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 15, HK design


title: PP LD-Delay 300, rep2


title: ZFA2_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 2, ME design

value: ME


title: ZFA4_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 4, ME design


title: PP LD-Delay 700, rep1

description:
Gene expression data from mice pars tuberalis at ZT0 in the long day delay condition.
Pooled samples from 25 mice.

source_name: long day delay, ZT0


title: 10 day schistosomula from M. fortis host v1


title: PP LD-Delay 1900, rep2


title: PP LD-Delay 2300, rep2

description:
Gene expression data from mice pars tuberalis at ZT16 in the long day delay condition.
Pooled samples from 25 mice.

source_name: long day delay, ZT16


title: 10 day schistosomula from Balb/C host v1


title: PP LD-Delay 700, rep2


title: BRCA1 - B1081

scan_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.

extract_protocol: As decribed in: Joosse SA, et al. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat. 2008 Aug 14

tag: organ

value: mammary gland

tag: disease

value: invasive ductal carcinoma

source_name: Women reference pool

tag: sample type

value: A pool of DNA from peripheral blood lymphocytes, from 6 apparently healthy women.


title: PP LD-Delay 2300, rep1

tag: tissue


title: PP LD-Advance 12, rep2

description:
Gene expression data from mice pars tuberalis at ZT12 in the long day advance condition.
Pooled samples from 25 mice.

source_name: long day advance, ZT12

value: long day advance


title: ZFA1_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 1, ME design

tag: zn finger

tag: platform_id design


title: BRCA1 - B1080

data_processing:
As described in:
Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.


title: ZFA4_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 4, HK design


title: ZFA5_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 5, HK design


title: BRCA1 - B1079


title: ZFA3_ME_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 3, ME design


title: PP LD-Delay 1100, rep1


title: BRCA1 - B1077


title: PP LD-Advance 8, rep2

description:
Gene expression data from mice pars tuberalis at ZT8 in the long day advance condition.
Pooled samples from 25 mice.

source_name: long day advance, ZT8


title: PP LD-Advance 12, rep1


title: BRCA1 - B1076


title: BRCA1 - B1075


title: PP LD-Advance 0, rep2

description:
Gene expression data from mice pars tuberalis at ZT0 in the long day advance condition.
Pooled samples from 25 mice.

source_name: long day advance, ZT0


title: ZFA2_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 2, HK design


title: ZFA3_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 3, HK design


title: PP LD-Advance 4, rep1

description:
Gene expression data from mice pars tuberalis at ZT4 in the long day advance condition.
Pooled samples from 25 mice.

source_name: long day advance, ZT4


title: BRCA1 - B1078


title: PP LD-Advance 20, rep2

description:
Gene expression data from mice pars tuberalis at ZT20 in the long day advance condition.
Pooled samples from 25 mice.

source_name: long day advance, ZT20


title: PP LD-Advance 4, rep2


title: BRCA1 - B1073


title: ZFA1_HK_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 1, HK design


title: ZFA169_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 169, ME design


title: ZFA188_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 188, ME design


title: PP LD-Advance 8, rep1


title: PP LD-Advance 16, rep2

description:
Gene expression data from mice pars tuberalis at ZT16 in the long day advance condition.
Pooled samples from 25 mice.

source_name: long day advance, ZT16


title: PP LD-Advance 0, rep1


title: PP LD 2300, rep2

description:
Gene expression data from mice pars tuberalis at ZT20 in the long day 2 weeks condition.
Pooled samples from 25 mice.

source_name: long day 2 weeks, ZT20

value: 8 weeks

value: long day 2 weeks


title: PP LD 2300, rep1


title: PP LD 1900, rep2

description:
Gene expression data from mice pars tuberalis at ZT16 in the long day 2 weeks condition.
Pooled samples from 25 mice.

source_name: long day 2 weeks, ZT16


title: PP LD-Advance 20, rep1


title: ZFA160_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 160, ME design


title: PP LD-Advance 16, rep1


title: ZFA152_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 152, ME design


title: PP LD 1500, rep2

description:
Gene expression data from mice pars tuberalis at ZT12 in the long day 2 weeks condition.
Pooled samples from 25 mice.

source_name: long day 2 weeks, ZT12


title: BRCA1 - B1072

source_name: Women reference pool


title: PP LD 700, rep2

description:
Gene expression data from mice pars tuberalis at ZT4 in the long day 2 weeks condition.
Pooled samples from 25 mice.

source_name: long day 2 weeks, ZT4


title: PP LD 1500, rep1


title: PP LD 700, rep1


title: ZFA107_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 107, ME design


title: PP LD 1100, rep1

description:
Gene expression data from mice pars tuberalis at ZT8 in the long day 2 weeks condition.
Pooled samples from 25 mice.

source_name: long day 2 weeks, ZT8


title: PP LD 1900, rep1


title: PP LD 1100, rep2


title: PP LD 300, rep1

description:
Gene expression data from mice pars tuberalis at ZT0 in the long day 2 weeks condition.
Pooled samples from 25 mice.

source_name: long day 2 weeks, ZT0


title: PP LD 300, rep2


title: ZFA145_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 145, ME design


title: PP SD 1900, rep2

description:
Gene expression data from mice pars tuberalis at ZT12 in the short day condition.
Pooled samples from 25 mice.

source_name: short day, ZT12

value: short day


title: PP SD 2300, rep2

description:
Gene expression data from mice pars tuberalis at ZT16 in the short day condition.
Pooled samples from 25 mice.

source_name: short day, ZT16

value: CBA/N


title: ZFA45_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 45, ME design


title: PP SD 2300, rep1

value: male


title: ZFA24_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 24, ME design


title: ZFA75_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 75, ME design


title: PP SD 300, rep2

description:
Gene expression data from mice pars tuberalis at ZT20 in the short day condition.
Pooled samples from 25 mice.

source_name: short day, ZT20

value: pars tuberalis


title: PP SD 300, rep1


title: ZFA93_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 93, ME design


title: Hs_pi3_LV

city: Innsbruck

first: Gilbert

last: Spizzo

address: Innrain 66

department: Experimental Oncology

country: Austria

institute: TCRI

description: Gene expression data from Hs578t cells transfected with pIRESpuro3

hyb_protocol: according to Affymetrix´ GeneChip Expression Analysis Technical Manual. Washing and staining: fluidics station (GeneChip? Fluidics Station450, Affymetrix) controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4., Fluidics protocol for eukaryotic 3´-expression arrays: EukGe_WSv4.

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix), controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4

data_processing: GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization and median-polish summarization on Affymetrix HGU133 plus 2.0 microarray probe-level data were performed using R 2.7.1 and Bioconductor 2.2. (gcrma package: justGCRMA function). The log2 transformed absolute expression values of the treatment sample (EpCAM positive line) were subtracted from the absolute expression values of the control sample (control line) in a gene-wise manner.

label_protocol: cDNA synthesis and in vitro-transcription: with Ambion´s Message Amp II 96 Kit

growth_protocol: 72h, phenol red free MEM medium (PAA) supplemented with 5mM glutamine (Gibco) and 10% fetal bovine serum (FBS superior, Biochrom) at 37°C under 5% CO2.

extract_protocol: Total RNA was isolated by using TRI-reagent (Molecular Research Centre) and RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer´s protocol.

value: mammary gland,

value: breast / carcinoma

tag: atcc number


title: Hs_pi3_Ep

description: Gene expression data from Hs578t cells transfected with pIRESpuro3_EpCAM

tag: cell line


title: ZFA8_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 8, ME design


title: ZFA15_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 15, ME design


title: ZFA57_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 57, ME design


title: WT_project III_LP

type: other

city: Bethesda

first: Eun-Hee

last: Park

state: MD

address: 6 Center Dr.

department: NICHD

institute: NIH

description: This sample is of wild-type YAJ3. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc. following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc. following their standard operating protocol. See www.nimblegen.com.

data_processing: The data was extracted from the scanned image and analyzed for normalized gene expression summary values (CALLS) by quantile normalization and the Robust Multi-array Average (RMA) algorithm (Irizarry et al. Biostatistics, 2003) using the NimbleScan software (NimbleGen). ArrayStar 3.0 software (DNASTAR; Madison, WI) was used to analyze the expression data provided by NimbleGen.

molecule: other

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae wilde-type YAJ3 (Jivotovskaya etal, MCB,2006)

label_protocol: Labeling was performed by NimbleGen Systems Inc. following their standard operating protocol. See www.nimblegen.com.

growth_protocol: WT strain YAJ3, eIF4G1 degron mutant YAJ41 , and eIF3 degron mutant YAJ34 were grown in liquid synthetic complete (SC) medium containing 2% raffinose as carbon source and 0.1 mM copper sulfate at 25°C (SCRaf + Cu2+, 25°C; permissive conditions) to an optical density (A600) of 0.15 to 0.6. After addition of galactose (2%), cells were incubated for an additional 30 min at 25°C followed by growth in SC containing 2% raffinose, 2% galactose, and 1 mM bathocuproinedisulfonic acid (BCS) at 36°C (SCRaf/Gal + BCS, 36°C; nonpermissive conditions) for up to 8h. Cycloheximide was added to a final concentration of 0.1 mg/mL, and the culture was chilled on ice for 10 min.

extract_protocol: Total RNA samples from the WCE or RNA samples from heavy/light polysomes were isolated using TRIZOL reagent (Invitrogen) according to the manufacturer's suggested protocol.

tag: genotype

value: Wild-type

tag: molecule type

value: light polysomes


title: WT_project III_T

value: total RNA


title: WT_project III_HP

value: heavy polysomes


title: ZFA10_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 10, ME design

value: ME


title: PP SD 1900, rep1

tag: strain


title: PP SD 1100, rep2

description:
Gene expression data from mice pars tuberalis at ZT4 in the short day condition.
Pooled samples from 25 mice.

source_name: short day, ZT4

tag: gender


title: 4G degron mutant_project III_T

description: This sample is of eIF4G degron mutant YAJ41 in which the chromosomal eIF4G2 (tif4632Δ) is deleted, harboring a temperature-sensitive degron allele of the gene encoding eIF4G1 (tif4631-td). The tif4631-td allele encodes ubiquitin and a thermolabile dihydrofolate reductase moiety fused to the N terminus of eIF4G1, expressed from a copper-dependent promoter, and is integrated into the chromosome in a manner that disrupts the resident wild-type (WT) TIF4631 allele. The strain also contains a galactose-inducible form of the gene encoding the ubiquitin ligase (Ubr1) required for proteasomal degradation of degron-tagged proteins by the “N-end rule” pathway. Shifting cells from medium containing copper and raffinose (as carbon source) at 25°C to medium containing galactose and raffinose but lacking copper at 36°C represses new synthesis and triggers proteasomal degradation of the existing degron-tagged eIF4G1-td protein. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.

source_name: Saccharomyces cerevisiae eIF4G1 degron mutant YAJ41 (Jivotovskaya etal, MCB,2006)

value: eIF4G1 degron mutant tif4631-td


title: PP SD 1500, rep1

description:
Gene expression data from mice pars tuberalis at ZT8 in the short day condition.
Pooled samples from 25 mice.

source_name: short day, ZT8

tag: age


title: ZFA5_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 5, ME design


title: PP SD 1500, rep2

tag: condition


title: WT_project II_HP

description: This sample is of wild-type YAJ3. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: WT_project II_LP


title: WT_project I_LP

description: This sample is of wild-type YAJ3. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: CFT073_LB_rep2

city: Montreal

first: Gabriela

last: Hidalgo

state: Quebec

address: 3610 University St

department: Chemical Engineering

country: Canada

institute: McGill University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® E. coli Genome 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with FlexArray 1.4.1 software program (http://genomequebec.mcgill.ca/FlexArray/). The data were normalized using the Robust Multi-Array Average algorithm (RMA). Comparison between the two data sets was done using the Randomized Variance Model (RVM) with a cut-off of a fold change of 2 (or -2) and a P-value of 0.05.

organism: Escherichia coli

source_name: CFT073 in LB, after 5 hours of growth.

label_protocol: Biotinylated cRNA were prepared according to the standard Prokaryotic Target Preparation protocol from Affymetrix (Affymetrix GeneChip® Expression Analysis Technical Manual) from 10 ug total RNA.

growth_protocol: Cultures of E. coli CFT073 were maintained at –80ºC in Luria-Bertani broth with 15% glycerol. Cultures were streaked onto LB agar plates and incubated (37°C, 24 h).  A single colony was inoculated into 150 mL of LB broth (in a 500 mL baffled flask).  Three inoculated flasks contained LB broth alone (controls), and three inoculated flasks were supplemented with cranberry derived PAC extract (100 µg/mL).Bacteria were incubated at 37°C, 5 h, 200 rpm to mid-log growth phase.

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

treatment_protocol: One volume of bacterial culture was added to two volumes of RNAprotect Bacteria Reagent (Qiagen) and RNA was extracted using RNeasy mini kit (Qiagen).  All samples were on-column treated with DNase I.

tag: growth condition

value: LB broth alone (control)


title: ZFA3_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 3, ME design


title: PP SD 700, rep2

description:
Gene expression data from mice pars tuberalis at ZT0 in the short day condition.
Pooled samples from 25 mice.

source_name: short day, ZT0

tag: time point


title: PP SD 1100, rep1


title: WT_project II_T


title: 4G degron mutant_project III_LP


title: WT_project I_T


title: CFT073_LB+PACs_rep3

source_name: CFT073 in LB+PACs (100 µg/mL), after 5 hours of growth.

value: LB broth supplemented with cranberry PACs (100 µg/mL)


title: 4G degron mutant_project II_T

description: This sample is of eIF4G degron mutant YAJ41 in which the chromosomal eIF4G2 (tif4632Δ) is deleted, harboring a temperature-sensitive degron allele of the gene encoding eIF4G1 (tif4631-td). The tif4631-td allele encodes ubiquitin and a thermolabile dihydrofolate reductase moiety fused to the N terminus of eIF4G1, expressed from a copper-dependent promoter, and is integrated into the chromosome in a manner that disrupts the resident wild-type (WT) TIF4631 allele. The strain also contains a galactose-inducible form of the gene encoding the ubiquitin ligase (Ubr1) required for proteasomal degradation of degron-tagged proteins by the “N-end rule” pathway. Shifting cells from medium containing copper and raffinose (as carbon source) at 25°C to medium containing galactose and raffinose but lacking copper at 36°C represses new synthesis and triggers proteasomal degradation of the existing degron-tagged eIF4G1-td protein. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.


title: ZFA1_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 1, ME design


title: CFT073_LB_rep3


title: WT_project I_HP


title: CFT073_LB+PACs_rep2


title: CFT073_LB+PACs_rep1


title: CFT073_LB_rep1


title: ZFA7_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 7, ME design


title: 4G degron mutant_project III_HP


title: PP SD 700, rep1


title: ZFA4_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 4, ME design


title: 4G degron mutant_project I_T

description: This sample is of eIF4G degron mutant YAJ41 in which the chromosomal eIF4G2 (tif4632Δ) is deleted, harboring a temperature-sensitive degron allele of the gene encoding eIF4G1 (tif4631-td). The tif4631-td allele encodes ubiquitin and a thermolabile dihydrofolate reductase moiety fused to the N terminus of eIF4G1, expressed from a copper-dependent promoter, and is integrated into the chromosome in a manner that disrupts the resident wild-type (WT) TIF4631 allele. The strain also contains a galactose-inducible form of the gene encoding the ubiquitin ligase (Ubr1) required for proteasomal degradation of degron-tagged proteins by the “N-end rule” pathway. Shifting cells from medium containing copper and raffinose (as carbon source) at 25°C to medium containing galactose and raffinose but lacking copper at 36°C represses new synthesis and triggers proteasomal degradation of the existing degron-tagged eIF4G1-td protein. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.


title: 4G degron mutant_project I_LP


title: Effects of hCG on the testicular transcriptome of S. senegalensis: Sample 2

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

description: Biological replicate 2 of 2

hyb_protocol: Hybridizations were carried out for 17 h at 60°C using Agilent's gaskets G2534-60002, G2534A hybridization chambers, and DNA Hybridization Oven G2545A, according to the manufacturer's instructions

scan_protocol: Microarray raw data were obtained using Agilent's DNA Microarray Scanner G2505B and Feature Extraction software (v10.1)

data_processing: Raw data were obtained using Agilent's DNA Microarray Scanner G2505B and Feature Extraction software (v10.1). The raw fluorescence intensity data were processed using the Polyphemus software, developed at Oryzon Genomics, which includes spatial data compensation, non-significant expressed data filtering, and data normalization. Data normalization was carried out by an improved version of the nonlinear Q-splines normalization method, enhanced with robust regression techniques.

organism: Solea senegalensis

source_name: Testis from saline-injected S. senegalensis

label_protocol: Total RNA (0.5 μg) from each sample was amplified and labelled with fluorescent cyanine dyes, Cy3 or Cy5, using the Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems) following the manufacturer's instructions with minor modifications

extract_protocol: Total RNA was extracted from testes from saline-injected fish using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

treatment_protocol: Fish were injected intraperitoneally with a saline solution and were sacrificed 24 hours after the injection

value: testis pieces

source_name: Testis from hCG-injected S. senegalensis

extract_protocol: Total RNA was extracted from testes from hCG-injected fish using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

treatment_protocol: Fish were injected intraperitoneally with human chorionic gonadotropin (hCG; 5IU/g body weight) and were sacrificed 24 hours after the injection


title: ZFA2_ME_8mer

description: platform design file: GPL11260

source_name: Artificial zinc finger array 2, ME design


title: 4G degron mutant_project II_LP


title: Effects of hCG on the testicular transcriptome of S. senegalensis: Sample 1

description: Biological replicate 1 of 2


title: 4G degron mutant_project II_HP


title: Asaf_12092SA_Mapping250_Sty

status: Public on Dec 01 2010

city: Jerusalem

first: Asaf

last: Hellman

address: Hadassah Medical School

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University

description: Exponentially grown EBV-transformed lymphocytes

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: As per manufacturer (Affymetrix).

data_processing:
See reference (Aran et al 2010).
DNA methylation: Cel files of MSRE-treated and untreated DNA samples from various tissues and cell lines, hybridized to Affymetrix SNP mapping microarrays. BED files with methylation score calculated as the 1-log2 of the hybridization intensities before/after MSRE treatment are added. Replication timing: Cel files of G1 and early-S fractions of the cell cycle, obtained from exponentially grown EBV-transformed lymphocytes, hybridized to Affymetrix SNP mapping microarrays. Bed file corresponding this calculation is added.

source_name: GM12092 Early-S

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: DNA samples were extracted using the QIAamp blood mini kit (Qiagene.com).

treatment_protocol: DNA methylation: One microgram of genomic DNA was digested at 37oC for16 hrs with a methylation sensitive restriction enzyme (MSRE) cocktail including AciI (20 units), BsaHI (1.3 units), HhaI (2.5 units), HpaII (2.5 units), and HpyCH4IV (10 units) (NewEngland Biolabs), in a 50 microliter reaction volume with 0.1 mg/ml BSA and 10% NEB buffer #4 (New England Biolabs), ethanol precipitated, and resuspended in TE at 50 ng/µl. Replication timing: none.

value: EBV transformed B-lymphcytes line GM12092

value: female


title: Asaf_12093GB_Mapping250_Sty

value: EBV transformed B-lymphcytes line GM12093


title: Asaf_12093SA_Mapping250_Sty

source_name: GM12093 Early-S


title: Asaf_12093SB_Mapping250_Sty


title: Asaf_12092SB_Mapping250_Sty


title: Asaf_12093GA_Mapping250_Sty


title: Asaf_12092GB_Mapping250_Sty


title: DnaB Chip-chip in B. Subtilis grown in MM_1

city: Nottingham

first: Panos

last: Soultanas

state: Nottinghamshire

address: University Park

department: School of Chemistry

country: United Kingdom

institute: University of Nottingham

description:
Bacillus subtilis strain 168 grown in MM; DnaB antisera
The antibodies against DnaD and DnaB were custom made by the 'Medical and Health Sciences Support Unit at the University of Nottingham, UK'. They were rabbit polyclonals. The secondary antibodies were Dynabeads M-280 coated with sheep anti-rabbit IgG from Invitrogen.

hyb_protocol: Slides were hybridised for 40 hours at 65C as per manufacturers instructions

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1)

data_processing: Data from the feature extraction without further processing.  The data was not normalized.  The negative values are from the Agilent control features on the array.  Negative signals are due to background subtraction where both foreground and background values are very low and the foreground is lower than the background.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Genomic DNA from Bacillus subtilis strain 168 IPd with anti-DnaB antisera.

label_protocol:
200-400ng ChIP or genomic DNA was labelled with Cy3 or Cy5 using a custom protocol utilizing the Invitrogen BioPrime labelling kit. Briefly this invovled the samples (20ul) and 2.5x random primers (20ul) were dentured at 94C for 3 minutes and then moved immediately to ice for 5 minutes.
The following mastermix was then added to each reaction 5ul dNTP mix (2mM dATP, 2mM dGTP, 2mM dTTP, 0.5mM dCTP), 3.75ul 1mM cy3 or cy5 d-CTP (GE healthcare and 1ul klenow enzyme. The reactions were then incubated at 37C for 6 hours and purified using Qiagen QiaQuick PCR cleanup columns. The resulting labelled DNA was then hybridisaed to Agilent slides as per manufacurers instructions.

growth_protocol: An overnight culture of Bacillus subtilis (strain 168) was used to inoculate 800 ml of LeMaster minimal medium. The culture was incubated at 30°C. During exponential growth (OD595 = 0.8).

extract_protocol: An overnight culture of Bacillus subtilis (strain 168) was used to inoculate 800 ml of LB or LeMaster minimal medium. The culture was incubated at 30°C. During exponential growth (OD595 = 0.8) 1% v/v formaldehyde was added for 20 min to cross-link protein-DNA complexes. The reaction was quenched by 0.5 M glycine. Cells were harvested and washed with 50 ml 10mM Tris–HCl pH 7.5, suspended in 2 ml lysis buffer (10mM Tris–HCl pH 8.0, 20% w/v sucrose, 50mM NaCl, 10mM EDTA, 10 mg/ml lysozyme) and incubated at 37 C for 30 min. Immunoprecipitation (IP) buffer (8 ml) was added (50mM HEPES–KOH pH 7.5, 150mM NaCl, 1mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 0.1% w/v sodium dodecyl sulfate and 1mM phenylmethylsulfonyl fluoride) and the solution sonicated 15 times (20 s bursts, 20 s rest on ice). The mixture was clarified by centrifugation (15 000g, 15 min at 4 C), the supernatant incubated with 300 ml anti-DnaB or anti-DnaD antibody (custom) overnight at 4 C on a rotating wheel and then with 150 ml of Dynabeads  M-280 sheep anti-rabbit IgG (Invitrogen) for 5 h at 4 C. The beads were washed twice with IP buffer, once with wash buffer (10mM Tris–HCl pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% v/v Nonident-P40 and 0.5% w/v sodium deoxycholate), once with wash buffer plus 0.02M NaCl and twice with TE buffer (10mM Tris–HCl pH 7.5, 1mM EDTA). After removing the TE buffer, the beads were suspended in 400 ml elution buffer (50mM Tris–HCl pH 7.5, 10mM EDTA, 1% w/v SDS) and incubated at 65 C for 10 min. Cross links were reversed by incubation with 0.8 mg/ml of proteinase K (Thermo Scientific) in 0.5  elution buffer at 42 C for 2 h and 65 C for 6 h. DNA was purified with a PCR purification kit (QIAGEN) and quantified by nanodrop.

treatment_protocol: 1% v/v formaldehyde was added for 20 min to cross-link protein-DNA complexes. The reaction was quenched by 0.5 M glycine. Cells were harvested and washed with 50 ml 10mM Tris–HCl pH 7.5, suspended in 2 ml lysis buffer (10mM Tris–HCl pH 8.0, 20% w/v sucrose, 50mM NaCl, 10mM EDTA, 10 mg/ml.

tag: chip antibody

value: anti-DnaB

source_name: control genomic DNA from Bacillus subtilis strain 168

value: control genomic DNA


title: DnaD Chip-chip in B. Subtilis grown in MM_2

description:
Bacillus subtilis strain 168 grown in MM; DnaD antisera
The antibodies against DnaD and DnaB were custom made by the 'Medical and Health Sciences Support Unit at the University of Nottingham, UK'. They were rabbit polyclonals. The secondary antibodies were Dynabeads M-280 coated with sheep anti-rabbit IgG from Invitrogen.

source_name: Genomic DNA from Bacillus subtilis strain 168 IPd with anti-DnaD antisera.

value: anti-DnaD


title: Asaf_12092GA_Mapping250_Sty


title: DnaB Chip-chip in the JMA201 B. Subtilis strain in LB

description:
Bacillus subtilis strain JMA201 grown in LB; DnaB antisera
The antibodies against DnaD and DnaB were custom made by the 'Medical and Health Sciences Support Unit at the University of Nottingham, UK'. They were rabbit polyclonals. The secondary antibodies were Dynabeads M-280 coated with sheep anti-rabbit IgG from Invitrogen.

organism: Bacillus subtilis

source_name: Genomic DNA from Bacillus subtilis strain JMA201 IPd with anti-DnaB antisera.

growth_protocol: An overnight culture of Bacillus subtilis (strain 168) was used to inoculate 800 ml of LB. The culture was incubated at 30°C. During exponential growth (OD595 = 0.8).

tag: pxis promoter

value: promoter is repressed (OFF)


title: H2A.Z ChIP from wild-type cells, alpha factor arrest, replicate 1

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

hyb_protocol: Amplified, labeled ChIP DNA were mixed, purified by microcon, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 55 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy5/Cy3) were calculated.

source_name: input (reference DNA obtained from the input MNAse digested chromatin prior to antibody addition)

label_protocol:
Cells were crosslinked with formaldehyde (2%), washed with water and zymolyase treated. Cells were then digested with MNase, and subjected to immunoprecipitation with with 10 ul Abcam rabbit anti-Htz1 polyclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.
The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

growth_protocol: Cells were grown to an OD of 0.2 in YPDextrose and arrested by adding alpha factor to a final concentration of 4 ug/ml and incubated for 2.5 hrs (wt) or 4.0 hrs (ino80D).

extract_protocol: DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.

tag: genotype/variation

value: WT

value: none (input)

source_name: Htz1 ChIP

value: anti-Htz1 polyclonal antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#


title: DnaB Chip-chip in B. Subtilis grown in LB_1

description:
Bacillus subtilis strain 168 grown in LB; DnaB antisera
The antibodies against DnaD and DnaB were custom made by the 'Medical and Health Sciences Support Unit at the University of Nottingham, UK'. They were rabbit polyclonals. The secondary antibodies were Dynabeads M-280 coated with sheep anti-rabbit IgG from Invitrogen.

tag: sample type


title: DnaB Chip-chip in the JMA264 B. Subtilis strain grown in LB

description:
Bacillus subtilis strain JMA264 grown in LB; DnaB antisera
The antibodies against DnaD and DnaB were custom made by the 'Medical and Health Sciences Support Unit at the University of Nottingham, UK'. They were rabbit polyclonals. The secondary antibodies were Dynabeads M-280 coated with sheep anti-rabbit IgG from Invitrogen.

source_name: Genomic DNA from Bacillus subtilis strain JMA264 IPd with anti-DnaB antisera.

value: promoter is constitutively ON


title: H2A.Z ChIP from wild-type cells, nocodazole arrest

growth_protocol: Cells were grown to an OD of 0.2 in YPDextrose and arrested by adding nocodazole to a final concentration of 20 ug/ml and incubated for 2.5 hrs (wt) or 4.0 hrs (ino80D).


title: Leaves-activated carbon (50 ug/ml) rep.2

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Applied Science

institute: University of Arkansas at Little Rock

description: Gene expression data from leaves of 10 days seedlings of tomato (cv. Micro-Tom)

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

organism: Solanum lycopersicum

source_name: 10 day old  leaves of wild type tomato

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix Eukaryotic two-cycle target labeling assay as specified in the GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

growth_protocol: Tomato seeds were germinated on MS medium (Magenta boxes) in light and harvested after 10 days of cultivation.

extract_protocol: Roots and first two leaves were isolated and immediately frozen in liquid nitrogen. The harvested root and leaf samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: No special tretments before harvesting were carried out.

value: Leaves  of 10 days-old tomato - Wild type (cv. Micro-Tom) grown on 50 ug/ml of CNTs

tag: cultivar

value: Micro-Tom

tag: tissue

value: Leaves

tag: protocol

value: grown on activated carbon (50 ug/ml)


title: H2A.Z ChIP from ino80D cells, alpha factor arrest, replicate 3


title: H2A.Z ChIP from ino80D cells, alpha factor arrest, replicate 2

label_protocol:
Cells were crosslinked with formaldehyde (2%), washed with water and zymolyase treated. Cells were then digested with MNase, and subjected to immunoprecipitation with with 10 ul Millipore rabbit anti-Htz1 polyclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.
The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

value: Millipore


title: H2A.Z ChIP from wild-type cells, alpha factor arrest, replicate 2

label_protocol:
Cells were crosslinked with formaldehyde (2%), washed with water and zymolyase treated. Cells were then digested with MNase, and subjected to immunoprecipitation with with 10 ul Millipore rabbit anti-Htz1 polyclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.
The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.


title: H2A.Z ChIP from ino80D cells, nocodazole arrest


title: H2A.Z ChIP from wild-type cells, alpha factor arrest, replicate 3


title: H2A.Z ChIP from ino80D cells, alpha factor arrest, replicate 1

label_protocol:
Cells were crosslinked with formaldehyde (2%), washed with water and zymolyase treated. Cells were then digested with MNase, and subjected to immunoprecipitation with with 10 ul Abcam rabbit anti-Htz1 polyclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.
The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.


title: DnaD Chip-chip in B. Subtilis grown in LB_2

description:
Bacillus subtilis strain 168 grown in LB; DnaD antisera
The antibodies against DnaD and DnaB were custom made by the 'Medical and Health Sciences Support Unit at the University of Nottingham, UK'. They were rabbit polyclonals. The secondary antibodies were Dynabeads M-280 coated with sheep anti-rabbit IgG from Invitrogen.


title: Leaves-activated carbon (50 ug/ml) rep.1


title: Leaves-CNTs (200 ug/ml) rep.2

value: Leaves  of 10 days-old tomato - Wild type (cv. Micro-Tom) grown on 200 ug/ml of CNTs

value: grown on 200 ug/ml of CNTs


title: Leaves-CNTs (100 ug/ml) rep.2

value: Leaves  of 10 days-old tomato - Wild type (cv. Micro-Tom) grown on 100 ug/ml of CNTs

value: grown on 100 ug/ml of CNTs


title: Leaves-CNTs (200 ug/ml) rep.1


title: Leaves-CNTs (100 ug/ml) rep.1


title: Ferret Lung, infecetd with SARS-CoV on Day 1, biological rep3

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

institute: Toronto General Research Institute

description: Gene expression data from ferret lung after infection with SARS-CoV on day 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PLIER using Expression Console Version 1.1 (Affymetrix) default analysis settings.

organism: Mustela putorius furo

source_name: Ferret

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA from blood was extracted with PAXgene Blood RNA Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Total RNA from lung was extracted with TRIzol (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: In experiments with SARS-CoV infection, intranasal infection of ferrets with 10^3 TCID SARS-CoV / Tor2 strain was performed. Ferrets were euthanized on day 0 (before infection), day 1 and day 2 (post infection). Peripheral blood was collected in PAXgene tubes ((BD®) and lung tissue was excised and put in RNAlater (Ambion, Austin, TX) immediately. In experiments with IFN-a2b,  subcutaneous injection of ferrets with 1 microgram/kilogram of IFN-a2b was performed on the back of ferrets. Ferrets were euthanized on day 0 (before injection), day 1 and day 2 (post injection). Peripheral blood was collected in PAXgene tubes and lung tissue was excised and put in RNAlater (Ambion, Austin, TX) immediately.

value: Lung

tag: virus strain

value: SARS-CoV


title: Roots-CNTs (50 ug/ml) rep.2

description: Gene expression data from roots of 10 days seedlings of tomato (cv. Micro-Tom)

source_name: 10 day old  roots of wild type tomato

value: Roots  of 10 days-old tomato - Wild type (cv. Micro-Tom) grown on 50 ug/ml of CNTs

value: Roots

value: grown on 50 ug/ml of CNTs


title: Ferret Lung, infecetd with SARS-CoV on Day 2, biological rep1

description: Gene expression data from ferret lung after infection with SARS-CoV on day 2


title: Leaves-control rep.1

value: Leaves  of 10 days-old tomato - Wild type (cv. Micro-Tom)- control

value: control


title: Leaves-CNTs (50 ug/ml) rep.1


title: Leaves-CNTs (50 ug/ml) rep.2


title: Roots-activated carbon (50 ug/ml) rep.1

value: Roots  of 10 days-old tomato - Wild type (cv. Micro-Tom) grown on activated carbon (50 ug/ml)


title: Roots-CNTs (100 ug/ml) rep.2

value: Roots  of 10 days-old tomato - Wild type (cv. Micro-Tom) grown on 100 ug/ml of CNTs


title: Ferret Lung, infecetd with SARS-CoV on Day 2, biological rep3


title: Roots-activated carbon (50 ug/ml) rep.2

value: Micro-Tom


title: Roots-CNTs (200 ug/ml) rep.1

value: Roots  of 10 days-old tomato - Wild type (cv. Micro-Tom) grown on 200 ug/ml of CNTs


title: Ferret Lung, infecetd with SARS-CoV on Day 2, biological rep2


title: Leaves-control rep.2

value: Leaves


title: Roots-CNTs (200 ug/ml) rep.2


title: Roots-CNTs (50 ug/ml) rep.1


title: Ferret Lung, infecetd with SARS-CoV on Day 1, biological rep2


title: Ferret Blood, infecetd with SARS-CoV on Day 2, biological rep4

description: Gene expression data from ferret blood after infection with SARS-CoV on day 2

value: Blood


title: Ferret Lung, uninfected, on Day 0, biological rep3

description: Gene expression data from ferret lung, uninfected

value: Uninfected


title: Ferret Lung, infecetd with SARS-CoV on Day 1, biological rep1


title: Ferret Lung, uninfected, on Day 0, biological rep1


title: Ferret Blood, infecetd with SARS-CoV on Day 2, biological rep2


title: Roots-CNTs (100 ug/ml) rep.1


title: Roots -control rep.2

value: Roots  of 10 days-old tomato - Wild type (cv. Micro-Tom) - control


title: 4G degron mutant_project I_HP

source_name: Saccharomyces cerevisiae eIF4G1 degron mutant YAJ41 (Jivotovskaya etal, MCB,2006)

tag: genotype

value: eIF4G1 degron mutant tif4631-td

tag: molecule type

value: heavy polysomes


title: Ferret Blood, infecetd with SARS-CoV on Day 2, biological rep3


title: Ferret Lung, uninfected, on Day 0, biological rep2

value: Lung


title: Ferret Blood, infecetd with SARS-CoV on Day 2, biological rep1

value: SARS-CoV


title: Ferret Blood, uninfected, on Day 0, biological rep3

description: Gene expression data from ferret blood, uninfected


title: Ferret Blood, uninfected, on Day 0, biological rep2


title: SFEB Day2 E-cad (+) [U74Bv2]

city: Kobe

first: Daisuke

last: Kamiya

address: 2-2-3 Minatojima-Minamimachi, Chuo

institute: RIKEN CDB

hyb_protocol: Samples were hybridized with Affymetrix Murine Genome U74B Version 2 Array and scanned at the RIKEN CDB Microarray Facility.

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

data_processing: The expression data were analyzed using an in-house-developed program (eXintegrator, http://www.cdb.riken.jp/scb/documentation/index.html). eXintegrator is a program that converts processed/normalized CHP data into the visual graphic.  Therefore, final processed/normalized data is CHP in our study. Algorithm: ExpressionStat 5.0.

molecule: polyA RNA

source_name: Differentiated cells (SFEB culture Day2)

label_protocol: Biotin labeled cRNA was synthesised by T7 RNA polymerase with Rnase inhibitor for 4hr at 37℃. RNA was purified by RNeasy Mini Kit.

growth_protocol: Mouse Sox1-GFP ES cells (129 derived) were maintained as described (http://www.ncbi.nlm.nih.gov/pubmed/15696161). The differentiation medium was GMEM supplemented with 10% Knockout Serum Replacement (KSR; Invitrogen), 2 mM glutamine, 1 mM pyruvate, 0.1 mM nonessential amino acids, and 0.1 mM 2-ME with or without 10% fetal calf serum (FCS; JRH). For the SFEBculture, ES cells were dissociated to single cells in 0.25% trypsin-EDTA (Invitrogen) and reaggregated in the differentiation medium (5*10^5 cells/dish) using bacterial grade dish.

extract_protocol: RNA was isolated from 1*10^6 cells of FACS sorted population with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. PolyA RNA was annealed by T7-dT primer and cDNA was synthesised by Superscript II (Invitrogen). cDNA was amplifed by T4 DNA polymerase and purified with Ph/Ch method.

tag: culture cells

value: ES cells were cultured with SFEB for 2days

tag: sorted for

value: E-cadherin+ cells


title: SFEB Day3 Sox1 (+) [U74Bv2]

source_name: Differentiated cells (SFEB culture Day3)

value: ES cells were cultured with SFEB for 3days

value: Sox1+ cells


title: Ferret Lung, injected with IFN-a2b on Day 2, biological rep4

description: Gene expression data from ferret lung after injection of IFN-a2b on day 2

value: Injected


title: SFEB Day4 Sox1 (+) [U74Bv2]

source_name: Differentiated cells (SFEB culture Day4)

value: ES cells were cultured with SFEB for 4days


title: Ferret Lung, injected with IFN-a2b on Day 1, biological rep2

description: Gene expression data from ferret lung after injection of IFN-a2b on day 1


title: Ferret Lung, injected with IFN-a2b on Day 1, biological rep3


title: SFEB Day4 Sox1 (+) [U74Cv2]

hyb_protocol: Samples were hybridized with Affymetrix Murine Genome U74C Version 2 Array and scanned at the RIKEN CDB Microarray Facility.


title: SFEB Day5 Sox1 (+) [U74Bv2]

source_name: Differentiated cells (SFEB culture Day5)

value: ES cells were cultured with SFEB for 5days


title: SFEB Day1 [U74Bv2]

source_name: Differentiated cells (SFEB culture Day1)

value: ES cells were cultured with SFEB for 1day


title: SFEB Day5 Sox1 (+) [U74Cv2]


title: SFEB Day2 E-cad (-) [U74Bv2]

value: E-cadherin- cells


title: Ferret Lung, injected with IFN-a2b on Day 1, biological rep4


title: Ferret Lung, injected with IFN-a2b on Day 2, biological rep2


title: Ferret Lung, injected with IFN-a2b on Day 2, biological rep3


title: Mouse ES 3 [U74Bv2]

source_name: Mouse ES cells (129 derived)

value: Mouse ES cells

value: E-cadherin+


title: Mouse ES 1 [U74Bv2]


title: Ferret Lung, injected with IFN-a2b on Day 2, biological rep1


title: Ferret Blood, injected with IFN-a2b on Day 2, biological rep4

description: Gene expression data from ferret blood on Day 2 after IFN-a2b injection

value: Blood


title: Ferret Blood, uninfected, on Day 0, biological rep1

value: Uninfected


title: SFEB Day3 Sox1 (-) [U74Bv2]

value: Sox1- cells


title: Ferret Lung, Not injected with IFN-a2b, on Day 0, biological rep3

description: Gene expression data from ferret lung not injected with IFN-a2b

value: Not injected


title: Ferret Lung, injected with IFN-a2b on Day 1, biological rep1

value: Lung


title: SFEB Day3 Sox1 (+) [U74Cv2]


title: Ferret Lung, Not injected with IFN-a2b, on Day 0, biological rep4


title: Mouse ES 2 [U74Bv2]


title: SFEB Day3 Sox1 (-) [U74Cv2]


title: Ferret Lung, Not injected with IFN-a2b, on Day 0, biological rep1


title: Ferret Lung, Not injected with IFN-a2b, on Day 0, biological rep2


title: Ferret Blood, injected with IFN-a2b on Day 2, biological rep3


title: Mouse ES 1 [U74Cv2]


title: Mouse ES 2 [U74Cv2]


title: Roots -control rep.1

value: Roots  of 10 days-old tomato - Wild type (cv. Micro-Tom)- control

value: Micro-Tom

value: Roots

value: control


title: SFEB Day2 E-cad (+) [U74Cv2]

value: ES cells were cultured with SFEB for 2days

value: E-cadherin+ cells


title: SFEB Day1 [U74Cv2]


title: SFEB Day2 E-cad (-) [U74Cv2]


title: Ferret Blood, injected with IFN-a2b on Day 2, biological rep2

value: Injected


title: Ferret Blood, injected with IFN-a2b on Day 2, biological rep1


title: Mouse ES 3 [U74Cv2]


title: Ferret Blood, injected with IFN-a2b on Day 1, biological rep4

description: Gene expression data from ferret blood on Day 1 after IFN-a2b injection


title: Ferret Blood, injected with IFN-a2b on Day 1, biological rep6


title: Ferret Blood, injected with IFN-a2b on Day 1, biological rep3


title: Ferret Blood, Not injected with IFN-a2b, on Day 0, biological rep1

description: Gene expression data from ferret blood not injected with IFN-a2b


title: Ferret Blood, injected with IFN-a2b on Day 1, biological rep2


title: 2228_T

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

description: Dog 12

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Canine Genome 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000.

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.4, Partek Inc., St. Louis, USA) and processed by the implemented gcRMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

organism: Canis lupus familiaris

source_name: mammary gland, tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 2ug total RNA.

extract_protocol: Tumor specimens were macrodissected to ensure high tumor or normal gland cellularity, respectively, and only sections that contained 70% tumor or non-neoplastic mammary epithelial cells, respectively, were included in the study. Tissue sections were transferred into 300 μl of lysis buffer (NucleoSpin RNA; Macherey&Nagel, Dueren, Germany) and homogenized (Precellyse 24, Bertin Technology, France). mRNA was extracted and purified using a commercial system (NucleoSpin RNA; Macherey&Nagel, Germany).

value: primary mammary carcinoma

tag: tissue type

value: tumor

tag: breed

value: Spitz-Mix

tag: age in years

tag: tumor size (cm)

tag: affected lymph node

value: inguinal

tag: postoperative survival (months)

tag: era


title: Ferret Blood, injected with IFN-a2b on Day 1, biological rep1


title: Ferret Blood, injected with IFN-a2b on Day 1, biological rep5


title: Ferret Blood, Not injected with IFN-a2b, on Day 0, biological rep4


title: Ferret Blood, Not injected with IFN-a2b, on Day 0, biological rep5


title: 1232_T_b

description: Dog 10

value: West Highland White Terrier


title: 2431_N

description: Dog 14

source_name: mammary gland, normal

value: mammary gland

value: normal

value: Mixed Breed


title: 2228_N

description: Dog 12


title: 1881_T

description: Dog 11

value: French Bulldog

value: not available


title: Ferret Blood, Not injected with IFN-a2b, on Day 0, biological rep3

value: Blood

value: Not injected


title: 1232_N

description: Dog 10


title: 2416_N

description: Dog 13

value: Beagle


title: 2416_T_b

description: Dog 13


title: 1881_N

description: Dog 11


title: 2431_T_b

description: Dog 14


title: Ferret Blood, Not injected with IFN-a2b, on Day 0, biological rep2


title: 61_T

description: Dog 9

value: Pudel


title: 2557_T_b

description: Dog 6

value: Golden Retriever


title: 2747_N

description: Dog 7


title: 2557_N

description: Dog 6


title: 2747_T_b

description: Dog 7

value: axillary


title: 1822_T_b

description: Dog 4

value: Dachshund


title: 2609_N

description: Dog 8


title: 2243_N

description: Dog 5

value: Bavarian Mountain Dog


title: 833_T_b

description: Dog 3

value: primary mammary carcinoma

value: tumor

value: Rottweiler


title: 825_N

description: Dog 2

value: Bobtail


title: SFEB Day3 Sox1 (+) [U74Av2]

hyb_protocol: Samples were hybridized with Affymetrix Murine Genome U74 Version 2 Array and scanned at the RIKEN CDB Microarray Facility.

value: ES cells were cultured with SFEB for 3days

value: Sox1+ cells


title: SFEB Day3 Sox1 (-) [U74Av2]

value: Sox1- cells


title: 2243_T_b

description: Dog 5

value: inguinal


title: 822_T

description: Dog 1

value: American Pittbull


title: 2627-08

scan_protocol: GeneChips were scanned using the Scanner G3000

source_name: canine mammary carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 2ug total RNA

extract_protocol: Tissue specimens were snap frozen in liquid nitrogen within 15 minutes after resection and stored at -80ºC until further use. Macrodissection was performed on all tumor specimens to ensure high tumor cellularity. Only sections with more than 70% carcinoma cells were included in the study as shown by digital image analysis (Scanscope T3, Aperio, Vista, USA; Zeiss Axiovision, Jena, Germany). For mRNA isolation, tissue sections were transferred into 300 µl of lysis buffer (NucleoSpin RNA XS; Macherey&Nagel, Dueren, Germany) and homogenized (Precellyse 24, Bertin Technology, France). RNA was extracted and purified using a commercial system (NucleoSpin RNA XS; Macherey&Nagel, Düren, Germany). The RNA quality was controlled using the BioAnalyzer (Agilent Technologies, USA) and only high quality RNA (RIN>8) was used for microarray analyses. Affymetrix GeneChip hybridization (Canine Genome 2.0 Array) was performed with 2 µg total RNA according to the manufacturer’s recommendations.

value: German Shepherd-Mix

tag: histologic grade

value: Grade III

value: none (no lymph node metastasis)

value: negative


title: 1822_N

description: Dog 4

value: mammary gland

value: normal


title: SFEB Day4 Sox1 (+) [U74Av2]

value: ES cells were cultured with SFEB for 4days


title: 2736_07

value: German-Shepherd-Mix


title: 2557_T

value: Golden Retriever


title: SFEB Day2 E-cad (-) [U74Av2]

value: ES cells were cultured with SFEB for 2days

value: E-cadherin- cells


title: SFEB Day5 Sox1 (+) [U74Av2]

value: ES cells were cultured with SFEB for 5days


title: Mouse ES 3 [U74Av2]

value: Mouse ES cells

value: E-cadherin+


title: SFEB Day1 [U74Av2]

value: ES cells were cultured with SFEB for 1day


title: 833_N

description: Dog 3

value: Rottweiler


title: 2747_T

value: West Highland White Terrier

value: Grade II

value: axillary


title: 2513_07

value: Pudel

value: none (no lymph node metastasis)


title: 2628_07

value: Miniature Pinscher

value: negative


title: 825_T_b

description: Dog 2

value: primary mammary carcinoma

value: tumor

value: Bobtail

value: inguinal


title: SFEB Day2 E-cad (+) [U74Av2]

value: ES cells were cultured with SFEB for 2days

value: E-cadherin+ cells


title: Mouse ES 2 [U74Av2]

value: Mouse ES cells


title: Mouse ES 1 [U74Av2]

value: E-cadherin+


title: 2431_T

value: Mixed Breed

value: Grade III


title: 2380_07

value: German Short Hair


title: 2047_07

value: Labrador


title: 2168_07

value: Soft coat. wheaten Terrier


title: 1937_07

value: Dalmatianr

value: Grade II


title: 1881T

value: French Bulldog


title: 2416_T

value: Beagle

value: negative


title: 61_08

value: Pudel


title: 822_07

value: American Pittbull


title: 2228T

value: Spitz-Mix

value: inguinal


title: 1232_T

value: West Highland White Terrier


title: 2194_07

value: Mischling

value: none (no lymph node metastasis)


title: 183_08

value: Great Dane


title: 1822_T

value: Dachshund


title: Gene expression profiles of Lkb1 WT #5 HSCs

city: Houston

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

institute: MD Anderson Cancer Center

description: Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 WT 5 HSCs.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: MAS5.0 was used to normalize arrays and to compute expression indices. Briefly, raw probe intensities were normalized across profiles. Expression values for each probe set were summarized. Differentially expressed probe sets were selected based on fold change as well as modified t-statistics after adjusting for multiple tests.

label: Biotin

source_name: LSK (Lin-, Sca-1+, c-Kit+) cells sorted from Lkb1 WT bone marrow cells

label_protocol: Approximately 10 ng of total RNA was first amplified by The RiboAmp® HS PLUS RNA Amplification Kit (Arcturus) and then processed to produce biotinylated cRNA targets.

extract_protocol: Bone marrow LSK cells were sorted from mice at 1 DPI (15,000-20,000 cells/sample). RNA from sorted LSK cells was extracted using PicoPure RNA Isolation Kit (Molecular Devices) per manufacturer's instructions, and cDNA was prepared utilizing Superscript II Rnase H-Reverse transcriptase (Invitrogen).

treatment_protocol: Here Lkb1 L/L mice treated with tamoxifen were used as Lkb1 WT mice. At 1 day post completing tamoxifen injection (DPI), we prepared single cell suspensions form bone marrow (from femoral and tibial bones), and stained and sorted LSK populations using FACSAria (Becton Dickinson, Mountain View, CA).

tag: strain

value: wild-type

value: bone marrow from femoral and tibial bones

tag: cell type

value: LSK (Lin-, Sca-1+, c-Kit+) cells


title: 1979_07

value: Irish Setter


title: 279_08

value: German-Shepherd-Mix

value: Grade III


title: 830_07

value: Cocker Spaniel-Mix


title: Gene expression profiles of Lkb1 KO #6 HSCs

description: Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #6 HSCs.

source_name: LSK (Lin-, Sca-1+, c-Kit+) cells sorted from Lkb1 KO bone marrow cells

treatment_protocol: To achieve somatic deletion of Lkb1 in mouse, we generated Lkb1 L/L, rosa26CreERT2 mice. In this model, the treatment of adult Lkb1 L/L, rosa26CreERT2 mice with tamoxifen results in efficient deletion of Lkb1 (Lkb1 KO mice) in hematopoietic organs and cells, including HSC-enriched LSK cells. At 1 day post completing tamoxifen injection (DPI), we prepared single cell suspensions form bone marrow (from femoral and tibial bones), and stained and sorted LSK populations using FACSAria (Becton Dickinson, Mountain View, CA).

value: Lkb1 knockout

tag: tissue


title: 2243_T

value: Bavarian Mountain Dog

value: negative


title: 825_T

value: Bobtail


title: Gene expression profiles of Lkb1 KO #7 HSCs

description: Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #7 HSCs.


title: 833_T

value: Rottweiler

value: inguinal


title: Gene expression profiles of Lkb1 KO #5 HSCs

description: Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #5 HSCs.


title: Gene expression profiles of Lkb1 WT #6 HSCs

description: Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 WT 6 HSCs.


title: 264_08


title: 8700LD

city: lleida

first: angela

last: canovas

state: lleida

address: 191, rovira roure

institute: irta

description: Duroc commercial line

hyb_protocol: Hybridisation protocol as recommented by Affymetrix using the Porcine Genome Array from Affymetrix.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A, as recommended by Affymetrix

data_processing: Data pre-processing, normalisation and class comparison analysis were carried out with the BRB-ArrayTools software version 3.7.1, which is available online at http://linus.nci.nih.gov/BRB-ArrayTools.html, as follows: microarray data normalisation was performed using the gcRMA algorithm, which corrects the intensity of each probe by its GC content; genes showing minimal variation across the set of arrays were excluded from the analysis, that is, only genes whose expression differed above 1.5 fold from the median in at least 20% of the arrays were retained. From the total 23937 spots of the array, 4299 spots passed these filtering conditions. For each probe, expression fold-change was calculated as the ratio between median values in both groups.

organism: Sus scrofa

source_name: longissimus thoracis et lumborum muscle from 190-days-old pigs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Duroc pigs were grown in standard commercial conditions, fed a commercial pellet diet and slaughtered at 190 days of age. Tissue samples were collected at slaughter, snap froxen in LN2 and stored at -80ºC until analysis

extract_protocol: total RNA was extracted from longissimus thoracis et lumborum muscle using Ribopure kit (AMBION) following the manufacturer's protocol

treatment_protocol: After slaughter, controled animals (n=350) were ranked based in 13 carcass, plasma and muscle fat deposition and fat composition traits. The top and bottom extreme of this distribution were selected to form the HIGH (n=10) and LOW (n=9) groups for longissimus thoracis et lumborum muscle microarrays experiment

tag: group

value: longissimus thoracis et lumborum muscle

tag: age

value: 190 days-old

value: Duroc


title: Gene expression profiles of Lkb1 WT #7 HSCs

description: Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 WT 7 HSCs.

tag: genotype


title: 2187LD

description: Duroc commercial line


title: 2172LD

description: Duroc commercial line


title: 1594LD

description: Duroc commercial line


title: Gcn4 deletion_2

city: Zurich

first: Uwe

last: Sauer

address: Auguste-Piccard-Hof 1

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

description: Gene expression of GCN4 deletion mutant during exponential growth in minimal media with glucose as carbon source.

hyb_protocol: Biotin-labeled cRNA samples were fragmented randomly to 35-200 bp at 94°C in fragmentation buffer (Affymetrix Inc., P/N 900371) and suspended in 100ml of hybridization mix (Affymetrix Inc., P/N 900720) containing a hybridization control and control oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip Yeast Genome 2.0 arrays for 16h at 45°C.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.) was used to determine the fluorescent intensity emitted by the labeled target.

data_processing: Affymetrix CEL files were processed using R (version 2.8.0) (R Development Core Team, 2008) and the Bioconductor affy package. Probe intensities were normalized for background by using the robust multiarray average method (RMA), using only perfect match (PM) probes. Normalization was performed using the qsplines algorithm. Gene expression values were calculated from the PM probes using the expression index calculation method (Li and Wong, 2001). All the normalization steps were done for pairwise conditions, i.e., mutant vs. wild-type.

source_name: GCN4 deletion mutant

label_protocol: Total RNA samples were reverse-transcribed with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using the Sample Cleanup Module (Affymetrix Inc.,P/N 900371). The purified double-stranded cDNAs were in vitro transcribed with biotin labeled nucleotides using the IVT Labeling Kit (Affymetrix Inc., P/N 900449).

growth_protocol: Minimal medium, glucose as carbon source, 30°C, 300 rpm, exponential growth in batch.

extract_protocol: Extraction as explained in the mechanical disruption protocol of the RNeasy Mini Kit (50), Qiagen.

treatment_protocol: Harvested as explained in the mechanical disruption protocol of the RNeasy Mini Kit (50), Qiagen.

tag: genotype/variation

value: GCN4 deletion


title: Gcn4 deletion_1


title: wild-type FY4_2, GCN4

description: Gene expression of wild-type FY4 during exponential growth in minimal media with glucose as carbon source.

source_name: wild-type (FY4)

value: wild-type


title: Pho2 deletion_1

description: Gene expression of PHO2 deletion mutant during exponential growth in minimal media with glucose as carbon source.

source_name: PHO2 deletion mutant

value: PHO2 deletion


title: wild-type FY4_3, GCN4


title: 1619LD

description: Duroc commercial line


title: Gcn4 deletion_3


title: 1539LD

description: Duroc commercial line


title: 1918LD

description: Duroc commercial line


title: 1550LD

description: Duroc commercial line


title: Pho2 deletion_2


title: 1540LD

description: Duroc commercial line


title: 1452LD

description: Duroc commercial line


title: 8697LD

description: Duroc commercial line


title: 1444LD

description: Duroc commercial line


title: wild-type FY4_1, GCN4


title: 1903LD

description: Duroc commercial line


title: 1533LD

description: Duroc commercial line


title: wild-type FY4_1, PHO2


title: 1612LD

description: Duroc commercial line


title: Bas1 deletion_3

description: Gene expression of BAS1 deletion mutant during exponential growth in minimal media with glucose as carbon source.

source_name: BAS1 deletion mutant

value: BAS1 deletion


title: 1468LD

description: Duroc commercial line


title: 2157LD

description: Duroc commercial line


title: wild-type FY4_2, PHO2


title: 2144LD

description: Duroc commercial line


title: wild-type FY4_3, PHO2


title: Bas1 deletion_2


title: 168-2

description: Pooled DNA samples2 MSRE1

source_name: Pool MSRE

value: blood

tag: gender

value: pool


title: ctrl3

description: Pooled DNA samples3 Genomic

source_name: Pool Genomic


title: 167-1

description: Pooled DNA samples2 Genomic5


title: 169-3

description: Pooled DNA samples2 MSRE2


title: 170-4

description: Pooled DNA samples2 MSRE3


title: 125 SNP-4

description: Pooled DNA samples2 Genomic4


title: ctrl3 MSRE

description: Pooled DNA samples3 MSRE


title: 1536LD

description: Duroc commercial line


title: wild-type FY4_1, BAS1


title: Bas1 deletion_1


title: wild-type FY4_2, BAS1


title: 124 SNP-3

description: Pooled DNA samples2 Genomic3


title: 307 SNP BJ80M

description: NHF PD80 MSRE

source_name: NHF PD80 MSRE

value: Primary foreskin fibroblasts PD80

value: male


title: 179 SNP-1

description: Pooled DNA samples1 Genomic


title: 122 SNP-1

description: Pooled DNA samples2 Genomic1


title: 306 SNP BJ80U

description: NHF PD80 Genomic

source_name: NHF PD80 Genomic


title: B cells from mice treated with R837 - rep 1

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

description: Gene expression from FACS-sorted B cells

hyb_protocol: Labeled targets were hybridized to GeneChip® Mouse Gene 1.0ST arrays (Affymetrix, Inc.), following Standard Nugen Protocols for target hybridization to the Affymetrix Gene Arrays. The hybridizations were run for 16 hours, 45oC, 60RPM in an Affymetrix Hybridization Oven 640. The Cartridge arrays were washed and stained using the Affyemtrix Fluidics Stations 450, following Affymetrix protocols.

scan_protocol: Scanning was performed on an Affymetrix GeneChip 3000 7G scanner, and Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

data_processing:
Probe sets of all 6 samples were normalized by RMA, which includes global background adjustment and quantile normalization. program-name = Expression Console; affymetrix-algorithm-name = rma-gene-default.
Each set of samples was subsequently normalized by z-score (number of standard deviation from mean) and treated as biological replicates.

label_protocol: All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies) and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies). The samples were amplified using the Nugen WT Pico Kit (NuGEN Technology) and the target reactions were run with 50ng of Total RNA.  The amplification products were processed through the EXON Module (NuGEN Technology) which creates sense-strand cDNA targets.  The sense strand cDNA Targets were then fragmented and labeled using NuGEN’s FL-Ovation™ cDNA Biotin Module V2 (NuGEN Technology).

extract_protocol: Total RNA from sorted B-cells (1.8 x 10^4 to 1.2 x 10^6 cells) was purified using Trizol® (Invitrogen, Life Technologies Corporation).

treatment_protocol: 8-12 week old C57BL/6 mice (Charles River Laboratories, Wilmington, MA) were immunized with 10µg of ovalbumin antigen in nanoparticles (suspended in 200µl of PBS), subcutaneously at the base of the tail. PLGA nanoparticles containing 37.5µg of MPL were used with the protein encapsulated particles. At day 7 post-immunization, activated, isotype switched B cells (TCRβ-CD11b-CD19+IgD-IgG+ cells) were isolated from draining lymph nodes (pooled) from immunized mice (n=5), sorted by FACS and RNA was isolated.

value: B-cell

tag: stimulation

value: R837 (TLR7 ligand)

tag: time

value: 7 days post-treatment

tag: cell markers

value: TCRbeta-CD11b-CD19+IgD-IgG+ B cells


title: B cells from mice treated with MPL and R837 - rep 1

source_name: MPL and R837-treated_1

value: MPL (TLR4 ligand) + R837 (TLR7 ligand)


title: 304 SNP BJ64U

description: NHF PD64 Genomic

source_name: NHF PD64 Genomic

value: Primary foreskin fibroblasts PD64


title: wild-type FY4_3, BAS1


title: B cells from mice treated with R837 - rep 2


title: 303 SNP BJ38M

description: NHF PD38 MSRE

source_name: NHF PD38 MSRE

value: Primary foreskin fibroblasts PD38


title: 302 SNP BJ38U

description: NHF PD38 Genomic

source_name: NHF PD38 Genomic


title: 305 SNP BJ64M

description: NHF PD64 MSRE

source_name: NHF PD64 MSRE


title: 123 SNP-2

description: Pooled DNA samples2 Genomic2


title: 184 SNP-8

description: Pooled DNA samples1 MSRE


title: 950_l

description: Lung MSRE

source_name: Lung MSRE

value: Lung


title: 950_k

description: Lung Genomic

source_name: Lung Genomic


title: 950_f

description: Blood 3 MSRE

source_name: Blood MSRE

value: Peripheral blood individual 3

value: female


title: MOILS_p_RA_Affy_meth_exp_GenomeWideSNP_6_H02_293642

description: EBV transformed B-lymphcytes Genomic 1

source_name: EBV transformed B-lymphcytes (GM10849) Genomic

value: EBV transformed B-lymphcytes line GM10849


title: MOILS_p_RA_Affy_meth_exp_GenomeWideSNP_6_H04_293646

description: EBV transformed B-lymphcytes MSRE 2

source_name: EBV transformed B-lymphcytes (GM12092) MSRE

value: EBV transformed B-lymphcytes line GM12089


title: MOILS_p_RA_Affy_meth_exp_GenomeWideSNP_6_H05_293648

description: EBV transformed B-lymphcytes Genomic 3

source_name: EBV transformed B-lymphcytes (GM12093) Genomic

value: EBV transformed B-lymphcytes line GM12093


title: B cells from mice treated with MPL and R837 - rep 2

source_name: MPL and R837-treated_2


title: MOILS_p_RA_Affy_meth_exp_GenomeWideSNP_6_H06_293650

description: EBV transformed B-lymphcytes MSRE 3

source_name: EBV transformed B-lymphcytes (GM12093) MSRE


title: MOILS_p_RA_Affy_meth_exp_GenomeWideSNP_6_H03_293644

description: EBV transformed B-lymphcytes Genomic 2

source_name: EBV transformed B-lymphcytes (GM12092) Genomic


title: B cells from mice treated with MPL - rep 2

value: MPL (TLR4 ligand)


title: 950_c

description: Blood 2 Genomic

source_name: Blood Genomic

value: Peripheral blood individual 2


title: 950_b

description: Blood 1 MSRE

value: Peripheral blood individual 1


title: 286-Olgen

description: Occipital lobe Genomic

source_name: Occipital lobe Genomic

value: Occipital lobe

value: male


title: MOILS_p_RA_Affy_meth_exp_GenomeWideSNP_6_H01_293640

description: EBV transformed B-lymphcytes MSRE 1

source_name: EBV transformed B-lymphcytes (GM10849) MSRE


title: B cells from mice treated with MPL - rep 1

value: B-cell


title: 950_p

description: Placenta MSRE

source_name: Placenta MSRE

value: Placenta


title: 950_d

description: Blood 2 MSRE


title: 950_o

description: Placenta Genomic

source_name: Placenta Genomic


title: 287-OLmsre

description: Occipital lobe MSRE

source_name: Occipital lobe MSRE


title: 237 - ICF3

description: EBV transformed B-lymphcytes ICF Genomic

source_name: EBV transformed B-lymphcytes ICF (GM08714) Genomic

value: EBV transformed B-lymphcytes GM08714


title: 950_e

description: Blood 3 Genomic


title: 950_a

description: Blood 1 Genomic


title: 238 - ICF3-MSRE

description: EBV transformed B-lymphcytes ICF MSRE

source_name: EBV transformed B-lymphcytes ICF (GM08714) MSRE


title: HNSCC cell - p63 si vs GFPsi - 48h - rep2

status: Public on Nov 23 2010

city: Boston

first: benjamin

middle: robert

last: ory

address: 55 fruit street

institute: Mas General Hospital Cancer Center

description:
supplementary_file_ch1:1_Exiqon_13889290_S01_Cropped.txt
supplementary_file_ch2:0_Exiqon_13889287_S01_Cropped.txt
After having passed sample quality control on the Bioanalyser2100, the samples were labelled using the miRCURY™ Hy3™/Hy5™ power labelling kit and hybridized on the miRCURY™ LNA Array (v.10.0) (Exiqon). Spike-in controls were added in various concentrations covering the full signal range, in both Hy3 and Hy5 labelling reactions giving the opportunity to evaluate the labelling reaction, hybridization and the performance of the array experiment in general.

hyb_protocol: Using Tecan hybridization stations the hybridization and washing steps are fully automated for excellent reproducibility

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays.

data_processing:
The data obtained is normalized using methods applicable to the performed experiment. The project customized data analysis is provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA).
The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. The data only represent the microRNAs that passed the filtering criteria across samples; Fold Change > 1.50.
normalised Hy3/Hy5 ratios (log2 transformed) from all 2 hybridizations. The ratios are tranferred from the excel-sheets named Slide-x.xls, and shown is the median of replicated measurements of the same miRNA from each slide

source_name: head and neck squamous cell carcinoma cell line

label_protocol: miRCURY™ LNA Array Power labeling kit allows highly efficient and uniform labeling of microRNAs with minimal sequence bias.

growth_protocol: RPMI FBS 10%

extract_protocol: For each sample, 2μg of Trizol extracted total RNA were purified using the RNeasy Mini Cleanup Kit (Qiagen) following manufacturer's instructions

treatment_protocol: p63-directed or control lentiviral shRNA for 48h

tag: cell line

value: human head and neck squamous cell carcinoma

tag: treatment

value: 48h lentiviral shRNA against p63

value: 48h lentiviral shRNA against GFP