title: B6 wildtype littermate 5

description:
11-0503_CB
both genotypes were littermates with each other

value: batch 1

value: homozygous for B6 in congenic region

value: female


title: KO_NonInf_replicate 2

status: Public on Jan 18 2012

type: RNA

city: Braunschweig

first: Sabin

last: Bhuju

address: Salzdhalumerstr

country: Germany

institute: Lionex

description: Gene expression in noninfected BMM from SOCS1 mutant

hyb_protocol: Following fragmentation, 1.8 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. Agilent micorarray were washed according to manufacture instruction.

scan_protocol: Agilent microchips  were scanned using the Feature extraction software FE 10.5 (Agilent)

data_processing: Scaling (Genespring GX 11, Agilent)

molecule: total RNA

organism: Mus musculus

source_name: SOCS1 mutant noninfected

label_protocol: Cy3 cRNA were prepared according to the standard Agilent protocol from 200 ng total RNA (Quick Amp Labeling Kit, Agilent).

growth_protocol: The bone marrow cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing glucose and supplemented with 2 mM L-glutamine, 10% FCS, 10 mM Hepes, 100 mg/ml streptomycin, 100 U/ml penicillin (all from Sigma, St Louis, MO), and 20 to 30% L929 cell-conditioned medium (as a source of macrophage-colony stimulating factor).

extract_protocol: Total RNA isolation

treatment_protocol: M. tuberculosis Harlingen strain were inoculated by the aerosol route by using a nose-only exposure unit

tag: genotype/variation

value: SOCS Knockout Mutant

tag: tissue

value: bone marrow derived macrophage (BMM)

tag: infection

value: Not Infected


title: heterozygous congenic 1

city: Chicago

first: Camron

middle: D

last: Bryant

state: IL

address: 920 E. 58th Street, CLSC 501

department: Human Genetics

country: USA

institute: The University of Chicago

description:
11-0496_CB
both genotypes were littermates with each other

hyb_protocol: The details for the hyb/wash/stain are in the Affy protocol: http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf.  Briefly, the hybridization cocktail was made with the Affy Hyb buffer, DMSO, Oligo B2 and 20X eukaryotic controls and hybridized to the gene arrays for 17hrs at 45C. The arrays were then washed and stained with SAPE (Streptavidin Phycoerythrin binds to the biotin) and scanned.

scan_protocol: Affymetrix GeneChip  Scanner 3000 7G.  Affymetrix GeneChip Command Console (AGCC) software generated the raw data files including the CEL files.

data_processing: Data were processed using both Affymetrix Gene Expression Console Software and Affymetrix Powertools robust multichip average (RMA) analysis.  Both gave the same results.  However, prior to generating RMA values, we eliminated 145 probes from analysis using the Affymetrix powertools kill list option.  We provide the text file named kill list that we used for probe masking.  After generating RMA values, we then corrected for batch effects (2 batches) using the ComBat.R script which is also provided.  Thus, the RMA values provided on the matrix template are those obtained following probe masking and following correction for batch effects.

label: biotin

source_name: left and right striatum

label_protocol: Precision Biomarker Resources processed the RNA and scanned the arrays.  Here is the protocol manual with all of the details for the amplification: http://tools.invitrogen.com/content/sfs/manuals/cms_064619.pdf.  Briefly, we started with 100ng of total RNA, subjected it to first strand and second strand cDNA generation followed by 16hr IVT amplification making cRNA. The cRNA was bead purified and then 10µg was put into the second cycle sscDNA reaction. 5.5µg of sscDNA was then fragmented and end labeled with biotin.

extract_protocol: RNA was extracted using Trizol® (Invitrogen, Carlsbad, CA) and chloroform and then precipitated with ethanol and resuspended.  The solution was then passed through RNeasy® columns (Qiagen), quality checked using the Agilent 2100 Bioanalyzer (Santa Clara, CA),

treatment_protocol: Mice were housed as same-sex littermates, 2-5 per cage.  Mice were naïve at the time of rapid decapitation for brain tissue harvesting.

tag: batch

tag: genotype

value: heterozygous for B6, A/J in congenic region

tag: Sex

tag: age (days old)


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-HDAC1 antibody_Array B

type: genomic

city: Madrid

first: Sara

last: Alvarez

address: C/Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: Three biological replicates per sample were prepared and hybridized on the same array set.

hyb_protocol: 1ug of each ChIP and Input labeled DNA were hybridized in Agilent hybridization chambers for up to 40 hours at 65ºC at 20rpm. The arrays were washed 5 minutes in wash buffer 1, and then 1 minute in wash buffer 2 at 37ºC.

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer´s protocol. The images obtained were processed using the Agilent Feature Extractor software application (v.9.5.3.1).

data_processing: The Agilent ChIP Analytics 1.3 software package was used to perform a linear scan across the regions represented on the promoter array. The software performs  both dye-bias and interarray normalization. A whole ChIP error model was used to calculate the confidence values from the enrichment ratio and the signal intensity of each probe.  It calculates the log of the ratio of intensity in the IP-enriched channel to intensity in the genomic DNA channel for each probe and use the neighborhood error model to calculate confidence vaues for each spot on each array (single-probe p value). This error model converts the intensity information in both channels to an X score which is dependent on both the absolute value of intensities and background noise in each channel. The X scores are assumed to be normally distributed, thus enabling a p value to be calculated for the enrichment ratio observed at each feature.

molecule: genomic DNA

organism: Homo sapiens

source_name: HDAC1 ChIP DNA from HSPC expressing the AML1/ETO fusion protein

label_protocol: ChIP or Input DNA were labeled using the Bioprime® DNA-Labeling system protocol (Life Technologies, Carlsbad, CA) with random priming and Cy5/Cy3 fluorescent dyes, respectively.

extract_protocol: ChIP assays were performed as described elsewhere (Ballestar et al., EMBO J., 2003 [PMID 14633992]). Three biological replicates were prepared and hybridized on the same array set. ChIP products were amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma, Saint Louis, MO) and purified using the UltraCleanTM GelSpinTM DNA purification kit (MO BIO laboratories, Inc., Carlsbad, CA).

treatment_protocol: HSPCs were 1% formaldehyde crosslinked after 12-17 weeks in culture.

value: cord blood

tag: cell type

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

tag: source

value: normal donors

tag: transduction

value: AML1/ETO fusion protein

tag: chip antibody

tag: antibody vendor

value: Affinity BioReagents

tag: antibody catalog number

tag: antibody lot number

source_name: Input DNA from HSPCs expressing the AML1/ETO fusion protein


title: WT_Inf_replicate 3

description: Gene expression after infecting wild type BMM with M. tuberculosis

source_name: Wild type infected

value: Wildtype

value: Infected


title: B6 wildtype littermate 4

description:
11-0501_CB
both genotypes were littermates with each other

value: male


title: B6 wildtype littermate 3

description:
11-0500_CB
both genotypes were littermates with each other


title: WT_Inf_replicate 4


title: WT_NonInf_replicate 2

description: Gene expression in noninfected wild type BMM

source_name: Wild type noninfected


title: WT_NonInf_replicate 1


title: Man1_DamID

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

description: supplementary_file_descriptions: Tab-delimited txt-files contain probe positions and log2 scores for all probes used in this analysis.

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

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

data_processing: CEL.files were analysed in R (http://www.r-project.org) using the Bioconductor (http://www. bioconductor.org) packages “affy”, “affxparser” and “preprocessCore” with standard parameters. Ima1/Heh2-DamID sample CEL-files were normalised together with their Dam Control sample CEL-files using quantile normalization with standard parameters. Probe sequences were mapped to the S.pombe genome draft downloaded from ftp://ftp.sanger.ac.uk/ on Nov 19, 2009. Any probes mapping to more than one location in the genome or mapping with more than one mismatch was excluded from further analysis.

organism: Schizosaccharomyces pombe

source_name: Man1 DamID gDNA

label_protocol: Biotin-labeled according to standard Affymetrix protocols.

growth_protocol: Cultures were grown at 30°C to a density of 7x10^6 cells/ml.

extract_protocol: Genomic DNA was extracted as described in Moreno et al., Methods Enzym. 1991.

tag: strain

source_name: DamCtrl DamID

growth_protocol: Cultures were grown at 30°C to a density of 7x106 cells/ml.


title: sas2∆-H4K16ac

city: Berlin

first: Ho-Ryun

last: Chung

address: Ihnestr. 75

department: Computational Molecular Biology

institute: Max-Planck-Institut for molecular Genetics

description:
H4K16ac sas2∆ ChIP Biological Replicates 1-3
processed_data_file_descriptions: = In each row there are three columns separated by tabs. The first column corresponds to the chromosome, the second column to the starting position of the probe and the third column to the sum of the normalized LogE signal intensities of the three biological replicates

hyb_protocol: Hybridization, washing and scanning of tiling arrays was performed according to the Affymetrix Chromatin Immunoprecipitation Assay protocol.

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

data_processing: Data was normalized using PMT. The sum of the normalized LogE signal intensities of the three biological replicates are reported.

organism: Saccharomyces cerevisiae

source_name: H4K16ac ChIP DNA from sas2∆

label_protocol: ChIP DNA (appr. 300 ng) was fragmented by DNaseI digestion to an average size of approximately 200bp and labeled with Terminal Deoxynucleotidyl Transferase using the reagents of the Human Mapping 250K Sty Assay Kit (Affymetrix).

growth_protocol: Yeast cell were grown to OD600 ~1 and cross linked with formaldehyd 30 min, rt. Cells were harvested and washed in TBS. Cells were lyses with ChIP lysis buffer and glass beads. Supernatant was sonicated.  Taken aliquots were preckeared with proteinG-agarose at 4 °C. Incubation with antibody was performed over night 4 °C. Immunoprecipitations were washed with wash buffers.

extract_protocol: DNA was extracted after RNase and Proteinase K digestion with Qiaquick Gel Extraction Kit.

tag: antibody


title: WT_NonInf_replicate 3


title: Ima1_DamID

source_name: Ima1 DamID gDNA


title: WT_Inf_replicate 1


title: KO_NonInf_replicate 1


title: B6 wildtype littermate 1

description:
11-0497_CB
both genotypes were littermates with each other


title: B6 wildtype littermate 6

description:
11-0507_CB
both genotypes were littermates with each other


title: MPTP and nonacupoints acupuncture-treated mouse 2 thalamic regions

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

description: Gene expression data from thalamic regions following nonacupoints-acupuncture-treatment to MPTP-intoxicated mouse

hyb_protocol: Following labeling, each cDNA was hybridized for 17 hr at 45℃ at 60 rpm on Affymetrix MouseGene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0007.

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

data_processing: The quality control was estimated by confirming the order of the signal intensities of the Poly-A controls and Hybridization controls using Expression Console Software (Affymetrix, USA). The microarray data was analyzed using a GenPlex V3.0 (ISTECH, Korea). The data were analyzed with Robust Multichip Analysis (RMA) quantification method as a probe set summarization algorithm for log transformation with base 2 (log2) and Quantile normalization method as a normalization method in the Preprocessing module of GenPlex V3.0. The mean signal intensities of all genes (35,557 probes (28,853 genes) in a platform) were obtained from 2 chips of each experimental group.

source_name: MPTP and nonacupoints acupuncture-treated mouse thalamic regions

label_protocol: Fragmented and biotinylated cDNA were prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual from 300 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual, Affymetrix).

growth_protocol: Six-week old male inbred C57BL/6 mice (20-22 g) were grown up.

extract_protocol: The total RNA in the bilateral thalamic tissues of each group (n=2 per each group) was extracted using an RNeasy Plus Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

treatment_protocol: While mice in the control group (n=9) were intraperitoneally injected with saline 0.9% (100 µl) once daily for four weeks, the mice in the MPTP group (n=9) were intraperitoneally injected with MPTP-HCl (20 mg/kg of free base) dissolved in saline 0.9% (100 µl) at twenty-four hr intervals for four weeks to produce the sustained chronic model of parkinsonism. Acupuncture was performed by hand two hr after the first MPTP injection and then at forty-eight hr intervals (fourteen total sessions). The acupuncture procedure (acupoint GB34 (Yanglingquan) and acupoint LR3 (Taichong) for acupoints; both sides of the hips for non-acupoints) was performed as previously reported. Mice in the acupoints group were immobilized by hand two hr after MPTP administration. Acupuncture needles were inserted bilaterally to depths of 1 mm at acupoint LR3 and 3 mm at acupoint GB34, and then turned at a rate of two spins per sec for fifteen sec as reported in a previous study. For the non-acupoints group, the needles were inserted to depths of 3 mm at both sides of the hips rather than at the acupoints GB34 and LR3 for the acupoints group, and then the same procedures were performed as with the acupoints.

tag: gender

value: Male

value: thalamic tissues

tag: developmental stage

value: Adult


title: WT-H4 control

description:
H4 WT ChIP Biological Replicates 1-3
processed_data_file_descriptions: = In each row there are three columns separated by tabs. The first column corresponds to the chromosome, the second column to the starting position of the probe and the third column to the sum of the normalized LogE signal intensities of the three biological replicates

source_name: H4 ChIP DNA from WT

value: Histone H4


title: germarium_apex of testes_134826673_rep4

city: Urbana

first: Amy

last: Cash

address: 1206 W. Gregory Dr

department: Biology

institute: University of Illinois

description:
CH1:  Oregon R strain of D. melanogaster, 5 day old males, 4 individual laser cut apex of testes pooled together for biological replicate 4
CH2:  Oregon R strain of D. melanogaster, 5 day old females, 4 individual laser cut germaria pooled together for biological replicate 4
All biological replicates were processed in parallel.

hyb_protocol: Microarrays were pre-treated for one hour at 42°C in pre-hybridization buffer (5 × SSC, 0.1%SDS, 1% I-block (Applied Biosystems)).  Amplified RNA with 50 pmol of dye incorporation from each sample were mixed with KREAblock (ULS aRNA Fluorescent Labeling kit) and 2 × formamide cDNA hybridization buffer (Genisphere), then heated at 80°C for 10 min. Labeled sampled were then added to microarray and hybridized overnight at 42°C.

scan_protocol: GenePix Scanner 4200 GenePix Pro 5.0 software

data_processing: Data normalized using OLIN in Bioconductor. Statistical testing done with the limma modified t-test with a false discovery rate correction.

organism: Drosophila melanogaster

source_name: apex of testes_rep4

label_protocol: 2 ug of amplified RNA (aRNA) was directly labeled with Cy3 using the Kreatech ULS aRNA Fluorescent Labeling Kit (Biomicrosystems).

growth_protocol: Flies were raised on standard corn meal agar medium at 25oC.

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual apex of the testes were pooled together before total RNA extraction, such that biological replicate 4 contained 4 testis tips. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).

value: Oregon R

tag: age

value: 5 day old

tag: tissue

value: apex of testes

tag: biological replicate

label_protocol: 2 ug of amplified RNA (aRNA) was directly labeled with Cy5 using the Kreatech ULS aRNA Fluorescent Labeling Kit (Biomicrosystems).

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual germarium were pooled together before total RNA extraction, such that biological replicate 4 contained 4 germaria. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).

value: female

value: germarium


title: WT-H4K16ac

description:
H4K16ac WT ChIP Biological Replicates 1-3
processed_data_file_descriptions: = In each row there are three columns separated by tabs. The first column corresponds to the chromosome, the second column to the starting position of the probe and the third column to the sum of the normalized LogE signal intensities of the three biological replicates

source_name: H4K16ac ChIP DNA from WT


title: sas2∆-H4 control

description:
H4 sas2∆ ChIP Biological Replicates 1-3
processed_data_file_descriptions: = In each row there are three columns separated by tabs. The first column corresponds to the chromosome, the second column to the starting position of the probe and the third column to the sum of the normalized LogE signal intensities of the three biological replicates

source_name: H4 ChIP DNA from sas2∆


title: WT_Inf_replicate 2

tag: genotype/variation

value: bone marrow derived macrophage (BMM)

tag: infection


title: germarium_apex of testes_134826672_rep3

description:
CH1:  Oregon R strain of D. melanogaster, 5 day old males, 4 individual laser cut apex of testes pooled together for biological replicate 3
CH2:  Oregon R strain of D. melanogaster, 5 day old females, 4 individual laser cut germaria pooled together for biological replicate 3
All biological replicates were processed in parallel.

source_name: apex of testes_rep3

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual apex of the testes were pooled together before total RNA extraction, such that biological replicate 3 contained 4 testis tips. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual germarium were pooled together before total RNA extraction, such that biological replicate 3 contained 4 germaria. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).


title: MPTP and nonacupoints acupuncture-treated mouse 1 thalamic regions


title: germarium_apex of testes_134826670_rep2

description:
CH1:  Oregon R strain of D. melanogaster, 5 day old females, 4 individual laser cut germaria pooled together for biological replicate 2
CH2:  Oregon R strain of D. melanogaster, 5 day old males, 4 individual laser cut apex of testes pooled together for biological replicate 2
All biological replicates were processed in parallel.

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual germarium were pooled together before total RNA extraction, such that biological replicate 2 contained 4 germaria. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).

source_name: apex of testes_rep2

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual apex of the testes were pooled together before total RNA extraction, such that biological replicate 2 contained 4 testis tips. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).


title: MPTP and acupoints acupuncture-treated mouse 2 thalamic regions

description: Gene expression data from thalamic regions following acupoints-acupuncture-treatment to MPTP-intoxicated mouse

source_name: MPTP and acupoints acupuncture-treated mouse thalamic regions


title: MPTP and acupoints acupuncture-treated mouse 1 thalamic regions

description: Gene expression data from thalamicl regions following acupoints-acupuncture-treatment to MPTP-intoxicated mouse


title: germarium_apex of testes_134826668_rep1

description:
CH1:  Oregon R strain of D. melanogaster, 5 day old females, 4 individual laser cut germaria pooled together for biological replicate 1
CH2:  Oregon R strain of D. melanogaster, 5 day old males, 4 individual laser cut apex of testes pooled together for biological replicate 1
All biological replicates were processed in parallel.

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual germarium were pooled together before total RNA extraction, such that biological replicate 1 contained 4 germaria. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).

source_name: apex of testes_rep1

extract_protocol:
Total RNA from laser cut samples were extracted using the Pico Pure RNA Isolation Kit (Molecular Devices).  The extraction buffers of 4 individual apex of the testes were pooled together before total RNA extraction, such that biological replicate 1 contained 4 testis tips. After sample pooling, total RNA extraction was performed according to standard Pico Pure RNA Isolation kit protocol.  Total RNA was eluted in 15 μl EB Buffer (Molecular Devices).  The quality of RNA was analyzed using a Pico Chip on the Agilent 2100 BioAnalyzer.  Total RNA was stored at -80 °C until amplification.
RNA amplification was performed for all biological samples.  Total RNA was incubated with 100 ng T7-oligo(dT) primer (Ambion) at 65°C for 10 min and then cooled on ice.  First strand DNA synthesis was performed by adding 2 ul 5X first strand buffer (Invitrogen), 1 ul 0.1 M DTT, 1 ul 10 mM dNTPs, 0.3 ul T4gp32 (USB, 13.4 ug/ul), 0.7 ul RNase Inhibitor (Ambion, 10 U/ul), and 1 ul Superscript II (Invitrogen, 200 U/ul), followed by incubation at 42°C for 2 hr, 65°C for 10 min, and then cooled on ice.  Second strand DNA synthesis occurred by the addition of 64 ul of second-stand master mix (45 ul water, 15 ul 5X second strand buffer, 1.5 ul 10 mM dNTPs, 2 ul DNA polymerase (Invitrogen, 10 U/ul), and 0.5 ul RNaseH (Invitrogen, 2 U/ul)), followed by incubation at 16°C for 2 hr.  cDNA clean-up was performed with MiniElute Reaction Cleanup columns (Qiagen) and eluted in 10 ul of elution buffer.  The volume was increased to 16 ul by addition of 7 ul of RNase-free water.  In vitro transcription (IVT) was performed using the MEGAscript kit (Ambion) with a 4 hour incubation at 37°C.  aRNA was purified with the RNeasy kit (Qiagen) and eluted in 100 ul RNase-free water. After adjusting the aRNA volume to 4 ul using a Speed Vac, 3 ug random primers (Invitrogen) were added and incubated at 65°C for 10 min and cooled on ice.  6 ul of first-strand mix was then added and reactions were incubated at 42°C for 2 hours.  Second round second strand synthesis, cDNA purification, IVT, and aRNA purification were all carried out as in the first round, with the following exception: the last wash of the aRNA purification was performed with 80% ethanol as opposed to Qiagen buffer RPE.  The final amplified antisense RNA product was quantified using a Nanodrop (Thermo Scientific).


title: Kasumi-3

city: Miyazaki

first: Yusuke

last: Saito

address: 5200 Kihara, Kiyotake

country: Japan

institute: Miyazaki University

hyb_protocol: the cRNA was linearly amplified with T7 polymerase, the biotinylated cRNA was cleaned with an RNeasy Mini Column Kit, fragmented to 50 to 200 nucleotides, and then hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChips were scanned using Affymetrics GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: AML

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Acute myloid leukemia cell lines were cultured in RPMI 1640 medium (Wako) supplemented with 10% fetal bovine serum (UCSD/AML1 : add 1 ng/ml granulocyte-macrophage colony-stimulating factor)..

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

tag: expression

value: EVI1 high AML

tag: cell line


title: MOLM1

source_name: CML in blast crisis


title: HNT-34


title: MPTP-treated mouse 1 thalamic regions

description: Gene expression data from thalamic regions of MPTP-intoxicated mouse

source_name: MPTP-treated C57BL/6 mouse thalamic regions


title: FKH-1

value: EVI1 low AML


title: NH

value: NH


title: LFS-adrenocortical carcinoma tumor 1

status: Public on Jan 19 2012

city: Toronto

first: Diana

middle: M

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing: Genotyping (CN5) and copy number analysis (Birdseed_v2) with the Affymetrix Genotyping Console. Standard export of copy number results (.CN5.CNCHP file)

source_name: LFS-adrenocortical carcinoma tumor 1

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tissues on dry ice by standard Proteinase K-SDS protocol, followed by phenol-chloroform extraction and ethanol precipitation.

tag: tumor type

value: adrenocortical carcinomas


title: MPTP-treated mouse 2 thalamic regions


title: UCSD/AML1


title: OIH1


title: Control mouse 2 thalamic regions

description: Gene expression data from normal thalamic regions

source_name: Control C57BL/6 mouse thalamic regions


title: THP1


title: K051


title: HL60


title: HEL

source_name: erythroleukemia

value: HEL


title: K052


title: ILK-expressing epidermis replicate 5

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

institute: Robarts Research Institute

description:
C'1 WT
Gene expression data from mouse # 10

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. 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 Partek Genomcis Suite using the GC_RMA normalization method

source_name: ILK-expressing epidermis

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: Mice were maintained in a 12-h dark/light cycle, with access to food and water ad libitum, and according to guidelines from the Canadian Council of Animal Care and the Animal Use Subcommittee of the University of Western Ontario. The genotype of the mice was determined as described in (Nakrieko et al. Mol Biol. Cell 19:2157, 2008)

extract_protocol: Qiagen Rneasy minikit, according to manufacturer's protocol

treatment_protocol: Skin digested with dispase (8 mg/ml) for 1 h at 37 degrees , to isolate the epidermis

tag: strain background

value: [Ilktm1Star (with Ilk alleles) x Tg(KRT14-cre)1Amc/J] x Ilktm1Star

tag: genotype/background

value: heterozygous for the KRT14-cre transgene and heterozygous (ILK-expressing) for the floxed Ilk alleles

value: 3 day-old

value: epidermis obtained from dispase treatment of skin


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-H3K9me3 antibody_Array A

description: Three biological replicates per sample were prepared and hybridized on the same array set.

source_name: H3K9me3 ChIP DNA from HSPC transduced with the empty vector

value: cord blood

tag: cell type

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

tag: source

value: normal donors

tag: transduction

value: vector

tag: chip antibody

tag: antibody vendor

value: Abcam

source_name: Input DNA from HSPCs transduced with the empty vector


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-H3K9me3 antibody_Array A

source_name: H3K9me3 ChIP DNA from HSPC expressing the AML1/ETO fusion protein

value: AML1/ETO fusion protein

tag: antibody catalog number

tag: antibody lot number

source_name: Input DNA from HSPCs expressing the AML1/ETO fusion protein


title: ILK-deficient epidermis replicate 5

description:
D'4 KO
Gene expression data from mouse # 9

source_name: ILK-deficient epidermis

value: heterozygous for the KRT14-cre transgene and homozygous (ILK-deficient) for the floxed Ilk alleles

tag: age


title: Control mouse 1 thalamic regions

tag: gender

value: Male

tag: strain

tag: tissue

value: thalamic tissues

tag: developmental stage

value: Adult


title: ILK-expressing epidermis replicate 4

description:
D'2 WT
Gene expression data from mouse # 8


title: ILK-deficient epidermis replicate 4

description:
D13 KO
Gene expression data from mouse # 7


title: Candida albicans T2 IL17A treated, biological rep2

city: PERUGIA

first: LUIGINA

last: ROMANI

address: VIA DEL GIOCHETTO

department: Department of Experimental Medicine and Biochemical Sciences

country: Italy

institute: University of Perugia

description: Biochip 11324

hyb_protocol: Hybridization was done automatically overnight (16 h) at 45 °C to febit Geniom Biochips according to febit internal hybridization protocol using Febit’s Geniom RT Analyzer Instrument.

scan_protocol: After hybridization the Geniom Biochip was washed automatically. For maximum sensitivity,  febit used biotin and its detection with streptavidin-phycoerythrin (SAPE), in  combination with febit’s Consecutive Signal Enhancement (CSE) procedure. The feature recognition (using Cy3  filter set) and signal calculation were done automatically within milliseconds. The Geniom  Technology showed accurate detection of mRNA profiles. The data correlates well with  qPCR data. There was no photo bleaching thus enabling repeated measurements and multiple  detection of each Biochip.

data_processing:
Starting from raw data files, analysis was performed using the PROP algorithm (at Febit, Germany). Microarray data were generated from two biological replicates. cDNA generated from cells exposed to drug vehicle alone was used as reference. Significantly modulated genes were selected from those whose expression was above two fold higher or lower than control samples.
We evaluated the effects of variance stabilizing normalization, mean normalization, median  normalization and quantile normalization on data. Especially for mRNAs, the quantile  normalization has been proven as a very suitable normalization method. Applying  quantile normalization, however, it is assumed that all arrays show similar data distributions.

organism: Candida albicans

source_name: Candida albicans blastospores growth in sabouraud solid medium

label_protocol: RNA was then amplified, biotin-labeled (MessageAmp II Biotin-Enhanced kit, Ambion Applied Biosystems, Monza, Italy) and purified on an affinity resin (RNeasy, Qiagen SpA, Milan, Italy).

growth_protocol: C. albicans SC5314 cells grown in RPMI-1640 medium

extract_protocol: Total RNA was extracted with mortar and pestle in the presence of liquid nitrogen. The resulting powder was resuspended in TRIZOL (Invitrogen Srl, Milan, Italy) and transferred to a 1.5-ml Eppendorf tube and gently vortexed and inverted two or three times to homogenize the sample.

treatment_protocol: C. albicans SC5314 cells were treated with either 10 ng/ml IL-17A (R&D Systems) or drug vehicle and incubated for 4 (T1) and 24 (T2) h at 37 °C.

value: Candida albicans blastospores

tag: treatment group

value: T2 IL17A treated


title: 96 hours after irradiation

city: Belo Horizonte

first: Priscila

last: Grynberg

state: Minas Gerais

address: Avenida Antonio Carlos, 6627

department: Departamento de Bioquímica e Imunologia

country: Brazil

institute: Universidade Federal de Minas Gerais

description: Analysis used non-irradiated T. cruzi epimastigote cells as control samples for comparison to irradiated epimastigote cells with RNA extracted 96 hours after irradiation. Two biological replicates (RI and RII).

hyb_protocol: Slides were pre-hybridized by placing them in coupling jars containing pre-hybridization solution (5× SSC, 0.1% SDS, 1%BSA) at 42 °C for one hour. Slides were washed twice by immersing 10 times in a beaker containing MilliQ water followed by dipping three times in isoamyl alcohol, and were subsequently spun dry. The slides containing 30 µL of samples in hybridization buffer were hybridized for 14 hours in a water bath at 42° C in the dark under cover slips inside Corning® hybridization chambers (Corning, USA). Slides were  then washed two times for five minutes each in a low stringency wash solution (2× SSC, 0.1% N-lauroysarcosine) at 42 °C (first wash) and RT (second wash), followed by two washes of five min in medium stringency wash (0.1× SSC, 0.1% N-lauroysarcosine) at RT and two washes for five minutes each in high stringency wash solution (0.1× SSC) at RT.

scan_protocol: Slides were spun dry and scanned using a microarray dual channel laser scanner (ScanExpress Lite da PerkinElmer®, USA) at 10 μm resolution, 100% laser power and PMT levels which were adjusted in order to obtain similar distributions of red and green signal intensities.

data_processing: For each time point, gene expression analysis was done based on information obtained from four slides, one dye-swap pair for each biological replicate. ScanArray Express (PerkinElmer®) software was used to generate the slide images and raw intensity data which were then analyzed using specific packages from the R statistical language. Spots of good quality (positive flag value) were considered to be analyzed. Data were inspected for spatial biases on both red and green channels (background and signal), for print-tip bias, dye bias, and bias dependent of intensity using the LIMMA and marray packages. Background correction was done with normexp method. Robust spline and aquantile methods were used for normalization within and between arrays, respectively. A linear model that incorporates biological and technical replication was used for statistical analysis. A list of differentially expressed genes was generated by applying adjusted p-values for multiple tests using ‘BH’ method, which works with the expected proportion of false-positives (FDR- False Discovery Rate) among the rejected hypothesis. Graphics were drawn using GraphPad version 5.03. Heatmap and cluster graphics were created using gplots package and personal scripts (R statistical language).

organism: Trypanosoma cruzi

source_name: T. cruzi epimastigote cells - irradiated (RNA extract 96 hours after irradiation)

label_protocol: Aminoallyl amplified RNA was labeled with Cy3 and Cy5 according to a modified version of the AminoAllyl MessageAmp II Kit (Ambion, USA) and TIGR's standard operational procedure – SOP #M008 (ftp://ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M008.pdf). Briefly, we followed the manufacturer’s instructions for the labeling step, but the initial amount of amplified RNA was changed to 8 μg. The Cy3 and Cy5 labeled samples were then combined. Labeled RNA was purified away from unincorporated dyes using YM-30 Microcon columns following manufacturer's specifications (Millipore®, USA). The final sample was dried again and resuspended in 30 µL of hybridization buffer (50% formamide, 5× SSC, 0.1% SDS, 0.1M DDT, and 6% salmon sperm as blocking agent) according to TIGR's SOP #M008. The solution was heated to 95 oC during 3 minutes and placed in ice for 30 seconds. After a brief centrifugation, the solution was dispensed onto the slide surface and covered with a coverslip.

growth_protocol: Epimastigote cells were cultivated at 28 ◦C in LIT medium (Liver Infusion Tryptone - liver digest neutralized) supplemented with complement-inactivated 10% fetal bovine serum, streptomycin sulfate (0.2 g/L), and penicillin (200,000 units/L).

extract_protocol: Epimastigote cells were subjected to RNA extraction using Trizol reagent (Invitrogen Life Technologies, USA) and RNA samples were purified using RNeasy® MiniEluteTM Cleanup Kit (Qiagen, German) according to the manufacturers’ instructions. Total RNA was quantified using a Nanodrop ND-100 UV/Vis spectrophotometer (NanoDrop Technologies, USA) and the overall RNA quality was assessed by denaturing gel electrophoresis [14]. Total RNA (2 μg) was amplified using the Amino Allyl MessageAmp II kit (Ambion, USA), according to the manufacturer’s specifications.

treatment_protocol: Cultures with 5×108 parasites in 20 mL of LIT medium (2x107 cells/mL) were exposed to a dose of 500 Gy (1578 Gy/h per 20 minutes) in a cobalt (60Co) irradiator located at Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Belo Horizonte, Brazil

value: CL Brener

source_name: T. cruzi epimastigote cells - control (Non-irradiated - Biological replicate I)


title: Candida albicans T1 IL17A treated, biological rep2

description: Biochip 11267

value: T1 IL17A treated


title: Candida albicans T2 IL17A treated, biological rep1

description: Biochip 11324


title: ILK-deficient epidermis replicate 3

description:
D12 KO
Gene expression data from mouse # 5

value: [Ilktm1Star (with Ilk alleles) x Tg(KRT14-cre)1Amc/J] x Ilktm1Star


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-H4Ac antibody_Array A

source_name: H4Ac ChIP DNA from HSPC transduced with the empty vector

extract_protocol: ChIP assays were performed as described elsewhere (Ballestar et al., EMBO J., 2003 [PMID 14633992]). Three biological replicates were prepared and hybridized on the same array set. ChIP products were amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma, Saint Louis, MO) and purified using the UltraCleanTM GelSpinTM DNA purification kit (MO BIO laboratories, Inc., Carlsbad, CA).

value: Millipore


title: Candida albicans T2 untreated, biological rep1

description: Biochip 11267

value: T2 untreated


title: Candida albicans T1 IL17A treated, biological rep1

description: Biochip 11267


title: Candida albicans T2 untreated, biological rep2

description: Biochip 11267


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-HDAC1 antibody_Array A

source_name: HDAC1 ChIP DNA from HSPC transduced with the empty vector

value: cord blood

value: Affinity BioReagents


title: ILK-deficient epidermis replicate 2

description:
D10 KO
Gene expression data from mouse # 3

value: 3 day-old

value: epidermis obtained from dispase treatment of skin


title: 24 hours after irradiation

description: Analysis used non-irradiated T. cruzi epimastigote cells as control samples for comparison to irradiated epimastigote cells with RNA extracted 24 hours after irradiation. Two biological replicates (RI and RII).

source_name: T. cruzi epimastigote cells - irradiated (RNA extract 24 hours after irradiation)


title: ILK-expressing epidermis replicate 1

description:
D3 WT
Gene expression data from mouse # 2

value: heterozygous for the KRT14-cre transgene and heterozygous (ILK-expressing) for the floxed Ilk alleles


title: 48 hours after irradiation

description: Analysis used non-irradiated T. cruzi epimastigote cells as control samples for comparison to irradiated epimastigote cells with RNA extracted 48 after irradiation. Two biological replicates (RI and RII).

source_name: T. cruzi epimastigote cells - irradiated (RNA extract 48 hours after irradiation)


title: ILK-expressing epidermis replicate 3

description:
D11 WT
Gene expression data from mouse # 6


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-H4Ac antibody_Array A

source_name: H4Ac ChIP DNA from HSPC expressing the AML1/ETO fusion protein

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

value: normal donors

value: AML1/ETO fusion protein


title: liver tissue received from control mice

city: Nicosia

first: Apostolos

last: Zaravinos

state: Nicosia

address: Kallipoleos 75

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

description:
liver tissue received from control mice
1_Exiqon_14084262_S01_Cropped.txt: Hy3
0_Exiqon_14084262_S01_Cropped.txt: Hy5

hyb_protocol: The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization, the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: Filtering was performed based on the signal intensity. Spots with no signal above the background (flags 1 and 2) were detected and removed. Background correction was performed to remove non-biological contributions (background) to the measured signal, by subtracting the median global background from the median local background from the signal intensity. A threshold of 1.5 (L12 versus L0) was set as cut-off. Normalization was performed using the Lowess regression algorithm, in order to remove certain systematic biases from microarray data, such as dye effects or intensity dependence. Normalized data were extracted, pre-processed and sorted with Microsoft Excel®.

source_name: Total RNA isolated from pooled livers from the L0 mice

label_protocol: One µg total RNA from sample and reference were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark). The Hy3™-labeled samples and the Hy5™-labeled samples were mixed pair-wise and hybridized to the miRCURY™ LNA array version 10.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for all species registered in the miRBASE version 11.0 at the Sanger Institute.

growth_protocol: Twenty male wild type mice C57BL6J (8 weeks old) fed a standard diet were used for the liver regeneration experiment.

extract_protocol: Liver tissue was excised from mice and was immediately submerged in RNA later solution (Ambion, Foster City, CA). For microRNA profiling, total RNA was isolated from pooled livers from the L0 and L12 mice using the TRIzol® reagent (Invitrogen, Carlsbad, CA) as the manufacturer instructed. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were housed in the animal facility of the University of Patras Medical School in temperature-, light- and humidity-controlled rooms with a 12-h light/dark cycle. All animal procedures were approved by the institutional review board of the University of Patras Medical School and were in accordance with EC Directive 86/609/EEC. A 2/3 partial hepatectomy (PH) was performed on 10 mice according to a recently published standardized protocol whereby the median and left lobes of the liver were removed and another 10 sham operated mice were used as the control group. The liver was allowed to regenerate and mice were sacrificed 12 hours after operation. Liver samples were collected from the sham operated mice (L0) and the hepatectomized mice at the end of the experiment (L12).

value: male

value: 8 weeks old

source_name: common reference pool


description:
liver tissue 12 hours after liver regeneration induced by 2/3 partial hepatectomy
1_Exiqon_14084263_S01_Cropped.txt: Hy3
0_Exiqon_14084263_S01_Cropped.txt: Hy5

source_name: Total RNA isolated from pooled livers from the L12 mice


title: ILK-expressing epidermis replicate 2

description:
D9 WT
Gene expression data from mouse # 4

source_name: ILK-expressing epidermis


title: Candida albicans T1 untreated, biological rep1

description: Biochip 11267

value: Candida albicans blastospores

value: T1 untreated


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-HDAC1 antibody_Array A

source_name: HDAC1 ChIP DNA from HSPC expressing the AML1/ETO fusion protein


title: Candida albicans T1 untreated, biological rep2

description: Biochip 11267


title: ILK-deficient epidermis replicate 1

description:
D1 KO
Gene expression data from mouse # 1

value: heterozygous for the KRT14-cre transgene and homozygous (ILK-deficient) for the floxed Ilk alleles


title: Candida albicans T0, biological rep2

description: Biochip 11267

value: T0 untreated


title: Candida albicans T0, biological rep1

description: Biochip 11267


title: Immediately after irradiation (0 hours)

description: Analysis used non-irradiated T. cruzi epimastigote cells as control samples for comparison to irradiated epimastigote cells with RNA extracted immediatelly after irradiation. Two biological replicates (RI and RII).

source_name: T. cruzi epimastigote cells - irradiated (RNA extract immediately after irradiation)

value: CL Brener


title: 4 hours after irradiation

description: Analysis used non-irradiated T. cruzi epimastigote cells as control samples for comparison to irradiated epimastigote cells with RNA extracted 4 hours after irradiation. Two biological replicates (RI and RII).

source_name: T. cruzi epimastigote cells - irradiated (RNA extract 4 hours after irradiation)


title: B6 wildtype littermate 2

description:
11-0499_CB
both genotypes were littermates with each other

source_name: left and right striatum

extract_protocol: RNA was extracted using Trizol® (Invitrogen, Carlsbad, CA) and chloroform and then precipitated with ethanol and resuspended.  The solution was then passed through RNeasy® columns (Qiagen), quality checked using the Agilent 2100 Bioanalyzer (Santa Clara, CA),

tag: batch

value: batch 1

tag: genotype

value: homozygous for B6 in congenic region

tag: Sex

tag: age (days old)


title: activated Treg, biological replica 1

city: Augusta

first: Piotr

last: Kraj

state: GA

address: 1120 15th Street

department: Centr. for Biotech. and Gen. Medicine

institute: Medical College of Georgia

hyb_protocol: Hybridization according to Affymetrix protocol, 45 degrees celcius, 16 hours, 50 rpm

scan_protocol: Scanned on Affymetrix scanner 3000 with 7G upgrade

data_processing: The data were condensed with RMA transformation algorithm using the R (Bioconductor) - an open source and open development software project for the analysis and comprehension of genomic data.

source_name: activated Treg cells

label_protocol: Biotin, total RNA was labeled according to Eberwine protocol using Target Amp kit, Epicentre

growth_protocol: Cells were activated in vitro by plate - bound anti-CD3, anti-CD28 antibodies

extract_protocol: Total RNA was isolated from the cells of different samples using RNeasy Mini Kit spin columns (Qiagen)

treatment_protocol: Adaptive Treg cells were generated in the presence of IL-2 (50 u/ml) and TGF-beta (3 ng/ml), actiavted Treg cells were produced by stimulation with  plate - bound anti-CD3, anti-CD28 antibodies

tag: genetic background

value: mixed, predominant C57BL/6

tag: cell type

value: activated Treg CD4+ Foxp3+  cells


title: Haematopoietic Stem/Progenitor cells transfected with empty vector_ChIP with anti-HA antibody_Array A

description:
Immunopurified anti-HA made in-house: clone H9658 Monoclonal Antibodies Unit, CNIO, Madrid, Spain.

Three biological replicates per sample were prepared and hybridized on the same array set.

source_name: HA-AML1/ETO ChIP DNA from HSPC transduced with the empty vector

value: cord blood

tag: source

tag: transduction

value: vector

value: anti-HA

source_name: Input DNA from HSPCs transduced with the empty vector


title: induced Treg, biological replica 1

source_name: induced Treg cells

value: induced Treg CD4+ Foxp3+  cells


title: induced Treg, biological replica 2


title: activated Treg, biological replica 2


title: Haematopoietic Stem/Progenitor cells expressing AML1/ETO-HA_ChIP with anti-HA antibody_Array A

source_name: HA-AML1/ETO ChIP DNA from HSPC expressing the AML1/ETO fusion protein

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

value: normal donors

tag: chip antibody

source_name: Input DNA from HSPCs expressing the AML1/ETO fusion protein


title: 162-1

status: Public on Jan 17 2012

city: Oslo

first: Anders

middle: Erik Astrup

last: Dahm

address: Kirkeveien 166

department: Hematology

country: Norway

institute: Oslo University Hospital

description: treatment group 3

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned using GeneChip ® Scanner 3000 (Affymetrix). Image analysis was performed using GeneChip ® Operating Software 1.4 (Affymetrix)

data_processing: The data were normalized using the farms package (Hochreiter 2006) in R (version 2.10.1), using the RMA (Irizarry 2003) method. Probes were summarized using the revised entrez-based probe annotation of Dai (Dai 2005, the package hgu133plus2hsentrezgcdf.db, version 12.1.0), and classified as informative or non-informative using the method of Talloen (Talloen 2007). Non-informative probe sets were discarded. The latter two methods reduced the number of probe sets from 54,675 on the original chip, to 17,788 after re-annotation, and to 3,640 after discarding non-informative probe sets (filtered data provided as a supplementary file on GSE24859). Differentially expressed probe sets were identified using the limma R package (Smyth 2004) by subtracting baseline measurement for each patient from the measurement at six weeks, and compare the resulting expression differences between patients with different treatments using limma's moderated t-test. P-values were corrected for multiple testing using the false discovery rate-controlling procedure of Benjamini and Hochberg (Benjamini 1995).

source_name: blood cells, baseline, before treatment with tibolone

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated from whole blood using the PAXgene® Blood RNA Kit 50 (Qiagen ref.762174). The total RNA was cleaned and concentrated to obtain smaller elution volumes using RNeasy® MinElute (Qiagen cat 74204).

value: cells from whole blood

value: female


title: 162-3

description: treatment group 3

source_name: blood cells, after 6 weeks treatment with tibolone


title: 160-3

description: treatment group 3


title: Colon cancer sample 7 using 75ng input DNA

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
Sample7_75ng
457612A04_MAF_S01_Cropped_635.pair [ch1 raw data file]
457612A04_MAF_S01_Cropped_532.pair [ch2 raw data file]

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: Median normalization in R/Bioconductor

source_name: colon cancer

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

tag: sample id

value: Colon cancer, FFPE

tag: input dna

source_name: Normal colon mucosa

value: Normal colon mucosa (Patient own normal, FFPE)


title: 193-1

description: treatment group 2

source_name: blood cells, baseline, before treatment with 2 mg 17b-estradiol/1 mg NETA


title: 160-1

description: treatment group 3


title: 164-3

description: treatment group 2

source_name: blood cells, after 6 weeks treatment with 2 mg 17b-estradiol/1 mg NETA


title: 174-1_NY

description: treatment group 2


title: 193-3

description: treatment group 2


title: 165-3

description: treatment group 2


title: 165-1

description: treatment group 2


title: 177-1

description: treatment group 2


title: 177-3

description: treatment group 2


title: Colon cancer sample 7 using 100ng input DNA

description:
Sample7_100ng
457612A03_MAF_S01_Cropped_635.pair [ch1 raw data file]
457612A03_MAF_S01_Cropped_532.pair [ch2 raw data file]


title: Colon cancer sample 4 using 250ng input DNA

description:
Sample4
383039A05_crop_635.pair [ch1 raw data file]
383039A05_crop_532.pair [ch2 raw data file]


title: 186-3_NY

description: treatment group 1

source_name: blood cells, after 6 weeks treatment with 1 mg 17b-estradiol/0.5 mg NETA


title: 157-1

description: treatment group 2


title: 157-3

description: treatment group 2


title: Colon cancer sample 7 using 50ng input DNA

description:
Sample7_50ng
US22502676A02_382992_S01_Cropped_635.pair [ch1 raw data file]
US22502676A02_382992_S01_Cropped_532.pair [ch2 raw data file]


title: 174-3_NY

description: treatment group 2


title: Colon cancer sample 3 using 250ng input DNA

description:
Sample3
383039A04_crop_635.pair [ch1 raw data file]
383039A04_crop_532.pair [ch2 raw data file]


title: Colon cancer sample 5 using 250ng input DNA

description:
Sample5
383039A06_crop_635.pair [ch1 raw data file]
383039A06_crop_532.pair [ch2 raw data file]


title: Colon cancer sample 1 using 250ng input DNA

description:
Sample1
383039A02_crop_635.pair [ch1 raw data file]
383039A02_crop_532.pair [ch2 raw data file]


title: Colon cancer sample 7 using 250ng input DNA

description:
Sample7_250ng
US22502676A01_382992_S01_Cropped_635.pair [ch1 raw data file]
US22502676A01_382992_S01_Cropped_532.pair [ch2 raw data file]


title: Colon cancer sample 7 using 150ng input DNA

description:
Sample7_150ng
457612A01_MAF_S01_Cropped_635.pair [ch1 raw data file]
457612A01_MAF_S01_Cropped_532.pair [ch2 raw data file]


title: Colon cancer sample 6 using 250ng input DNA

description:
Sample6
383039A07_crop_635.pair [ch1 raw data file]
383039A07_crop_532.pair [ch2 raw data file]


title: Colon cancer sample 2 using 250ng input DNA

description:
Sample2
383039A03_crop_635.pair [ch1 raw data file]
383039A03_crop_532.pair [ch2 raw data file]


title: 178-3

description: treatment group 1


title: 172-3

description: treatment group 1


title: 178-1

description: treatment group 1

source_name: blood cells, baseline, before treatment with 1 mg 17b-estradiol/0.5 mg NETA


title: 172-1

description: treatment group 1


title: 159-1

description: treatment group 1


title: 154-3

description: treatment group 1


title: 167-3

description: treatment group 1


title: 159-3

description: treatment group 1


title: 186-1_NY

description: treatment group 1


title: 154-1

description: treatment group 1


title: 167-1

description: treatment group 1


title: OE::rsmA-rep2.3

type: mixed

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

institute: Dickinson College

description: Biological replicate 3 of 3 for Run 2. Experimental OE::rsmA cells.

hyb_protocol: Arrays were hybridized in a NimbleGen hybridization system 12 (BioMicro) following the standard NimbleGen operating protocol. See www.nimblegen.com.  As the arrays are four-plex arrays, sample tracking controls were also included.

scan_protocol: Arrays were scanned using a GenePix 4000B scanning laser (Molecular Devices) following the standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al.  (2004) Genome Biol 5: R80).  The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3).

organism: Aspergillus nidulans

source_name: Aspergillus nidulans OE::rsmA (native)

label_protocol: Sample labeling was performed as described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414, using cyanine dyes (Amersham), Superscript III (Invitrogen), and amino-allyl-dUTP (Ambion).  RNA collected from either wild-type RDIT9.32 (veA) or OE::rsmA was labeled with Cy5 dye and was directly compared to a genomic DNA reference sample labeled with Cy3 dye.

growth_protocol: Aspergillus nidulans cultures were grown in liquid minimal media at 37˚C for 48 h, with shaking at 250 rpm.

extract_protocol: Mycelia were collected, lyophilized overnight, and ground with spatula.  To 100 µL mycelia, 1 mL Trizol was added, followed by 250 µL chloroform.  RNA was precipitated with EtOH.  Following total RNA isolation, RNA was further purified with LiCl and RNeasy Mini kit (Qiagen).  RNA concentration was determined by NanoDrop spectrophotometer (Thermo Scientific).

tag: treatment

value: liquid minimal media at 37˚C for 48 h in dark, with shaking at 250 rpm

value: overexpression of rsmA at the native locus under the control of gpdA promoter

source_name: Aspergillus nidulans RDIT9.32 (veA) genomic DNA

value: Genomic DNA was extracted from cells grown in liquid minimal media with yeast extract (5 g/liter) overnight at 37˚C in the light condition


title: OE::rsmA-rep2.1

description: Biological replicate 1 of 3 for Run 2. Experimental OE::rsmA cells.


title: OE::rsmA-rep2.2

description: Biological replicate 2 of 3 for Run 2. Experimental OE::rsmA cells.


title: 164-1

description: treatment group 2

tag: gender


title: 778_Tel+ parental

city: Houston

first: Jian

last: Hu

state: TX

address: 1515 Holcombe Blvd

department: Cancer Biology

institute: MD Anderson Cancer Center

hyb_protocol: Hybridization was performed with the Tecan HS Pro hybridization station.

scan_protocol: Scanning was performed with Agilent scanner equipped Agilent Scanner Control software v7.0.

data_processing: Data were processed with the Feature Extraction (FE) software v9.5, normalized using LOcally-WEighted regression Scatterplot Smoother.

label_protocol: The fragmented product is labeled via exo-Klenow with Cyanine 3-dUTP.

extract_protocol: Total genomic DNA were extracted with Qiagen DNeasy Blood & Tissue Kit following according to the manufacturer's instructions.

treatment_protocol: Various generations of Atm-/-TERT-ER mice treated with 4-OHT or vehicle. Recipient SCID mice injected with G3 Atm-/-TERT-ER T-cell lymphomas were maintained either on 4-OHT or vehicle

tag: recipient strain

value: SCID

tag: genotype/variation

value: Atm-/-TERT-ER

tag: telomere maintanence mechanism

value: Telomerase

tag: generations

tag: passages

value: parental


title: 778_ALT+ 1

value: ALT

value: Vehicle


title: 778_Tel+ 3


title: 778_Tel+ 2


title: WT-rep2.3

description: Biological replicate 3 of 3 for Run 2. Control wild-type RDIT9.32 (veA) cells.

source_name: Aspergillus nidulans wild-type RDIT9.32 (veA)

tag: genotype

value: wild-type RDIT9.32 (veA)


title: 778_Tel+ 1


title: 2072P_G3_OHT


title: 2186T_G3_OHT


title: 2783_G1_OHT


title: 778_ALT+ 2


title: 2797_G1_OHT


title: 1283_G1_OHT


title: 2186P_G3_OHT


title: 1548_G3_OHT


title: breast cancer no-treatment surgical specimen subject 26 FL1735 R54594

first: TAKAYUKI

last: IWAMOTO

department: Breast medical Oncology

institute: UT MD Anderson

description: Gene expression data from breast cancer FNA biopsy, pre-treatment

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized to affymetrix U133A arrays overnight at 42C. Microarrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.

data_processing: The data were normalized using dChip version 1.3 followed by logrithm-base-10 transformation. The dChip version 1.3 was used to calculate Model Based Expression Index (MBEI) values of the arrays using the digital standard microarray MDA-BCNorm.CEL and the probe sensitivity index file UTMDACC-BreastCancerNormalizer.psi as described in Hess, et. al, Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and 5-Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer, Journal of Clinical Oncology, 24 (26), 2006.

source_name: breast cancer surgical specimens no treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 ug total RNA using the BioArray High Yield RNA transcript labeling kit (Enzo Laboratories).

extract_protocol: total RNA was extracted from the FNA and surgical specimens using Qiagen RNeasy kit following the manufacturer’s instructions (http://www.qiagen.com).

tag: array qc

value: Pass

value: No Treatment

tag: prepost-pair

tag: molecular subtype

value: Basal

tag: er status

value: ERneg

tag: her2 status

tag: disease state

value: breast cancer

tag: tissue

value: breast cancer surgical specimen


title: 2072T_G3_OHT


title: 2588_G3_VEH


title: 2668_G3_VEH


title: 2737_G3_OHT


title: 2628_G3_VEH


title: 778_ALT+ 3


title: 2657_G1_OHT


title: breast cancer no-treatment surgical specimen subject 25 FL1739 R54067

value: LumA

value: ERpos


title: 778_ALT+ 4


title: 1561_G3_OHT


title: 2713_G3_OHT


title: 2582_G3_VEH


title: 2486_G1_OHT


title: 2714_G1_OHT


title: OE::rsmA-rep1.3

description: Biological replicate 3 of 3 for Run 1. Experimental OE::rsmA cells.

source_name: Aspergillus nidulans OE::rsmA (plasmid)

value: liquid minimal media at 37˚C for 48 h in dark, with shaking at 250 rpm

value: overexpression of rsmA on plasmid pMS65 under the control of gpdA promoter


title: WT-rep2.1

description: Biological replicate 1 of 3 for Run 2. Control wild-type RDIT9.32 (veA) cells.

value: Genomic DNA was extracted from cells grown in liquid minimal media with yeast extract (5 g/liter) overnight at 37˚C in the light condition


title: OE::rsmA-rep1.2

description: Biological replicate 2 of 3 for Run 1. Experimental OE::rsmA cells.


title: breast cancer no-treatment surgical specimen subject 24 FL1767 R53548


title: breast cancer post-treatment surgical specimen subject 22 FL1762 R51365

source_name: breast cancer surgical specimens

value: post-neoadjuvant systemic therapy


title: 778_G3_OHT

value: SCID

value: Atm-/-TERT-ER

value: Telomerase


title: 2032_G3_OHT


title: 2275_G1_OHT


title: 852_G3_OHT

value: ALT


title: 202-3

description: treatment group 4

source_name: blood cells, after 6 weeks treatment with raloxifene

value: cells from whole blood

value: female


title: 2637_G3_VEH

value: Vehicle


title: 2379_G1_OHT


title: 691N_G1_OHT


title: 192-3

description: treatment group 4


title: WT-rep1.1

description: Biological replicate 1 of 3 for Run 1. Control wild-type RDIT9.32 (veA) cells.

value: wild-type RDIT9.32 (veA)


title: breast cancer post-treatment surgical specimen subject 18 FL1634 R50065

value: Pass

value: ERneg


title: OE::rsmA-rep1.1

description: Biological replicate 1 of 3 for Run 1. Experimental OE::rsmA cells.


title: WT-rep1.2

description: Biological replicate 2 of 3 for Run 1. Control wild-type RDIT9.32 (veA) cells.


title: WT-rep1.3

description: Biological replicate 3 of 3 for Run 1. Control wild-type RDIT9.32 (veA) cells.


title: breast cancer post-treatment surgical specimen subject 20 FL1747 R50893

value: Basal

value: breast cancer

value: breast cancer surgical specimen


title: breast cancer no-treatment surgical specimen subject 17 FL1740 R50012

value: No Treatment


title: breast cancer post-treatment surgical specimen subject 19 FL1787 R50659


title: 202-1

description: treatment group 4

source_name: blood cells, baseline, before treatment with raloxifene


title: 537_G3_OHT


title: 180-3

description: treatment group 4


title: 180-1

description: treatment group 4


title: 192-1

description: treatment group 4


title: 169-3

description: treatment group 4


title: 477_G3_OHT


title: 484_G3_OHT


title: 691_G3_OHT


title: 169-1

description: treatment group 4


title: 411_G1_OHT


title: breast cancer post-treatment surgical specimen subject 16 FL1637 OCT R49615

value: LumA

value: ERpos


title: 166-3

description: treatment group 4


title: 166-1

description: treatment group 4


title: 199-1

description: treatment group 3


title: 199-3

description: treatment group 3


title: 163-3_NY

description: treatment group 4


title: Compound 1 (5uM) 3h rep3

city: Dallas

first: liang

last: zhang

state: Texas

address: 5323 harry hines blvd k2.202

institute: utsw

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: HBEC_Compound 1 (5uM) 3h

label_protocol: Biotinylated cRNA were prepared according  to UT Southwestern Microarray protocol for Illumina arrays

growth_protocol: HBEC cells were plated in 10 cm diameter dishes in keratinocyte serum-free medium and grown overnight to just reach confluency.

extract_protocol: For each sample total RNA was isolated with RNeasy Mini Kit and RNA was delivered to the UT Southwestern Microarray Core Facility.

treatment_protocol: Reagents were added at the concentrations and for the times listed on each sample.

tag: tissue source

value: bronchial


title: 191-3

description: treatment group 3


title: Compound 1 (5uM) 3h rep2


title: breast cancer post-treatment surgical specimen subject 14 FL1745 R48910

value: post-neoadjuvant systemic therapy

value: Normal


title: Compound 1 (5uM) 3h rep1


title: breast cancer post-treatment surgical specimen subject 13 FL1742 R48906


title: 179-3

description: treatment group 3


title: 191-1

description: treatment group 3

source_name: blood cells, baseline, before treatment with tibolone


title: breast cancer post-treatment surgical specimen subject 12 FL1636 OCT R48486


title: breast cancer post-treatment surgical specimen subject 15 FL1743 R49009


title: 171-3

description: treatment group 3

source_name: blood cells, after 6 weeks treatment with tibolone


title: breast cancer post-treatment surgical specimen subject 11 FL1699 R47984


title: 171-1

description: treatment group 3


title: 475_G3_OHT

value: SCID

value: Atm-/-TERT-ER

value: Telomerase


title: DMSO 3h rep2

source_name: HBEC_DMSO 3h


title: DMSO 3h rep3


title: DMSO 3h rep1


title: 179-1

description: treatment group 3

value: cells from whole blood

value: female


title: breast cancer post-treatment surgical specimen subject 10 FL1633 R47527


title: breast cancer post-treatment surgical specimen subject 23 FL1765 R51874


title: WT-rep2.2

description: Biological replicate 2 of 3 for Run 2. Control wild-type RDIT9.32 (veA) cells.

value: liquid minimal media at 37˚C for 48 h in dark, with shaking at 250 rpm

value: wild-type RDIT9.32 (veA)

value: Genomic DNA was extracted from cells grown in liquid minimal media with yeast extract (5 g/liter) overnight at 37˚C in the light condition


title: breast cancer post-treatment surgical specimen subject 9 FL1786 R46409

value: Pass


description:
Sample7_50ng
Colon cancer sample 7 using 50ng input DNA
US22502676_252252210371_S01_CGH_105_Dec08_1_3.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

source_name: colon cancer

tag: sample id

value: Colon cancer, FFPE

tag: input dna

source_name: Normal colon mucosa

value: Normal colon mucosa (Patient own normal, FFPE)


title: 163-1_NY

description: treatment group 4

tag: gender


title: breast cancer post-treatment surgical specimen subject 8 FL1764 R45280

tag: treatment

value: ERneg

value: breast cancer

value: breast cancer surgical specimen


description:
Sample7_75ng
Colon cancer sample 7 using 75ng input DNA
US22502676_252252210371_S01_CGH_105_Dec08_1_2.txt


title: breast cancer post-treatment surgical specimen subject 7 FL1635 OCT R44209

value: LumB

value: ERpos


description:
Sample7_100ng
Colon cancer sample 7 using 100ng input DNA
US22502676_252252210371_S01_CGH_105_Dec08_1_1.txt


title: 13 DAS, biological rep2

city: Zwijnaarde

first: Megan

last: Andriankaja

address: 927 Technologiepark

country: Belgium

institute: VIB-PSB

description: 13 days after stratification

hyb_protocol: Standard agronomics protocol

scan_protocol: Standard agronomics protocol

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). The TAIR9 CDFwas used.

organism: Arabidopsis thaliana

label_protocol: Standard agronomics protocol

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: RNeasy plant mini kit (Qiagen) , according to manufacturer protocol

tag: ecotype

value: leaf 3

tag: age

value: 13 days after stratification


title: 13 DAS, biological rep1

description: 13 days after stratification


title: 11 DAS, biological rep3

description: 11 days after stratification

value: 11 days after stratification


title: 12 DAS, biological rep2

description: 12 days after stratification

value: 12 days after stratification


title: 13 DAS, biological rep3

description: 13 days after stratification


title: 12 DAS, biological rep1

description: 12 days after stratification


title: 671_G3_OHT

tag: recipient strain

value: SCID

tag: genotype/variation

value: Atm-/-TERT-ER

tag: telomere maintanence mechanism

value: Telomerase

tag: generations


title: breast cancer post-treatment surgical specimen subject 6 FL1688 R44130

tag: array qc

value: post-neoadjuvant systemic therapy

tag: prepost-pair

value: LumA


description:
Sample7_150ng
Colon cancer sample 7 using 150ng input DNA
US22502676_252252210370_S01_CGH_105_Dec08_1_2.txt


title: breast cancer post-treatment surgical specimen subject 5 FL1572 R42161_2

value: Pass

tag: molecular subtype

value: Normal

tag: er status


title: 11 DAS, biological rep1

description: 11 days after stratification


title: breast cancer post-treatment surgical specimen subject 2 FL1687 R36494

tag: her2 status

tag: disease state


title: 12 DAS, biological rep3

description: 12 days after stratification

tag: tissue


title: 10 DAS, biological rep3

description: 10 days after stratification

value: 10 days after stratification


title: 9 DAS, biological rep2

description: 9 days after stratification

value: 9 days after stratification


title: Colon cancer sample 6 using 250ng input DNA

description:
Sample6
Colon cancer sample 6
US22502676_252252210027_S01_CGH_105_Dec08_1_3.txt

tag: sample id

value: Colon cancer, FFPE

value: Normal colon mucosa (Patient own normal, FFPE)


title: breast cancer post-treatment surgical specimen subject 4 FL1783 R40764

value: ERneg

value: breast cancer

value: breast cancer surgical specimen


title: breast cancer post-treatment surgical specimen subject 3 FL2216 R39970_3

value: ERpos


title: 10 DAS, biological rep2

description: 10 days after stratification

value: leaf 3


title: 11 DAS, biological rep2

description: 11 days after stratification

value: 11 days after stratification


title: 9 DAS, biological rep3

description: 9 days after stratification


description:
Sample7_250ng
Colon cancer sample 7 using 250ng input DNA
US22502676_252252210370_S01_CGH_105_Dec08_1_1.txt

tag: input dna


title: 10 DAS, biological rep1

description: 10 days after stratification


title: 9 DAS, biological rep1

description: 9 days after stratification


title: 8 DAS, biological rep3

description: 8 days after stratification

value: 8 days after stratification


title: Colon cancer sample 4 using 250ng input DNA

description:
Sample4
Colon cancer sample 4
US22502676_252252210025_S01_CGH_105_Dec08_1_3.txt


title: Colon cancer sample 3 using 250ng input DNA

description:
Sample3
Colon cancer sample 3
US22502676_252252210025_S01_CGH_105_Dec08_1_2.txt


title: breast cancer no-treatment biopsy subject 25 FL2739_808

description: Gene expression data from breast cancer FNA biopsy, pre-treatment

source_name: breast cancer FNA biopsy, no-treatment

value: No Treatment

value: breast cancer tumor


title: Colon cancer sample 1 using 250ng input DNA

description:
Sample1
Colon cancer sample 1
US22502676_252252210028_S01_CGH_105_Dec08_1_2.txt


title: 8 DAS, biological rep1

description: 8 days after stratification


title: MS, day 10, biological rep2

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). The TAIR9 CDF was used.

value: control

tag: sample type


title: MS, day 9, biological rep3

tag: treatment


title: MS, day 10, biological rep3

tag: ecotype


title: Colon cancer sample 2 using 250ng input DNA

description:
Sample2
Colon cancer sample 2
US22502676_252252210028_S01_CGH_105_Dec08_1_3.txt


title: 8 DAS, biological rep2

description: 8 days after stratification

tag: age


title: MS, day 9, biological rep1


title: breast cancer no-treatment biopsy subject 26 FL830-791(B)

value: Basal


title: MS, day 10, biological rep1


title: breast cancer post-treatment surgical specimen subject 1 FL1736 R30324

value: Pass

value: post-neoadjuvant systemic therapy


title: MS, day 9, biological rep2


title: breast cancer pre-treatment biopsy subject 23 FL1290 703

source_name: breast cancer FNA biopsy, pre-treatment

value: pre-neoadjuvant systemic therapy

value: Normal


title: norflurazon, day 10, biological rep1

value: norflurazon treatment


title: norflurazon, day 10, biological rep2


title: norflurazon, day 9, biological rep3


title: norflurazon, day 10, biological rep3


title: breast cancer pre-treatment biopsy subject 20 FL688-647


title: breast cancer pre-treatment biopsy subject 22 FL2738_688


title: breast cancer pre-treatment biopsy subject 18 U133A_80-FL-214-FL378-595_09_01_06


title: norflurazon, day 9, biological rep1


title: breast cancer pre-treatment biopsy subject 19 FL2737_667


title: breast cancer no-treatment biopsy subject 24 FL1753 816

value: LumA


title: norflurazon, day 9, biological rep2


title: MSK0130 NSP

first: Qingxia

last: Wei

address: 101 College Street

department: Development Biology

institute: Hospital for Sick Children

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The raw data were normalized using robust multi-array average (RMA) algorithm15

label: Biotin

source_name: Soft tissue sarcoma

label_protocol: 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module

growth_protocol: Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).

extract_protocol: For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.

treatment_protocol: For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).

tag: cells

value: Primary Malignant Fibrous Histiocytoma

tag: phenotype

value: MFH (myofibrosarcoma)

tag: subpopulation

value: non-SP


title: MSK0130 SP

value: SP


title: ALT+ P4-5

hyb_protocol: The biotinylated cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

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

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #5 on vehicle passage 4

label_protocol: The fragmented product is labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3’-hydroxyl end of the fragmented cDNA.

extract_protocol: Total RNAs were extracted with Qiagen Rneasy kit following according to the manufacturer's instructions.

treatment_protocol: Recipient SCID mice were maintained either on 4-OHT or vehicle

tag: recipient strain

value: SCID

tag: genotype/variation

value: G3 Atm-/-TERT-ER

tag: cell type

value: T-cell lymphoma

tag: telomere maintanence mechanism

value: alternative lengthening of telomeres (ALT)


title: breast cancer pre-treatment biopsy subject 16 U133A_80-FL-215-FL379-604_09_08_06

tag: array qc

tag: prepost-pair

tag: molecular subtype

tag: er status

value: ERpos

value: breast cancer

value: breast cancer tumor


title: breast cancer no-treatment biopsy subject 17 FL2736_609

value: Pass

value: No Treatment

value: Basal

value: ERneg

tag: her2 status

tag: disease state

tag: tissue


title: ALT+ P4-4

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #4 on vehicle passage 4


title: MSK0306 NSP

value: STS(soft tissue sarcoma)-MFH (myofibrosarcoma)


title: MSK0293 SP

value: STS(soft tissue sarcoma)-MFH (myofibrosarcoma), GRD.1


title: ALT+ P4-3

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #3 on vehicle passage 4


title: breast cancer pre-treatment biopsy subject 15 FL600-566

tag: treatment

value: pre-neoadjuvant systemic therapy

value: LumA


title: MSK0306 SP

value: Primary Malignant Fibrous Histiocytoma


title: tbf1-mSA-1

city: Birmingham

first: Karolina

last: Pajerowska-Mukhtar

state: Alabama

address: 1300 University Blvd

department: Department of Biology

institute: University of Alabama at Birmingham

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A) for 16 hours at 45C with rotation at 60rpm.

scan_protocol: Immediately following hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the GeneChip® FS450 fluidic station and are then scanned on the GeneChip® Scanner 3000 7G Plus where patterns of hybridization are detected.

data_processing: The data were normalized with RMA algorithm using Gene-Spring GX default analysis settings

label_protocol: RNA probes were labelled using MessageAmp Premier RNA Amplification Kit (Ambion)

growth_protocol: Arabidopsis plants (Columbia-0 and tbf1 mutant) were grown on soil (Metro Mix 360) at 22˚C under a 16/8 hr light/dark cycle for 3 weeks

extract_protocol: The RNA was extracted with TRIzol (Ambion)

treatment_protocol: Treated with 1 mM SA for 6 hrs (spray) or 10 µM elf18 for 2 hrs (infiltration into leaves). Mock treatments with water were included for both spray and infiltration.

value: mature leaf

tag: genotype

value: tbf1 mutant

value: water for 6 hrs (spray)

tag: biological replicate


title: MSK0282 SP

tag: cells

value: STS(soft tissue sarcoma)-MFH (myofibrosarcoma), GRD.3

value: SP


title: breast cancer pre-treatment biopsy subject 13 U133A_80-FL-107_FL283-569_05_19_06

value: ERpos


title: breast cancer pre-treatment biopsy subject 12 U133A_80-FL-205-FL369-570_08_25_06

value: breast cancer


title: ALT+ P4-2

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #2 on vehicle passage 4

value: SCID

value: G3 Atm-/-TERT-ER

value: T-cell lymphoma

value: alternative lengthening of telomeres (ALT)


title: Telomerase+ P4-2

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #2 on 4-OHT passage 4

value: Telomerase


title: MSK0227 SP

tag: phenotype

value: MFH (myofibrosarcoma) III/III


title: MSK0282 NSP

tag: subpopulation

value: non-SP


title: tbf1-mSA-2


title: ALT+ P4-1

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #1 on vehicle passage 4

tag: recipient strain


title: Telomerase+ P4-3

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #3 on 4-OHT passage 4

tag: genotype/variation


title: MSK0227 NSP


title: breast cancer pre-treatment biopsy subject 11 FL2735_517

value: Pass

value: pre-neoadjuvant systemic therapy

value: Normal

value: ERneg

value: breast cancer tumor


title: tbf1-mSA-3

value: mature leaf

value: tbf1 mutant

value: water for 6 hrs (spray)


title: MSK0366 NSP

value: Primary Malignant Fibrous Histiocytoma

value: pleomorphic undifferentiated sarcoma


title: MSK0293 NSP

value: STS(soft tissue sarcoma)-MFH (myofibrosarcoma), GRD.1


title: WT-elf-2

source_name: WT-elf

value: wild type

value: 10 µM elf18 for 2 hrs (infiltration into leaves)


title: Telomerase+ P4-1

source_name: G3 Atm-/-TERT-ER T-cell lymphoma #1 on 4-OHT passage 4

value: SCID

value: G3 Atm-/-TERT-ER

tag: cell type

value: T-cell lymphoma


title: breast cancer pre-treatment biopsy subject 14 U133A_80-FL-213-FL377-572_09_01_06

value: Basal

value: breast cancer


title: Telomerase+ parental

source_name: G3 Atm-/-TERT-ER T-cell lymphoma parental

tag: telomere maintanence mechanism

value: Telomerase


title: breast cancer pre-treatment biopsy subject 8 U133A_FL60-439_07_28_05

tag: array qc

value: Pass

value: pre-neoadjuvant systemic therapy


title: Non-side population, biological rep 4

hyb_protocol: Following fragmentation, GeneChips were washed and stained using EukGE-WS2v4

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

data_processing: The .cel files where imported into Genespring GX11 program and summarized using RMA normalization. The expression value of each gene from the SP and NSP fraction of each distinct tumour is normalized to the expression value of that particular gene from the NSP fraction. The NSP normalized matrix is provided as a supplementary file on the Series record.

source_name: NSP 864

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The tumours were freshly harvested from human.

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

treatment_protocol: The tumours were stained with Hoeschst Dye, and sorted via flow-cytomentry

value: soft-tissue sarcoma

value: Non-side population cells


title: breast cancer pre-treatment biopsy subject 10 U133A_FL99_521_10_05_05

tag: prepost-pair

value: ERneg

value: breast cancer tumor


title: breast cancer pre-treatment biopsy subject 7 U133A_FL41-380_07_07_05

tag: molecular subtype

value: ERpos


title: Non-side population, biological rep 3

source_name: NSP 265


title: breast cancer pre-treatment biopsy subject 5 FL2733_307

tag: er status