title: Mouse_colon_LEC_rep4

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

LEC_4

value: male


title: SPC-06 Undifferentiated Replicate 1

status: Public on Jun 16 2012

type: RNA

city: London

first: Graham

last: Cocks

address: The James Black Centre, 125 Coldharbour Lane

department: Neuroscience

country: United Kingdom

institute: King's College London

description: Clone 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Sample probe profile were exported from GenomeStudio. Data were then imported into lumi (bioconductor) and Variance Stabilizing transformation applied, Quantile Normalized and log2 transformed.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human spinal cord neural stem cell line 06, undifferentiated

label_protocol: Biotinylated cDNA were prepared using the Custom Illumina® TotalPrep™-96 Kit (Ambion)

growth_protocol: Cells were maintained as described by Pollock K et al, Exp Neurol. 2006 May;199(1):143-55.

extract_protocol: Standard Trizol extraction followed by DNase treatment, RNA dissolved in water.

tag: gender

value: Female

tag: tissue

value: Spinal cord

tag: embryonic age

value: 10 weeks


title: Mouse_colon_BEC_rep2

city: Zurich

first: Giorgia

last: Jurisic

address: Wolfgang-Pauli Strasse 10

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

BEC_2

hyb_protocol: Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.

label: biotin

organism: Mus musculus

source_name: Mouse, colon, normal, blood endothelial cells

label_protocol: Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.

growth_protocol: Mice were maintained under conventional conditions.

extract_protocol: Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).

treatment_protocol: Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).

tag: strain

value: female

tag: age

value: 8 weeks

value: colon

tag: cell type

value: blood vascular endothelial cells

tag: condition

value: normal, healthy

tag: cell isolation method

value: FACS


title: SPC-04 Undifferentiated Replicate 1

description: Clone 4

source_name: Human spinal cord neural stem cell line 04, undifferentiated


title: meiS HU rec8 delete replicate 3

status: Public on Jun 15 2012

type: genomic

city: Cambridge

first: Stephen

middle: P

last: Bell

state: MA

address: 68-630, 77 Massachusetts Ave.

department: Biology

country: USA

institute: MIT

description:
biological replicate 3 of 3 of meiS HU replication profile from rec8 delete cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from rec8 delete cells
rec8HU_3.txt

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: meiS HU replication profile from rec8 delete cells [G1 control]

label_protocol: 5 μg of gDNA was labeled with Cy3-dUTP or Cy5-dUTP (GE Healthcare) by random priming without denaturation using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: To induce synchronous meiosis, strains were pre-inoculated at OD600 = 0.2 in YPA (1% yeast extract, 2% bactopeptone, 1% potassium acetate, for meiS profiles), or BYTA medium (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phtlhalate, for all HU profiles), grown for 16 hours at 30°C, washed twice with water, and resuspended at OD600 = 2.0 in SPO medium (0.3% potassium acetate, pH7.0) at 30°C. For mitS phase profiles, cells were inoculated into fresh YPD medium containing 5 μg/ml alpha-factor for 3 hours and released by washing cells in 2 volumes of sterile water and resuspending in YPD at 30°C at OD600=0.6. MeiS cells containing the ime2-as1 allele were synchronized by incubation in SPO + 20 μM 1-NA-PP1 (Toronto Research Chemicals) for 4 hours, the cells were washed with 2 volumes of sterile water and resuspended in SPO medium. Samples of 1.5 mls were removed every 5 minutes for mitS profiles and every 7.5 minutes for meiS profiles. All DNA samples inclusive of S phase (those which showed cells in S phase in the FACS profiles, as well as two time points before and after) were pooled for processing. For hydroxyurea (HU) experiments, cells from BYTA cultures were inoculated into YPD containing 200 mM HU (OD600=1) or SPO (OD600=2.0) containing 20 mM HU for 4 hours at 30°C.

extract_protocol: Cells were lysed by bead beating in 500μl phenol/chloroform and 500μl of breakage buffer (10mM TRIS, pH 8.0, 1mM EDTA, 100mM NaCL, 2% Triton X-100, 1% SDS).  After centrifugation, the aqueous phase was precipitated with ethanol and resuspended in 500 μl TE7.6 (10 mM TRIS, pH7.6, 1mM EDTA) with 30 μg RNase. DNA was resuspended and samples were incubated at 50°C for 3 hours. DNA was sheared by sonicating at 100% output and lowest power for 10 seconds using a Branson sonicator. DNA was extracted with 500μl phenol/chloroform, precipitated with ethanol and resuspended in 100 μl of TE7.6

tag: type of dna

value: mitotic budding yeast cells

source_name: meiS HU replication profile from rec8 delete cells [HU 4 hours]

value: HU 4 hours

value: meiotic budding yeast cells


title: SPC-01 Undifferentiated Replicate 1

description: Clone 1

source_name: Human spinal cord neural stem cell line 01, undifferentiated


title: meiS HU spo11 delete replicate 3

description:
biological replicate 3 of 3 of meiS HU replication profile from spo11 delete cells
Series supplementary file contains mean of 3 biological replicate of meiS HU replication profile from spo11 delete cells
spo11HU_3.txt

source_name: meiS HU replication profile from spo11 delete cells [G1 control]

source_name: meiS HU replication profile from spo11 delete cells [HU 4 hours]


title: meiS HU rec8 delete replicate 1

description:
biological replicate 1 of 3 of meiS HU replication profile from rec8 delete cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from rec8 delete cells
rec8HU_1.txt


title: SPC-06 Undifferentiated Replicate 2

description: Clone 6


title: meiS HU spo11 delete replicate 2

description:
biological replicate 2 of 3 of meiS HU replication profile from spo11 delete cells
Series supplementary file contains mean of 3 biological replicate of meiS HU replication profile from spo11 delete cells
spo11HU_2.txt


title: Mouse_colon_BEC_rep1

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

BEC_1


title: no MLD, biallelic AML MLL_00265

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

country: Germany

institute: Munich Leukemia Laboratory

description: no MLD, biallelic

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

tag: ID

value: PBMC

tag: disease state

value: no Multilineage dysplasia, acute myeloid leukemia, biallelic


title: HCC 827 ER1

city: San Francisco

first: Elton

last: Chan

state: California

address: 600 16th Street Rm N216R

department: Medicine

institute: UCSF

description: Gene expression data from the Erlotinib-resistant cell line, HCC827 ER1

hyb_protocol: 5.5 μg of single stranded cDNA was fragmented, labeled and hybridized to the Affymetrix array for 16 hours. Post hybridization staining and washing was performed according to the manufacturer’s instructions (Affymetrix).

scan_protocol: chips were scanned with a high-numerical Aperture and flying objective (FOL) lens in the GS3000 scanner (Affymetrix). Images were quantified using GCOS 1.4 (GeneChip Operating Software, Affymetrix).

data_processing: Raw CEL files were processed with Aroma Affymetrix (Bengtsson et al., 2008) using standard RMA background adjustment and quantile normalization. Summarization was fit to both exons and RefSeq transcripts using the HuEx-1_0-st-v2,main,A20071112,EP CDF annotation. Additionally, outlier profiles for all transcripts and outlier assignments in all tumors were determined from normalized expression data as detailed in Experimental Procedures and as previously described (Ghosh and Chinnaiyan, 2009).

source_name: HCC827 ER1

label_protocol: 1-2 μg of total RNA were depleted of ribosomal RNA, (Ribominus Eukaryote kit, Invitrogen). Efficiency of the depletion was checked on BioAnalyzer. Resulting material was labeled using the Affymetrix WT Sense Target Labeling Assay (Affymetrix).

growth_protocol: Grown and subcultured as according to ATCC protocol for HCC827

extract_protocol: Qiagen's RNeasy kit was used according to the manufacturer's instructions

treatment_protocol: Growth media was treated with drug (Erlotinib), which was dissolved in 10 mM concentrate (1000x), or vehicle control (DMSO only).

tag: cell line

value: HCC 827

value: Lung

tag: erlotinib resistance

value: Yes


title: meiS HU rec8 delete replicate 2

description:
biological replicate 2 of 3 of meiS HU replication profile from rec8 delete cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from rec8 delete cells
rec8HU_2.txt


title: ssDNA in cdc6-mn dmc1 cells replicate 1

description:
biological replicate 1 of 2 of ssDNA in dmc1 cells
Series supplementary file contains mean of 2 biological replicates of ssDNA in dmc1 cells
ssDNA_cdc6_1.txt

data_processing:
Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).
Replicate datesets are the normalized log2 ratio (experimental ssDNA signal (5 hours timepoint) / control ssDNA (0 hour timepoint)). The final values are average of the individual replicate log2 ratios.

source_name: ssDNA in dmc1 cells [0hr in SPO]

label_protocol: 1.5 μg of ssDNA was labeled with Cy3-dUTP or Cy5-dUTP (GE Healthcare) by random priming without denaturation using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours. Samples were isolated at the indicated timepoints.

extract_protocol: To isolate ssDNA, ~10^9 cells were fixed in 70% ethanol at –20°C. Cells were spheroplasted in sorbitol buffer (1M sorbitol, 1% beta-mercaptoethanol, 0.2 mg/ml zymolyase 100T, 0.1M EDTA, pH 7.4), lysed in NDS (0.6% SDS, 300mM EDTA, 10mM Tris.HCl, pH 9.5). DNA was deproteinated with proteinase K (0.25mg/ml; Roche) at 50°C, twice phenol extracted, treated with RNase A, and stored in TE (1mM EDTA, 10mM Tris.HCl, pH 7.5) at 4°C. 25 μg DNA were digested to completion with EcoRI (New England Biolabs). ssDNA was enriched by batch absorption to BND cellulose (Sigma). Briefly, a 50% slurry of BND-cellulose was equilibrated in NET (1M NaCl, 10mM Tris, pH 7.6, 1mM EDTA). Digested DNA was adjusted to 1M NaCl and ssDNA was incubated with a 500 μl bed volume of BND-cellulose for 5 minutes. Resin was washed with five bed volumes of NET. ssDNA was eluted five times with 600 μl NET + 1.8% caffeine. DNA was precipitated and concentrated for microarray analysis.

tag: time in spo (hours)

source_name: ssDNA in dmc1 cells [5hrs in SPO]

value: meiotic budding yeast cells, 0 or 5 hours in SPO-medium


title: HCC 827 ER2

description: Gene expression data from the Erlotinib-resistant cell line, HCC827 ER2

source_name: HCC827 ER2


title: HCC 827

description: Gene expression data from the parental cell line, HCC827

source_name: HCC 827

value: No


title: ssDNA in cdc6-mn dmc1 cells replicate 2

description:
biological replicate 2 of 2 of ssDNA in dmc1 cells
Series supplementary file contains mean of 2 biological replicates of ssDNA in dmc1 cells
ssDNA_cdc6_2.txt


title: no MLD, biallelic AML MLL_00267

description: no MLD, biallelic


title: no MLD, biallelic AML MLL_00269

description: no MLD, biallelic


title: Mouse_colon_BEC_rep4

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

BEC_4

value: male


title: meiS HU spo11 delete replicate 1

description:
biological replicate 1 of 3 of meiS HU replication profile from spo11 delete cells
Series supplementary file contains mean of 3 biological replicate of meiS HU replication profile from spo11 delete cells
spo11HU_1.txt


title: SPC-01 Undifferentiated Replicate 2

description: Clone 1

value: Female

value: Spinal cord

value: 10 weeks


title: SPC-04 Undifferentiated Replicate 2

description: Clone 4


title: Mouse_colon_LEC_rep1

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

LEC_1

source_name: Mouse, colon, normal, lymphatic endothelial cells

value: female

value: 8 weeks

value: colon

value: lymphatic endothelial cells


title: Mouse_colon_LEC_rep2

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

LEC_2

value: normal, healthy

value: FACS


title: meiS HU sml1 delete replicate 3

description:
biological replicate 3 of 3 of meiS HU replication profile from sml1 delete cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from sml1 delete cells
sml1HU_3.txt

source_name: meiS HU replication profile from sml1 delete cells [G1 control]

value: mitotic budding yeast cells

source_name: meiS HU replication profile from sml1 delete cells [HU 4 hours]

value: HU 4 hours

value: meiotic budding yeast cells


title: meiS HU sml1 delete replicate 2

description:
biological replicate 2 of 3 of meiS HU replication profile from sml1 delete cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from sml1 delete cells
sml1HU_2.txt


title: no MLD, biallelic AML MLL_00264

description: no MLD, biallelic

value: PBMC

value: no Multilineage dysplasia, acute myeloid leukemia, biallelic


title: no MLD, biallelic AML MLL_00239

description: no MLD, biallelic


title: meiS HU wild type replicate 3

description:
biological replicate 3 of 3 of meiS HU replication profile from wild-type cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from wild-type cells
meiHU_3.txt

source_name: meiS HU replication profile from wild-type cells [G1 control]

source_name: meiS HU replication profile from wild-type cells [HU 4 hours]


title: no MLD, biallelic AML MLL_00257

description: no MLD, biallelic


title: meiS HU sml1 delete replicate 1

description:
biological replicate 1 of 3 of meiS HU replication profile from sml1 delete cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from sml1 delete cells
sml1HU_1.txt


title: mitS HU replicate 2

description:
biological replicate 2 of 3 of mitS HU replication profile from wild-type cells
Series supplementary file contains mean of 3 biological replicates of mitS HU replication profile from wild-type cells
mitHU_2.txt

source_name: mitS HU replication profile from wild-type cells [HU 4 hours]

source_name: mitS HU replication profile from wild-type cells [G1 control]


title: meiS replicate 2

description:
biological replicate 2 of 3 of meiS pooled S-phase replication profile
Series supplementary file contains mean of 3 biological replicates of meiS pooled S-phase replication profile
meiS_2.txt

source_name: meiS pooled S-phase replication profile [G1 control]

source_name: meiS pooled S-phase replication profile [pooled S phase]

value: pooled S phase


title: meiS HU wild type replicate 1

description:
biological replicate 1 of 3 of meiS HU replication profile from wild-type cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from wild-type cells
meiHU_1.txt


title: MLD, biallelic AML MLL_00268

description: MLD, biallelic

value: Multilineage dysplasia, acute myeloid leukemia, biallelic


title: mitS HU replicate 3

description:
biological replicate 3 of 3 of mitS HU replication profile from wild-type cells
Series supplementary file contains mean of 3 biological replicates of mitS HU replication profile from wild-type cells
mitHU_3.txt


title: no MLD, biallelic AML MLL_00263

description: no MLD, biallelic


title: MLD, biallelic AML MLL_00255

description: MLD, biallelic


title: MLD, biallelic AML MLL_00261

description: MLD, biallelic


title: G1 control replicate 3

description:
biological replicate 3 of 3 of G1 control profile
Series supplementary file contains mean of 3 biological replicates of G1 control profile
G1_3.txt

source_name: G1 control profile


title: no MLD, biallelic AML MLL_00233

description: no MLD, biallelic


title: mitS HU replicate 1

description:
biological replicate 1 of 3 of mitS HU replication profile from wild-type cells
Series supplementary file contains mean of 3 biological replicates of mitS HU replication profile from wild-type cells
mitHU_1.txt


title: no MLD, biallelic AML MLL_00262

description: no MLD, biallelic


title: MLD, biallelic AML MLL_00259

description: MLD, biallelic


title: no MLD, biallelic AML MLL_00245

description: no MLD, biallelic


title: no MLD, biallelic AML MLL_00237

description: no MLD, biallelic


title: meiS replicate 1

description:
biological replicate 1 of 3 of meiS pooled S-phase replication profile
Series supplementary file contains mean of 3 biological replicates of meiS pooled S-phase replication profile
meiS_1.txt


title: MLD, biallelic AML MLL_00266

description: MLD, biallelic


title: MLD, biallelic AML MLL_00252

description: MLD, biallelic


title: meiS replicate 3

description:
biological replicate 3 of 3 of meiS pooled S-phase replication profile
Series supplementary file contains mean of 3 biological replicates of meiS pooled S-phase replication profile
meiS_3.txt


title: meiS HU wild type replicate 2

description:
biological replicate 2 of 3 of meiS HU replication profile from wild-type cells
Series supplementary file contains mean of 3 biological replicates of meiS HU replication profile from wild-type cells
meiHU_2.txt


title: G1 control replicate 1

description:
biological replicate 1 of 3 of G1 control profile
Series supplementary file contains mean of 3 biological replicates of G1 control profile
G1_1.txt


title: MLD, biallelic AML MLL_00248

description: MLD, biallelic


title: G1 control replicate 2

description:
biological replicate 2 of 3 of G1 control profile
Series supplementary file contains mean of 3 biological replicates of G1 control profile
G1_2.txt


title: Red1 ChIP in clb5 clb6 delete cells replicate 2

description:
biological replicate 2 of 2 of Red1 ChIP in clb5 clb6 delete cells
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in clb5 clb6 delete cells
clb5clb6_Red1ChIP_2.txt

source_name: biological replicate 2 of 2 of Red1 ChIP in clb5 clb6 delete cells [input]

label_protocol: Half of the immunoprecipitated DNA or one tenth of the input DNA was labeled with Cy3- or Cy5-dUTP (GE Healthcare) by random priming using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: For mitotic Mcm2-7 chromatin immunoprecipitation, cells were inoculated into fresh YPD medium containing 5 μg/ml alpha-factor for 3 hours. For all other ChIP experiments, cells were pre-grown in presporulation medium YPA or BYTA) and transferred into sporulation medium (SPO) at 0 hours at OD600=2.0. Samples were isolated at 1 hours for Mcm2-7 analysis and 3 hours for Rec8, Hop1 and Red1 analysis.

extract_protocol: 25 mls of cells were harvested for all sporulating cultures and 50 ml of culture was collected from YPD for pre-mitotic Mcm2-7 analysis. Chromatin immunoprecipitation was performed as described (Aparicio et al., 1997). One tenth of the lysate was removed as an input sample. Proteins were immunoprecipitated with the indicated antibodies in combination with 20 µl GammaBind-Sepharose (GE Healthcare) for 16 hours at 4°C.

tag: ip or input

value: input

source_name: biological replicate 2 of 2 of Red1 ChIP in clb5 clb6 delete cells [IP]

value: IP

tag: chip antibody

value: 2 µl anti-Red1 (Nancy Hollingsworth)


title: Red1 ChIP in clb5 clb6 delete cells replicate 1

description:
biological replicate 1 of 2 of Red1 ChIP in clb5 clb6 delete cells
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in clb5 clb6 delete cells
clb5clb6_Red1ChIP_1.txt

source_name: biological replicate 1 of 2 of Red1 ChIP in clb5 clb6 delete cells [IP]

source_name: biological replicate 1 of 2 of Red1 ChIP in clb5 clb6 delete cells [input]


title: Red1 ChIP in cdc6-mn cells replicate 1

description:
biological replicate 1 of 2 of Red1 ChIP in cdc6-mn cells
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in cdc6-mn cells
cdc6_Red1ChIP_1.txt

source_name: biological replicate 1 of 2 of Red1 ChIP in cdc6-mn cells [IP]

source_name: biological replicate 1 of 2 of Red1 ChIP in cdc6-mn cells [input]


title: Hop1 ChIP in clb5 clb6 delete cells replicate 1

description:
biological replicate 1 of 2 of Hop1 ChIP in clb5 clb6 delete cells
Series supplementary file contains mean of 2 biological replicates of Hop1 ChIP in clb5 clb6 delete cells
clb5clb6_Hop1ChIP_1.txt

source_name: biological replicate 1 of 2 of Hop1 ChIP in clb5 clb6 delete cells [IP]

value: 2 µl anti-Hop1 (Nancy Hollingsworth)

source_name: biological replicate 1 of 2 of Hop1 ChIP in clb5 clb6 delete cells [input]


title: Red1 ChIP in wild-type cells +HU replicate 1

description:
biological replicate 1 of 2 of Red1 ChIP in wild-type cells +HU
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in wild-type cells +HU
WT_Red1ChIPHU_1.txt

source_name: biological replicate 1 of 2 of Red1 ChIP in wild-type cells +HU [input]

source_name: biological replicate 1 of 2 of Red1 ChIP in wild-type cells +HU [IP]


title: control MLL_00116

description: control

value: control


title: Red1 ChIP in wild-type cells replicate 1

description:
biological replicate 1 of 2 of Red1 ChIP in wild-type cells
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in wild-type cells
WT_Red1ChIP_1.txt

source_name: biological replicate 1 of 2 of Red1 ChIP in wild-type cells [IP]

source_name: biological replicate 1 of 2 of Red1 ChIP in wild-type cells [input]


title: MLD, biallelic AML MLL_00230

description: MLD, biallelic


title: control MLL_00109

description: control


title: control MLL_00107

description: control


title: Red1 ChIP in wild-type cells +HU replicate 2

description:
biological replicate 2 of 2 of Red1 ChIP in wild-type cells +HU
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in wild-type cells +HU
WT_Red1ChIPHU_2.txt

source_name: biological replicate 2 of 2 of Red1 ChIP in wild-type cells +HU [input]

source_name: biological replicate 2 of 2 of Red1 ChIP in wild-type cells +HU [IP]


title: Hop1 ChIP in clb5 clb6 delete cells replicate 2

description:
biological replicate 2 of 2 of Hop1 ChIP in clb5 clb6 delete cells
Series supplementary file contains mean of 2 biological replicates of Hop1 ChIP in clb5 clb6 delete cells
clb5clb6_Hop1ChIP_2.txt

source_name: biological replicate 2 of 2 of Hop1 ChIP in clb5 clb6 delete cells [input]

source_name: biological replicate 2 of 2 of Hop1 ChIP in clb5 clb6 delete cells [IP]


title: Hop1 ChIP in cdc6-mn cells replicate 2

description:
biological replicate 2 of 2 of Hop1 ChIP in cdc6-mn cells
Series supplementary file contains mean of 2 biological replicates of Hop1 ChIP in cdc6-mn cells
cdc6_Hop1ChIP_2.txt

source_name: biological replicate 2 of 2 of Hop1 ChIP in cdc6-mn cells [input]

source_name: biological replicate 2 of 2 of Hop1 ChIP in cdc6-mn cells [IP]


title: control MLL_00112

description: control


title: Hop1 ChIP in cdc6-mn cells replicate 1

description:
biological replicate 1 of 2 of Hop1 ChIP in cdc6-mn cells
Series supplementary file contains mean of 2 biological replicates of Hop1 ChIP in cdc6-mn cells
cdc6_Hop1ChIP_1.txt

source_name: biological replicate 1 of 2 of Hop1 ChIP in cdc6-mn cells [IP]

source_name: biological replicate 1 of 2 of Hop1 ChIP in cdc6-mn cells [input]


title: control MLL_00114

description: control


title: Hop1 ChIP in wild-type cells +HU replicate 2

description:
biological replicate 2 of 2 of Hop1 ChIP in wild-type cells +HU
Series supplementary file contains mean of 2 biological replicates of Hop1 ChIP in wild-type cells +HU
WT_Hop1ChIPHU_2.txt

source_name: biological replicate 2 of 2 of Hop1 ChIP in wild-type cells +HU [IP]

source_name: biological replicate 2 of 2 of Hop1 ChIP in wild-type cells +HU [input]


title: control MLL_00118

description: control


title: Red1 ChIP in cdc6-mn cells replicate 2

description:
biological replicate 2 of 2 of Red1 ChIP in cdc6-mn cells
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in cdc6-mn cells
cdc6_Red1ChIP_2.txt

source_name: biological replicate 2 of 2 of Red1 ChIP in cdc6-mn cells [input]

source_name: biological replicate 2 of 2 of Red1 ChIP in cdc6-mn cells [IP]


title: Hop1 ChIP in wild-type cells +HU replicate 1

description:
biological replicate 1 of 2 of Hop1 ChIP in wild-type cells +HU
Series supplementary file contains mean of 2 biological replicates of Hop1 ChIP in wild-type cells +HU
WT_Hop1ChIPHU_1.txt

source_name: biological replicate 1 of 2 of Hop1 ChIP in wild-type cells +HU [input]

source_name: biological replicate 1 of 2 of Hop1 ChIP in wild-type cells +HU [IP]


title: Red1 ChIP in wild-type cells replicate 2

description:
biological replicate 2 of 2 of Red1 ChIP in wild-type cells
Series supplementary file contains mean of 2 biological replicates of Red1 ChIP in wild-type cells
WT_Red1ChIP_2.txt

source_name: biological replicate 2 of 2 of Red1 ChIP in wild-type cells [input]

source_name: biological replicate 2 of 2 of Red1 ChIP in wild-type cells [IP]


title: control MLL_00117

description: control


title: Rec8 ChIP in clb5 clb6 delete cells replicate 1

description:
biological replicate 1 of 2 of Rec8 ChIP in clb5 clb6 delete cells
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in clb5 clb6 delete cells
clb5clb6_Rec8ChIP_1.txt

source_name: biological replicate 1 of 2 of Rec8 ChIP in clb5 clb6 delete cells [input]

source_name: biological replicate 1 of 2 of Rec8 ChIP in clb5 clb6 delete cells [IP]


title: control MLL_00111

description: control


title: Rec8 ChIP in cdc6-mn cells replicate 2

description:
biological replicate 2 of 2 of Rec8 ChIP in cdc6-mn cells
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in cdc6-mn cells
cdc6_Rec8ChIP_2.txt

source_name: biological replicate 2 of 2 of Rec8 ChIP in cdc6-mn cells [input]

source_name: biological replicate 2 of 2 of Rec8 ChIP in cdc6-mn cells [IP]


title: control MLL_00106

description: control


title: control MLL_00110

description: control


title: Rec8 ChIP in clb5 clb6 delete cells replicate 2

description:
biological replicate 2 of 2 of Rec8 ChIP in clb5 clb6 delete cells
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in clb5 clb6 delete cells
clb5clb6_Rec8ChIP_2.txt

source_name: biological replicate 2 of 2 of Rec8 ChIP in clb5 clb6 delete cells [IP]

source_name: biological replicate 2 of 2 of Rec8 ChIP in clb5 clb6 delete cells [input]


title: Liver sample from Alcoholic hepatitis group (CA28)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'gcrma' function of the Bioconductor package (v2.4) 'gcrma' in R.2.9.1

source_name: liver biopsy sample

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: liver sample group

value: :Alcoholic hepatitis


title: Rec8 ChIP in cdc6-mn cells replicate 1

description:
biological replicate 1 of 2 of Rec8 ChIP in cdc6-mn cells
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in cdc6-mn cells
cdc6_Rec8ChIP_1.txt

source_name: biological replicate 1 of 2 of Rec8 ChIP in cdc6-mn cells [IP]

source_name: biological replicate 1 of 2 of Rec8 ChIP in cdc6-mn cells [input]


title: Liver sample from Alcoholic hepatitis group (CA5)


title: Liver sample from Alcoholic hepatitis group (CA77)


title: Rec8 ChIP in wild-type cells replicate 2

description:
biological replicate 2 of 2 of Rec8 ChIP in wild-type cells
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in wild-type cells
WT_Rec8ChIP_2.txt

source_name: biological replicate 2 of 2 of Rec8 ChIP in wild-type cells [input]

source_name: biological replicate 2 of 2 of Rec8 ChIP in wild-type cells [IP]


title: Liver sample from Alcoholic hepatitis group (CA80)


title: Rec8 ChIP in wild-type cells +HU replicate 1

description:
biological replicate 1 of 2 of Rec8 ChIP in wild-type cells +HU
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in wild-type cells +HU
WT_Rec8ChIPHU_1.txt

source_name: biological replicate 1 of 2 of Rec8 ChIP in wild-type cells +HU [input]

source_name: biological replicate 1 of 2 of Rec8 ChIP in wild-type cells +HU [IP]


title: Liver sample from Alcoholic hepatitis group (CA39)


title: exp3+NaHS

city: Shanghai

first: Xu

last: Jia

address: Yi Xue Yuan Road 138

department: School of Pharmacy, Institute of Biomedical Science

country: China

institute: Fudan University

description: S.pombe with NaHS-3_50, biological rep1

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm using GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Schizosaccharomyces pombe

source_name: with NaHS

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The wild type S. pombe cells were grown in liquid medium to OD600=0.5

extract_protocol: Total RNA was extracted from cells using a hot phenol method and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by  RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: 50μM of NaHS (Sigma, St Louis, MO, USA) were used for treatment of wild type cells for 30 min at 30℃.

tag: genotype/variation

tag: growth condition

value: liquid medium to OD600=0.5


title: Liver sample from Alcoholic hepatitis group (CA22)


title: Rec8 ChIP in wild-type cells +HU replicate 2

description:
biological replicate 2 of 2 of Rec8 ChIP in wild-type cells +HU
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in wild-type cells +HU
WT_Rec8ChIPHU_2.txt

source_name: biological replicate 2 of 2 of Rec8 ChIP in wild-type cells +HU [IP]

source_name: biological replicate 2 of 2 of Rec8 ChIP in wild-type cells +HU [input]


title: Liver sample from Alcoholic hepatitis group (CA92)


title: exp1+NaHS

description: S.pombe with NaHS-1_50, biological rep1


title: exp3

description: S.pombe without NaHS-3, biological rep1

source_name: without NaHS


title: exp1

description: S.pombe without NaHS-1, biological rep1


title: Liver sample from Alcoholic hepatitis group (CA47)


title: exp2+NaHS

description: S.pombe with NaHS-2_50, biological rep1


title: Liver sample from Alcoholic hepatitis group (CA20)


title: Liver sample from Alcoholic hepatitis group (CA51)


title: Liver sample from Alcoholic hepatitis group (CA82)


title: mitS replicate 3

description:
biological replicate 3 of 3 of mitS pooled S-phase replication profile
Series supplementary file contains mean of 3 biological replicates of mitS pooled S-phase replication profile
mitS_3.txt

source_name: mitS pooled S-phase replication profile [pooled S phase]

source_name: mitS pooled S-phase replication profile [G1 control]


title: mitS replicate 2

description:
biological replicate 2 of 3 of mitS pooled S-phase replication profile
Series supplementary file contains mean of 3 biological replicates of mitS pooled S-phase replication profile
mitS_2.txt


title: exp2

description: S.pombe without NaHS-2, biological rep1


title: Liver sample from Alcoholic hepatitis group (CA45)


title: Liver sample from Alcoholic hepatitis group (CA64)


title: Liver sample from Control group (N53)

description: Liver sample from Control group

value: :Control


title: Liver sample from Alcoholic hepatitis group (CA62)


title: Liver sample from Control group (N17)

description: Liver sample from Control group


title: MLD, biallelic AML MLL_00235

description: MLD, biallelic


title: pre-meiotic Mcm2-7 ChIP replicate 3

description:
biological replicate 3 of 3 of pre-meiotic Mcm2-7 ChIP
Series supplementary file contains mean of 3 biological replicates of pre-meiotic Mcm2-7 ChIP
meiMcm_3.txt

source_name: biological replicate 3 of 3 of pre-meiotic Mcm2-7 ChIP [input]

source_name: biological replicate 3 of 3 of pre-meiotic Mcm2-7 ChIP [IP]

value: 2 µl UM185 (Stephen P. Bell)


title: pre-meiotic Mcm2-7 ChIP replicate 2

description:
biological replicate 2 of 3 of pre-meiotic Mcm2-7 ChIP
Series supplementary file contains mean of 3 biological replicates of pre-meiotic Mcm2-7 ChIP
meiMcm_2.txt

source_name: biological replicate 2 of 3 of pre-meiotic Mcm2-7 ChIP [IP]

source_name: biological replicate 2 of 3 of pre-meiotic Mcm2-7 ChIP [input]


title: Liver sample from Control group (N54)

description: Liver sample from Control group

source_name: liver biopsy sample


title: S. lycopersicum galls 14 dpi vs control cells Rep 2

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

institute: CNB-CSIC

description: Biological replicate 2 of 3. Gene expression of Galls 14 dpi vs control cells

hyb_protocol: Pre-hybridization: TOM 1 microarray slides from the Center for Gene Expression Profiling (CGEP) at the Boyce Thompson Institute (BTI), Cornell University (see the Functional Genomics Database, http://ted.bti.cornell.edu/) were pre-hybridized in a humidified hybridization chamber for 45 min at 42°C using 80 µl of pre-heated buffer containing 5x SSC, 0.1% SDS, 1% BSA, 10 mM of EDTA pH 8 and DEPC water, covered with a clean glass LifterSlip 22x601-2-4861(Erie Scientific, Portsmouth, NH, USA). The slides were removed from the chamber and washed five times with MiliQ water at room temperature, dipped in isopropanol and dried by centrifugation (2000 rpm. for 1 min).   Hybridization: A hybridization mix was prepared with 250 pmol each of either Cy5 or Cy3 labeled aRNA (in 17 µl), 4 µl of 0.5 M EDTA pH 8 and 2 µl of poly(A)+ DNA to a final volume of 40 µl. Probes were denatured at 65°C for 3 min, followed by instant cooling on ice for 1 min and combined with 40 µl of hybridization buffer containing 50% formamide, 5x SSC and 0.1% SDS. Probe solution was pipetted on the spotted surface of the slide and the hybridization was carried out under a LifterSlip in the dark within a humidified hybridization chamber for 16-24 h in a water bath at 42°C. Three slides were hybridized independently with aRNA from three biological replicates, including one dye-swap. Two independent treatments were essayed (3 and 7 dpi GCs versus CCs).  Post-hybridization: after hybridization, the slides were washed using a black jar as follows: two washes at 42°C for 5 min in 0.5x SSC/0.2% SDS, twice for 5 min in 0.1x SSC at room temperature, one wash for 5 min in 0.05X SSC at room temperature and one quick wash in MiliQ water at room temperature. Slides were dried by immediately centrifuging at 2000 rpm for 1 min.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Solanum lycopersicum

source_name: control cells

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Meloidogyne javanica populations were maintained under sterile conditions on cucumber roots in vitro. Tomato seeds (Solanum lycopersicum Mill, cv. Moneymaker) were surface-sterilized by soaking for 30 min in 20% commercial bleach with 0.1% v/v Triton X-100, followed by eight washes with Milli-Q water. Forty seeds were germinated in vitro in Petri dishes (125 mm) on Gamborg B5 medium supplemented with 20 g/L sucrose and 1.5% Daishin agar, pH 6.2. The plates were tilted horizontally and kept in the dark at 4°C for 48 h. They were then placed vertically, to allow the roots to grow along the surface, in the dark at 28°C and 65% humidity for 3 days. Between 8 and 10 seedlings were transferred to new Gamborg plates. Each primary tomato root was inoculated just behind the root tip with sterile, freshly-hatched M. javanica (20–30 juveniles stage 2, J2). The growth of the root tips from non-inoculated and inoculated seedlings, as well as the galls formed after penetration of J2, were carefully monitored every 24 h by labeling the bottom of the plates. Therefore, we collected galls for microdissection at two different time points (48 to 72 hours post-infection, and 6-7 dpi, respectively; for simplification we will refer as 3 and 7 dpi). The plates were incubated at 28°C vertically in the dark during the infection time course. Finally, tissues were collected at different dpi. This protocol it is described by Portillo et al., 2009 Isolation of RNA from laser-capture-microdissected giant cells at early differentiation stages suitable for differential transcriptome analysis. Molecular Plant Pathology 10 (4), 523–535.

extract_protocol: Total RNA of galls was extracted from 100 mg of hand-dissected tissue and from their equivalent uninfected controls at 1, 3, 7 and 14 days post-infection (dpi), using TRI Reagent (Molecular Research Center, Inc., Cincinnati, Ohio, USA) with the mortar homogenization-maceration procedure as described Portillo et al., 2006, Evaluation of different RNA extraction methods for small quantities of plant tissue combined effects of reagent type and homogenization procedure on RNA quality-integrity and yield. Physiologia Plantarum 128 (1), 1-7. After isolation, total RNA was further purified by RNeasy Mini Kit columns (Quiagen Inc., Valencia, CA, USA) and it concentration, quality and integrity were assessed.    Total RNA isolated of GCs and CCs at 3 and 7 dpi were performed as described in Portillo et al., 2009. Isolation of RNA from laser-capture-microdissected giant cells at early differentiation stages suitable for differential transcriptome analysis. Molecular Plant Pathology 10 (4), 523–535.The RNA from LCM cells was immediately extracted using the Absolutely RNA Nanoprep kit (Stratagene, CA, USA) according to the manufacturer’s instructions, with minor modifications. Briefly, 100 µl of lysis buffer was applied to the cap via the ExtracSure Sample Extraction Device that was then connected to a 0.5-ml microcentrifuge tube. After vortexing, the sample was incubated at 60°C for 5 min. The lysis buffer was then collected and mixed with an equal volume (ca. 100 µl) of 70% ethanol before being applied to the RNA-binding column. DNase was added and incubated at room temperature for 10 min, followed by washing. Finally, the RNA was eluted twice in 10 µl of DEPC-treated water.

tag: cultivar

value: S. lycopersicum Mill, cv. Moneymaker

tag: tissue type

value: control cells (CCs) from the uninfected root vascular cylinder

source_name: Galls

value: Galls from early stages of development formed during the interaction of Meloidogyne javanica with tomato (Solanum lycopersicum) roots

tag: dpi

value: 14 dpi


title: S. lycopersicum galls 7 dpi vs control cells Rep 3

description: Biological replicate 3 of 4. Gene expression of Galls 7 dpi vs control cells

value: 7 dpi


title: Liver sample from Control group (C12)

description: Liver sample from Control group


title: Rec8 ChIP in wild-type cells replicate 1

description:
biological replicate 1 of 2 of Rec8 ChIP in wild-type cells
Series supplementary file contains mean of 2 biological replicates of Rec8 ChIP in wild-type cells
WT_Rec8ChIP_1.txt

source_name: biological replicate 1 of 2 of Rec8 ChIP in wild-type cells [input]

tag: strain

tag: cell type

value: meiotic budding yeast cells

source_name: biological replicate 1 of 2 of Rec8 ChIP in wild-type cells [IP]


title: S. lycopersicum galls 14 dpi vs control cells Rep 1

description: Biological replicate 1 of 3. Gene expression of Galls 14 dpi vs control cells


title: Liver sample from Control group (C9)

description: Liver sample from Control group


title: fun30∆ transcritome replicate 2

city: marseille

first: bertrand

last: llorente

address: 31 chemin josephh aiguier

country: France

institute: cnrs

hyb_protocol: Breifly, DNA arrays were prehybridized using DIG Easy Hyb (Roche Applied Science) and single stranded DNA for 2 hours at 42 Celcius degrees, prior to over night hybridization in similar conditions. Two washes in with 0.1X SSC and 0.1% SDS were performed followed by one wash in with 0.1X SSC only.

scan_protocol: Scans of the microarrays were done on a GenePix 4000B scanner using the GenePix Pro software.

data_processing: print−tip Lowess normalisation using Goulphar R script ( Lemoine et al, BMC Bioinformatics, 2006)

source_name: S288C background, rich medium, exponential phase

label_protocol: cDNA random priming using CyScribe lebelling kit from Amersham.

growth_protocol: Rich medium (YPD), exponential phase

extract_protocol: RNA was extracted using standard yeast protocol involving mechanical cell lysis with glass beads and vortex in the presence of phenol chloroform isoamyl alcohol (24:24:1). For details see Chanfreau et al. EMBO 1998.

value: fun30 homozygote diploid from the systematic deletion library


title: mitS replicate 1

description:
biological replicate 1 of 3 of mitS pooled S-phase replication profile
Series supplementary file contains mean of 3 biological replicates of mitS pooled S-phase replication profile
mitS_1.txt

value: pooled S phase

value: mitotic budding yeast cells


title: Liver sample from Control group (C7)

description: Liver sample from Control group


title: fun30∆ transcritome replicate 1


title: Liver sample from Alcoholic hepatitis group (CA79)


title: S. lycopersicum galls 14 dpi vs control cells Rep 3

description: Biological replicate 3 of 3. Gene expression of Galls 14 dpi vs control cells


title: Liver sample from Control group (N52)

description: Liver sample from Control group


title: pre-meiotic Mcm2-7 ChIP replicate 1

description:
biological replicate 1 of 3 of pre-meiotic Mcm2-7 ChIP
Series supplementary file contains mean of 3 biological replicates of pre-meiotic Mcm2-7 ChIP
meiMcm_1.txt

source_name: biological replicate 1 of 3 of pre-meiotic Mcm2-7 ChIP [IP]

value: IP

source_name: biological replicate 1 of 3 of pre-meiotic Mcm2-7 ChIP [input]

value: input


title: pre-mitotic Mcm2-7 ChIP replicate 3

description:
biological replicate 3 of 3 of pre-mitotic Mcm2-7 ChIP
Series supplementary file contains mean of 3 biological replicates of pre-mitotic Mcm2-7 ChIP
mitMcm_3.txt

source_name: biological replicate 3 of 3 of pre-mitotic Mcm2-7 ChIP [IP]

source_name: biological replicate 3 of 3 of pre-mitotic Mcm2-7 ChIP [input]


title: pre-mitotic Mcm2-7 ChIP replicate 1

description:
biological replicate 1 of 3 of pre-mitotic Mcm2-7 ChIP
Series supplementary file contains mean of 3 biological replicates of pre-mitotic Mcm2-7 ChIP
mitMcm_1.txt

source_name: biological replicate 1 of 3 of pre-mitotic Mcm2-7 ChIP [IP]

source_name: biological replicate 1 of 3 of pre-mitotic Mcm2-7 ChIP [input]


title: pre-mitotic Mcm2-7 ChIP replicate 2

description:
biological replicate 2 of 3 of pre-mitotic Mcm2-7 ChIP
Series supplementary file contains mean of 3 biological replicates of pre-mitotic Mcm2-7 ChIP
mitMcm_2.txt

source_name: biological replicate 2 of 3 of pre-mitotic Mcm2-7 ChIP [IP]

source_name: biological replicate 2 of 3 of pre-mitotic Mcm2-7 ChIP [input]


title: S. lycopersicum galls 7 dpi vs control cells Rep 2

description: Biological replicate 2 of 4. Gene expression of Galls 7 dpi vs control cells


title: S. lycopersicum galls 7 dpi vs control cells Rep 1

description: Biological replicate 1 of 4. Gene expression of Galls 7 dpi vs control cells


title: S. lycopersicum galls 1 dpi vs control cells Rep 3

description: Biological replicate 3 of 4. Gene expression of Galls 1 dpi vs control cells

value: 1 dpi


title: S. lycopersicum galls 3 dpi vs control cells Rep 4

description: Biological replicate 4 of 4. Gene expression of Galls 3 dpi vs control cells

value: 3 dpi


title: S. lycopersicum galls 1 dpi vs control cells Rep 4

description: Biological replicate 4 of 4. Gene expression of Galls 1 dpi vs control cells


title: S. lycopersicum galls 3 dpi vs control cells Rep 2

description: Biological replicate 2 of 4. Gene expression of Galls 3 dpi vs control cells


title: S. lycopersicum galls 3 dpi vs control cells Rep 3

description: Biological replicate 3 of 4. Gene expression of Galls 3 dpi vs control cells


title: S. lycopersicum Giant cells 7 dpi vs control cells Rep 2

description: Biological replicate 2 of 3. Gene expression of Giant cells 7 dpi vs control cells

source_name: Giant cells

value: sample highly enriched in individual GCs from early stages of development formed during the interaction of Meloidogyne javanica with tomato (Solanum lycopersicum) roots


title: S. lycopersicum galls 1 dpi vs control cells Rep 1

description: Biological replicate 1 of 4. Gene expression of Galls 1 dpi vs control cells


title: S. lycopersicum Giant cells 3 dpi vs control cells Rep 3

description: Biological replicate 3 of 3.Gene expression of Giant cells 3 dpi vscontrol cells


title: HBrCa_54

city: Farmington

first: Kevin

last: Claffey

state: CT

address: 263 Farmington Ave

institute: UConn Health Center

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

data_processing: Samples were normalized untilizing rank invariant normalization.

source_name: primary breast tumor

label_protocol: Biotinylated RNA was amplified using the Illumina® TotalPrep™ RNA Amplification Kit from Ambion/Invitrogen.

extract_protocol: Total RNA was isolated using the RNeasy kit from Qiagen according to the standard protocol. RNA qaulity was evaluated with a Agilent Bioanalyzer.

tag: lymph node status

value: postive

tag: subject age


title: HBrCa_34

description: replicate 1

value: negative


title: S. lycopersicum galls 3 dpi vs control cells Rep 1

description: Biological replicate 1 of 4. Gene expression of Galls 3 dpi vs control cells


title: HBrCa_25

description: replicate 1

value: positive


title: S. lycopersicum galls 1 dpi vs control cells Rep 2

description: Biological replicate 2 of 4. Gene expression of Galls 1 dpi vs control cells

value: S. lycopersicum Mill, cv. Moneymaker


title: HBrCa_40

description: replicate 1


title: S. lycopersicum Giant cells 7 dpi vs control cells Rep 3

description: Biological replicate 3 of 3.Gene expression of Giant cells 7 dpi vs control cells

value: control cells (CCs) from the uninfected root vascular cylinder


title: S. lycopersicum Giant cells 3 dpi vs control cells Rep 1

description: Biological replicate 1 of 3. Gene expression of Giant cells 3 dpi vs control cells


title: HBrCa_19

description: replicate 1


title: S. lycopersicum Giant cells 3 dpi vs control cells Rep 2

description: Biological replicate 2 of 3. Gene expression of Giant cells 3 dpi vs controlcells


title: S. lycopersicum Giant cells 7 dpi vs control cells Rep 1

description: Biological replicate 1 of 3. Gene expression of Giant cells 7 dpi vs control cells


title: HBrCa_11

description: replicate 1


title: DR pool 2 with RU486 treatment

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

hyb_protocol: Sample Hybridization was done according to the manufacturers’ protocol for the 12-plex Gene Expression array platform. NimbleGen’s Sample Tracking Controls (05223512001), Hybridization Kit reagents (05583683001) and Wash Buffers (05584507001) were used. Each 12-plex array was sealed with a H12 mixer, provided with the Gene Expression array. 4μg of each Cy3 labeled sample was loaded onto an array on the 12-plex chip, using a Gilson M100 pipette. Hybridization was done overnight on a NimbleGen Hybridization System 4 unit, at 42°C for 16hrs

scan_protocol: After the 12-plex chip was washed and dried, the chip was scanned on a GenePix 4200A scanner at 300PMT, 100POW. Arrays were then quantitated using NimbleGen’s NimbleScan2 software.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003)

organism: Drosophila melanogaster

source_name: pools of 35 individual female 13 day old flies on DR food for 10 days with RU486

label_protocol: 150ng of total RNA was amplified for each experimental sample using Sigma’s TransPlex Complete Whole Transcriptome Amplification Kit (WTA2). Only 1/5th of the amplified sample library was used for the secondary amplification reaction. Amplified dscDNA samples were then purified using Qiagen’s QIAquick PCR Purification Kit (28104) and processed on the QIAcube according to the manufacturers’ standard protocol, “QIAquick PCR Purification-Standard.” Sample quality and concentration were assessed using a Nanodrop and Agilent’s Bioanalyzer (DNA 7500 Kit (5067-1506)). Amplification was randomized across experimental groups. 1μg of dscDNA was labeled with Cy3 for each experimental sample, using the NimbleGen (Roche) One-Color DNA Labeling Kit (05223555001) according to the manufacturers’ protocol. Cy3 labeling was randomized across experimental groups.

extract_protocol: Total RNA was extracted from approximately 35 flies collected in 1.5ml tubes for each experimental sample using Qiagen’s Rneasy Lipid Tissue Mini Kit (74804). The samples were initially transferred to a Qiagen 2ml sample tube (990381) and then digested using Qiagen’s Qiazol lysis buffer. Lysis was aided with the use of Qiagen’s TissueLyser, which pulverized the samples in lysis buffer for nine minutes at 20Hz. The samples were then processed on Qiagen’s QIAcube robot, with an on-column Dnase digestion, using a modified version of Qiagen’s QIAcube standard protocol, “RNeasy Lipid Tissue Mini-Animal Tissues-Aqueous Phase.” The total RNA samples were processed according to the manufacturers’ protocol, and their quality and concentration were assessed using a Nanodrop and Agilent’s Bioanalyzer (RNA 6000 Nano Kit (5067-15811)). Total RNA extraction was randomized across experimental groups


title: DR pool 4 with RU486 treatment


title: DR pool 3 with RU486 treatment


title: HBrCa_30

description: replicate 1


title: DR pool 5 with RU486 treatment


title: DR pool 3

source_name: pools of 35 individual female 13 day old flies on DR food for 10 days


title: DR pool 1 with RU486 treatment


title: DR pool 5


title: Dik-Vbar2f_Vbar2fx4-39_bar2-full-length_dikaryon_biological-replication_rep2

city: Jena

first: Erika

last: Kothe

address: Neugasse 25

department: Microbial Communication, Institute of Microbiology

institute: Friedrich-Schiller-University

description: blanks (only one single “T” nucleotide) are used for background corrections

hyb_protocol: Hybridization was done automatically over night (16 hours) at 45°C using RT-Analyzer from febit. The biotin labeling was detected with streptavidinphycoerythrin (SAPE), in combination with Consecutive Signal Enhancement (CSE) procedure from febit.

scan_protocol: The feature recognition, using Cy3 filter set, and signal calculation were done automatically within milliseconds using the Geniom RT Analyzer.

data_processing:
Background  correction  was  performed  using  the intensities of blank probes which consist only of one single ”T” nucleotide. The median background intensity was subtracted from spot intensity. After converting any negative values to a low positive value (7), signal intensities were log2-transformed. The obtained data  were  processed using quantile normalization, and duplicate spots were averaged.
By R and Bioconductor computed log2 transformed and quantil normalized signal intensity

organism: Schizophyllum commune

source_name: mated mycelium, Vbar2fx4-39, compatible interaction, mycelium from the side of Vbar2f

label_protocol: For each array 1 µg of total RNA was labeled using the MassageAmpTM-Biotin Enhanced RNA Kit from Ambion.

growth_protocol: The S. commune strains were grown on solid medium (CYM) at 28°C. Mycelium of a mating interaction was transferred onto a cellophane membrane onto fresh CYM plates and grown for 3 days.

extract_protocol: Total RNA was isolated from < 100 mg tissue powder using “Qiagen Rneasy plant mini kit” (Qiagen, Hilden, Germany), quality controlled with Agilent 2100 Bioanalyzer, using RNA 6000 Nano Kit, and a NanoDropTM 1000 Spectrophotometer (Thermo Scientific).

treatment_protocol: Mycelium was harvested, frozen in liquid nitrogen and ground with mortar and pestle to a powder.

tag: developmental stage

value: dikaryon

tag: strain(s)

value: Vbar2f x 4-39

tag: mating type loci

tag: genotype

tag: stage of clamp formation

value: mostly pseudoclamps


title: Thin-phenotype_W22thin_monokaryon_biological-replication_rep1

source_name: strain W22 showing thin-phenotype

value: thin-phenotype

value: no clamps


title: Aon_W22x4-39_semicompatible-interaction_technical-replication_rep2

source_name: mated mycelium, W22x4-39, Aon, mycelium from barrage zone

value: common B heterokaryon

value: no clamps, pseudoclamps in barrage zone


title: HBrCa_28

description: replicate 1


title: Bon_W21x4-39_flat_biological-replication_rep2

source_name: mated mycelium, W21x4-39, Bon, flat, mycelium from the side of W21

value: common A heterokaryon, flat-phenotype


title: Bon_W21x4-39_flat_biological-replication_rep1


title: Dikaryon_W22x12-43_compatible-interaction_technical-replication_rep1

source_name: mated mycelium, dikaryon

value: clamps


title: Dik-Vbar2f_Vbar2fx4-39_bar2-full-length_dikaryon_biological-replication_rep1


title: Thin-phenotype_W22thin_monokaryon_biological-replication_rep2


title: Dikaryon_W22x12-43_compatible-interaction_technical-replication_rep2


title: Monokaryon1_12-43_technical-replication_rep2

source_name: strain 12-43, monokaryon

value: monokaryon

value: ura-


title: Monokaryon1_12-43_technical-replication_rep1


title: Aon_W22x4-39_semicompatible-interaction_technical-replication_rep1


title: DR pool 1


title: Dik-Vbar2t_Vbar2tx4-39_bar2-truncated_dikaryon_biological-replication_rep2

source_name: mated mycelium, Vbar2tx4-39, compatible interaction, mycelium from the side of Vbar2t

value: Vbar2t x 4-39


title: AL pool 1

source_name: pools of 35 individual female 13 day old flies


title: DR pool 4


title: Monokaryon2_4-39_biological-replication_rep2

source_name: strain 4-39, monokaryon


title: DR pool 6


title: DR pool 6 with RU486 treatment


title: Primary ovarian tumour patient 11242

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

country: Australia

institute: PeterMacCallum Cancer Centre

hyb_protocol: Samples were hybridized to GeneChip® Human Gene 1.0 ST arrays according to the Affymetrix protocol (GeneChip® WT Terminal Labeling and Hybridization User Manual). GeneChips were washed in an Affymetrix fluidics station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: Raw data were normalized using the RMA normalization method available in the R/Bioconductor package affy.

source_name: primary ovarian tumor tissue collected at primary surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT Terminal Labeling and Hybridization User Manual).

growth_protocol: Frozen tissues were sectioned on a cryostat and lysed immediately.

extract_protocol: Total RNA was isolated using the Ambion mirVANA RNA isolation kit. The quality of RNA samples was checked by BioAnalyzer.

tag: gender

value: female

tag: tissue

value: primary ovarian tumor

tag: patient identifier


title: AL pool 6


title: AL pool 5


title: AL pool 3


title: Pouch of Douglas patient 11242

source_name: pouch of Douglas tissue collected at primary surgery

value: pouch of Douglas


title: AL pool 2


title: Dik-Vbar2t_Vbar2tx4-39_bar2-truncated_dikaryon_biological-replication_rep1


title: AL pool 4 with RU486 treatment

source_name: pools of 35 individual female 13 day old flies with RU486


title: Colon nodule patient 7899

source_name: colon nodule tissue collected at primary surgery

value: colon nodule


title: Primary ovarian tumour patient 6496


title: Monokaryon2_4-39_biological-replication_rep1


title: AL pool 1 with RU486 treatment


title: Omentum patient 8479

source_name: omentum tissue collected at primary surgery

value: omentum


title: AL pool 4


title: Primary ovarian tumour patient 7899


title: Primary ovarian tumour patient 8479


title: HD-iPSC culture 8

hyb_protocol: The arrays were hybridized and washed as per the manufacturers instructions via a 4-bay MAUI hybridization unit (Roche).

scan_protocol: Scanning was carried out on a GenePix 4200 Scanner (Molecular devices USA), at a PMT to ensure saturation was not achieved.

data_processing: Arrays were normalized using ArrayStar (DNAStar, Madison, WI, USA)

source_name: HD-iPSC cultured cells

label_protocol: All samples passed QC and integrity checks, and were then reverse transcribed and amplified with one round of whole-transcriptome amplification via the WTA2 complete whole transcriptome kit from Sigma (Sigma-Aldrich, St Louis, MO, USA). After amplification, the resulting omniplex cDNA library was then further purified using a Qiagen PCR purification chip (Qiagen), and evaluated for integrity and yield via Bioanalyzer. The resulting cDNA libraries were then labeled via the one color Nimblegen (Cy3) labeling kit as per the manufacturers instructions (Roche Nimblegen, Madison, WI, USA).

extract_protocol: Total RNA was purified from iPSCs or NSCs using RNeasy Mini kit (Qiagen) after growth on matrigel coated plates and conditioned medium containing 8 ng/ml bFGF. A minimum of 2 passages growth in tandem was established prior to collection of mRNA for comparative analysis

tag: cell line

value: HD patient-derived iPSC line HD-iPS4


title: DR pool 2


title: AL pool 6 with RU486 treatment


title: AL pool 2 with RU486 treatment


title: HD-iPSC culture 7


title: HD-iPSC culture 5


title: AL pool 5 with RU486 treatment


title: Ileum mesenteric nodule patient 6496

source_name: ileum mesenteric nodule tissue collected at primary surgery

value: ileum mesenteric nodule


title: AL pool 3 with RU486 treatment


title: JR121 (pJR29;VapC) (cy3) vs. JR121 (pJR230; VapBC) (cy5) rep4

city: Dunedin

first: Jennifer

middle: R

last: Robson

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: Biological replicate 4 of 4.

hyb_protocol: Hybrization performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Scanned Genepix 4000A scanner . Images were quantified using Spotfinder (TIGR).

data_processing: Total normalization and LOWESS normalization with MIDAS software (TIGR)

organism: Mycolicibacterium smegmatis

source_name: Batch culture HdB 0.2% glycerol

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: M. smegmatis ΔvapBC mutant (JR121) strain harboring either pJR29 (pMind_vapC) or pJR230 (pMind_vapBC) was used for conditional expression with tetracycline of the toxin VapC or the toxin-antitoxin complex VapBC. Strains were grown in 400 ml of Hartmans de Bont (HdB) minimal medium supplemented with 0.2% glycerol and hygromycin B (50  μg/ml) in 2 l flasks at 37°C with agitation (200 rpm). Strains JR121(pJR29) and JR121(pJR230) were grown to an optical density (600nm) of ~0.1. Protein expression was then induced with tetracycline (20 ng/ml). Cells were then harvested after 60 minutes post-induction for RNA extraction.

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

tag: genotype/variation

value: JR121ΔvapBC (pJR29,VapC)

value: JR121ΔvapBC (pJR230,VapBC)


title: Subject 47H

city: Menlo Park

first: Denise

last: Nishita

address: 333 Ravenswood Ave.

department: Molecular Genetics

institute: SRI International

scan_protocol: As described by manufacturer's protocol written by Fluidigm respectively

data_processing: In order to generate calibration curves for each of the six chips, the triplicate Ct values, SD, and CV for each point on the standard curve were averaged. Two different types of differential gene expression analyses were performed – the comparative standard curve (CSC) or delta delta CT method, and the relative standard curve (RSC) method. In the former method, the target gene amount is a function (2 to the – power) of the difference in normalized target assay cycle threshold between the sample and a calibrator (a standard curve). In the latter method, the sample Ct values are transformed into nanogram (ng) amounts based upon the standard curve produced from the aggregation of data from across all six chips.  The normalized signal, NormNg, calculated for each sample, is the ratio of the transformed ng in the target gene to the geometric mean of the transformed ng amounts of the four reference genes. Two-sided t-tests, as well as upper and lower one-sided t-tests, were performed for all assays in both methods of analysis.  False discovery rates were calculated and post-hoc multiple regression tests incorporating covariates were performed.

label: EvaGreen

source_name: High Salivary Stress

label_protocol: Fluidigm standard protocol

extract_protocol: Saliva biospecimens were collected using the Oragene•RNA for Expression Analysis Self-Collection Kits, RE-100 (DNA Genotek, Ontario, Canada) and the manufacturer’s protocol, described in the Supplemental File.

tag: sample id

tag: stress (0-low, 1-high)

tag: sex (0-male 1-female)

tag: smoking status (0-non smoker, 1-former smoker, 2-current smoker)

tag: rna integrity score

tag: rna yield (ug)


title: HD-iPSC culture 4


title: Subject 48H


title: HD-iPSC culture 6


title: TF_1_shTRAF6_d2.5_rep1

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

hyb_protocol: Hybridizations were with the standard Probe Array Cartidge (GeneChip Human Gene 1.0 ST Array; Affymetrix). Create a hybridization cocktail for a single probe array that contains 2.5 µg of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20× Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1× Hybridization Buffer.  Heat hybridization cocktail to 99°C for 2 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 90 µL of 1× Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1× Hybridization Buffer and fill probe array with 90 µL of the hybridization cocktail. Incubate at 45°C for 18 hrs in the Hybridization Oven rotating at 60 rpm.

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000 7G, and data were collected with Genechip Operating Software (Affymetrix).

data_processing:
Use RMA to normalize all arrays (samples) for a project. Average means of replicate samples. Create interpretations to compare different groups. Filter raw data to remove entities (genes) not being expressed. Perform fold change analysis, create list of genes with a  FC  1.5 or higher. Then use a statistical test, T Test unpaired with a p-value cutoff of 0.05 and multiple testing correction using Benjamini-Hochberg.
probe group file: HuGene-1_0-st-v1.pgf
meta-probeset file: HuGene-1_0-st-v1.csv

source_name: TF-1 cells, shTRAF6, d2.5

label_protocol: A total of 1-20ng of total RNA was reversed transcribed and labeled with the Ovation Pico WTA System (Nugen), the WT-Ovation Exon Module v1.0 (NuGEN), and the Encore Biotin Module (NuGEN).

growth_protocol: TF-1 cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum, 100U/mL Penicillin and 100ug/mL Streptomycin, and 10ng/mL hIL-3.

extract_protocol: Total RNA was extracted and purified with Quick-RNA MiniPrep Kit from Zymo Research (Cat#R1054) according to the manufacturer's instructions.

treatment_protocol: Short hairpin RNA targeting human TRAF6 was expressed in pLKO.1-puro lentiviral expression vector, and provided by the Lenti-shRNA library core CCHMC. The clones for TRAF6 is TRCN0000007348. Puromycin resistance gene was replaced by green fluorescent protein (GFP). The vector targeting scramble sequences was used as control. All the plasmids were packaged into pseudo lentivirus for transient and stable knockdown. Lentiviruses were pseudotyped with VSV-G, produced by 293-FT cells, and concentrated through ultracentrifugation at 20,000rpm for 2 hours at 4°C. Cells at 1×10^5/mL were transduced with lentivirus at an multiplicity of infection (MOI) of 0.5~1 and in the presence of 8μg/mL of polybrene (No. TR-1003-G; Millipore). At 2.5 days post-transduction, GFP positive cells were purified via fluorescence-activated cell sorting (FACS).

tag: treatment

value: TRAF6 knockdown


title: TF_1_shTRAF6_d2.5_rep2


title: Subject 44H


title: Subject 45H


title: pRS-kdm3a 6d 2

city: Brussels

first: Sarah

last: Dedeurwaerder

address: Route de Lennik, 808

country: Belgium

institute: Université Libre de Bruxelles

description:
biological replicate 2
Sample 12

hyb_protocol: cRNA was hybridized on the MouseWG-6 v2 array according to the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina)

data_processing: The data were normalized using quantile normalization with the 'beadarray' package in R

source_name: F9 cells

label_protocol: Biotinylated cRNA were prepared from 200 ng of total RNA with the Illumina® TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: Total RNA was isolated by the Tripure method (Roche) according to the manufacturer's instructions and purified on RNeasy minicolumns (Qiagen)

tag: kdm3a expression

value: Knock-down

value: Retinoin acid during 3 days and then retinoic acid + cAMP during 3 additional days


title: Subject 46H


title: HD-iPSC culture 2


title: JR121 (pJR29;VapC) (cy5) vs. JR121 (pJR230; VapBC) (cy3) rep3

description: Biological replicate 3 of 4.


title: CTL 6d 2

description:
biological replicate 2
Sample 10

value: WT


title: Subject 43H


title: TF_1_control_d2.5_rep2

source_name: TF-1 cells, pLKO, d2.5

value: control


title: Subject 42H


title: Subject 41H


title: pRS-kdm3a 6d 1

description:
biological replicate 1
Sample 11


title: Corrected HD-iPSC culture 6

source_name: Corrected HD-iPSC cultured cells

value: Corrected HD-iPSC line C127


title: HD-iPSC culture 3


title: Corrected HD-iPSC culture 8


title: HD-iPSC culture 1


title: CTL 6d 1

description:
biological replicate 1
Sample 9


title: Corrected HD-iPSC culture 2


title: JR121 (pJR29;VapC) (cy5) vs. JR121 (pJR230; VapBC) (cy3) rep1

description: Biological replicate 1 of 4.


title: JR121 (pJR29;VapC) (cy3) vs. JR121 (pJR230; VapBC) (cy5) rep2

description: Biological replicate 2 of 4.


title: Subject 40H


title: TF_1_control_d2.5_rep1


title: 245 stretched

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

institute: University of Cambridge

description: myometrium

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: VST and quantile normalised in Lumi v 2.40

source_name: myometrium

label_protocol: Illumina

growth_protocol: Strips of myometrium maintained in culture medium (Phenol red-free DMEM, 10% charcoal-stripped serum; 2mM L-glutamine, antibiotics) under 0.6g tension for approx. 65hrs

extract_protocol: Trizol method, according to manufacturer's (Invitrogen) instructions

treatment_protocol: Cultured as above but under 2.4 g tension

tag: condition

value: pregnant

tag: Stage

value: term, non-laboring

tag: tension

value: high (2.4g)


title: pRS-kdm3a 72h 1

description:
biological replicate 1
Sample 7

value: Retinoic acid during 3 days


title: Corrected HD-iPSC culture 1


title: Subject 37H


title: pRS-kdm3a 72h 2

description:
biological replicate 2
Sample 8


title: Subject 36H


title: Subject 39H


title: pRS-kdm3a 0h 2

description:
biological replicate 2
Sample 4

value: No treatment


title: Corrected HD-iPSC culture 7


title: Subject 34H


title: CTL 0h 1

description:
biological replicate 1
Sample 1


title: Corrected HD-iPSC culture 3


title: Corrected HD-iPSC culture 4


title: Corrected HD-iPSC culture 5


title: CTL 72h 2

description:
biological replicate 2
Sample 6


title: Huh7/5-2 infected 72 h biological replicate 2

city: Vienna

first: Kumaran

last: Kandasamy

state: Vienna

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: Center for Molecular Medicine

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

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner with G7 update.

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

source_name: Huh7/5-2 HCV infected 72h

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

growth_protocol: standard cell culture in DMEM supplemented with 10% FCS, NEA, L-Glut and Pen/Strep

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), following the manufacturer's protocol.

treatment_protocol: HCV infection was done as described in the summary field

tag: cell type

tag: time point

tag: hcv infection

value: true


title: Subject 38H


title: 245 control

description: myometrium


title: 244 control

description: myometrium


title: CTL 72h 1

description:
biological replicate 1
Sample 5


title: Huh7/5-2 infected 48 h biological replicate 1

source_name: Huh7/5-2 HCV infected 48h


title: pRS-kdm3a 0h 1

description:
biological replicate 1
Sample 3


title: Huh7/5-2 infected 72 h biological replicate 1


title: 240 stretched

description: myometrium


title: Subject 35H


title: Huh7/5-2 uninfected 48 h biological replicate 1

source_name: Huh7/5-2 uninfected 48h

value: false


title: 244 stretched

description: myometrium


title: CTL 0h 2

description:
biological replicate 2
Sample 2


title: Huh7/5-2 infected 48 h biological replicate 2


title: 243 stretched

description: myometrium


title: 242 stretched

description: myometrium


title: Subject 33H


title: 243 control

description: myometrium


title: Subject 31H


title: Subject 32H


title: Subject 30H


title: Huh7/5-2 infected 24 h biological replicate 2

source_name: Huh7/5-2 HCV infected 24h


title: Subject 29H


title: Subject 26H


title: Subject 25H

tag: sex (0-female 1-male)


title: 242 control

description: myometrium


title: Subject 27H


title: Huh7/5-2 infected 24 h biological replicate 1


title: Subject 24L

source_name: Low Salivary Stress


title: Subject 28H


title: Huh7/5-2 infected 12 h biological replicate 1

source_name: Huh7/5-2 HCV infected 12h


title: 236 stretched

description: myometrium


title: 240 control

description: myometrium


title: Huh7/5-2 uninfected 48 h biological replicate 2


title: Subject 23L


title: Huh7/5-2 infected 4 h biological replicate 1

source_name: Huh7/5-2 HCV infected 4h


title: Huh7/5-2 uninfected 4 h biological replicate 2

source_name: Huh7/5-2 uninfected 4h


title: Huh7/5-2 infected 12 h biological replicate 2


title: 237 stretched

description: myometrium


title: 238 stretched

description: myometrium


title: 238 control

description: myometrium


title: Huh7/5-2 infected 4 h biological replicate 2


title: 234 stretched

description: myometrium


title: 4E IP 2Gy 6h 1

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: MDA-MB-231 cells

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were grown in DMEM with 10% FBS in an atmosphere of 5% CO2/95% air at 37°C

extract_protocol: MBL International Rip Chip kit procedure was follwed according to manufacturers protocol

treatment_protocol: Cell cultures were irradiated using 320 X-ray source (Precision XRay Inc.) at a dose rate of 2.3 Gy/min.

tag: cell line

value: MDA-MB-231 cells

tag: antibody

value: 2 Gy

tag: time

value: 6 h

tag: antibody manufacturer

value: MBL International

tag: antibody catalog #

tag: antibody lot #


title: 237 control

city: Cambridge

description: myometrium


title: TM2_22

city: Montréal

first: Diala

last: Abed-Rabbo

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

hyb_protocol: A measure of 15 mg of cRNA was hybridized to an Affymetrix HuGeneFL microarray. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Microarrays were scanned with a Hewlett Packard Gene Array scanner.

data_processing: Gene expression data were corrected for background using the Robust Multiarray Averaging (RMA) package, normalized using the Quantile method and summarized using the Median Polish method. Differentially-expressed probesets (DEPS) were identified on the basis of a moderated t-statistic computed with the Bioconductor Limma package for each contrast of two a priori classes of samples. The Benjamini and Hochberg (BH) correction method was applied to control the false discovery rate across all genes. DEPS retained as candidates correspond to probesets with q-value (adjusted BH p-values) ≤ 0.05 for most of the comparisons with the exception of the M1/2 vs. TM1/2 contrast where q-value was ≤ 0.2.

label_protocol: Reverse Transcription was performed on 1 µg of total RNA with the SuperScriptTM First-Strand Synthesis System (Invitrogen Canada Inc., Burlington, Ontario, Canada) and random hexamers, according to the procedure recommended by the manufacturer. c-DNA samples were diluted at 1/3 or 1/6 in water prior to q-RT-PCR. Three µl of this dilution were used for each experiment. An in vitro transcription was performed on this cDNA and the resulting cRNA was biotinylated via incorporation of biotinylated dUTP and dCTP. DNA from samples was fragmented in 40mM Tris acetate, 100mM potassium acetate, and 30mM MgCl2 (pH 8.1) at 951C in order to reduce secondary structure.

growth_protocol: After rinsing, an explant of the surgical specimen was placed in 35-mm culture dishes, and held surface down so that the ovarian surface epithelium was maintained in a small amount of medium in contact with the bottom of the culture dishes, allowing the NOSEs to colonize the plastic. The cells were then passaged at 80% of confluence. A subgroup of NOSEs was cultivated in a modified medium (MM) i.e. the standard OSE medium supplemented with epidermal growth factor, hydrocortisone, insulin and bovine pituitary extract. Finally, tumors of ovaries (TOVs) were established in OSE medium supplemented with 10% FBS.

extract_protocol: Total RNA was extracted with TRIzolTM reagent (Gibco/BRL, Life Technologies Inc., Burlington, ON, Canada). RNA was extracted directly from homogenized cells grown to 80% confluence in 100-mm Petri dishes. RNA quality was monitored with a 2100 Bioanalyzer and RNA 6000 Nano LabChip kit (Agilent Technologies, Missisauga, Ontario, Canada) according to the manufacturer’s protocol.

treatment_protocol: Morphologically normal surface epithelium cells were obtained by gently scraping, 2-3 times with a rubber scraper, the ovarian surface epithelium of the surgical specimen provided by the pathologist. The cells collected were then seeded in standard OSE medium consisting of 50:50 medium 199:105 (Sigma) supplemented with 15% fetal bovine serum (FBS), 2.5 µg/mL amphotericin B and 50 µg/mL gentamicin.

tag: age at surgery

tag: cancer history

value: Familial cancer history

tag: carrier

value: Yes

tag: familial mutation

value: BRCA2 8765delAG

value: IV

tag: grade

tag: cell origin

value: Primary culture - Ascitis cells - Cystadenocarcinoma Serous papillary

tag: culture medium

value: OSE

tag: passage

tag: class


title: 236 control

description: myometrium

tag: condition

value: pregnant

tag: Stage

tag: tension


title: Huh7/5-2 uninfected 4 h biological replicate 1

tag: cell type

tag: time point

tag: hcv infection


title: TM1_21

value: BRCA1 4446C>T

value: Primary culture - Ascitis cells - Cystadenocarcinoma Endometrioid


title: TM1_20

value: IIIC

value: Primary culture - Ascitis Cells Cystadenocarcinoma Serous


title: 4E IP 2Gy 6h 3

tag: cell line

tag: antibody

tag: treatment

tag: time

tag: antibody manufacturer

tag: antibody catalog #


title: M2_14

tag: age

tag: cancer history

tag: carrier

tag: familial mutation

value: Not Applicable

tag: grade

value: Morphologically normal ovarian surface epithelium cells


title: TM1_19

tag: age at surgery

tag: cell origin

value: Primary culture - Epiploon Cystadenocarcinoma Serous

tag: culture medium

tag: passage

tag: class


title: Subject 20L

tag: sample id

tag: stress (0-low, 1-high)

tag: sex (0-male 1-female)

tag: smoking status (0-non smoker, 1-former smoker, 2-current smoker)

tag: rna integrity score

tag: rna yield (ug)


title: Subject 21L


title: Subject 22L


title: Subject 19L


title: Subject 18L


title: Subject 17L


title: Subject 16L


title: 4E IP Control 3

tag: cell line

value: MDA-MB-231 cells

tag: antibody

tag: treatment

value: control

tag: time

tag: antibody manufacturer

tag: antibody catalog #

tag: antibody lot #


title: Subject 15L


title: Subject 14L


title: 4E IP Control 1

value: MBL International


title: 4E IP 2Gy 6h 2

value: 2 Gy

value: 6 h


title: M2_12

tag: age

tag: cancer history

value: Colon cancer at the age of 47, breast cancer at the age of 49 and familial cancer history

tag: carrier

value: Yes

tag: familial mutation

value: BRCA2 G6085T

tag: Stage

tag: grade

tag: cell origin


title: Subject 13L

tag: sample id

tag: stress (0-low, 1-high)

tag: sex (0-male 1-female)

tag: smoking status (0-non smoker, 1-former smoker, 2-current smoker)


title: IgG 2Gy 6h 2

tag: cell line

tag: antibody

value: IgG


title: 4E IP Control 2

tag: treatment

tag: time


title: Subject 12L

tag: rna integrity score

tag: rna yield (ug)


title: NM_7

tag: age

value: No

tag: culture medium

value: OSE

tag: passage

tag: class

value: NM


title: M1_10

tag: cancer history

value: Familial cancer history

tag: carrier

tag: familial mutation

value: BRCA1 2953del3+C

tag: Stage


title: M2_13

value: BRCA2 8765delAG

value: Not Applicable

tag: grade

tag: cell origin


title: M1_9

value: BRCA1 C4446T

value: Morphologically normal ovarian surface epithelium cells


title: Subject 10L

tag: sample id

tag: stress (0-low, 1-high)

tag: sex (0-male 1-female)

tag: smoking status (0-non smoker, 1-former smoker, 2-current smoker)


title: IgG 2Gy 6h 3

tag: cell line

value: MDA-MB-231 cells

tag: antibody

tag: treatment

tag: time


title: 234 control

description: myometrium

tag: condition

value: pregnant

value: term, non-laboring

tag: tension


title: IgG Control 2

value: control


title: NM_5

tag: age

tag: culture medium

tag: passage

tag: class


title: Subject 11L

tag: rna integrity score

tag: rna yield (ug)


title: NM-3

tag: cancer history

tag: carrier

tag: familial mutation

tag: Stage

tag: grade

tag: cell origin


title: Subject 9L

tag: sample id

tag: stress (0-low, 1-high)

tag: sex (0-male 1-female)

tag: smoking status (0-non smoker, 1-former smoker, 2-current smoker)


title: Stationary abcR1abcR1, biological rep 1

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: Gene expression data from stationary phase 2308 cells containing abcR1 abcR2 double mutation

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on a B. abortus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

organism: Brucella abortus

source_name: Brucella abortus stationary phase

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to early stationary phase in brucella broth at 37C with aeration

extract_protocol: Total bacterial RNA was isolated using Trizol according to the manufacturer's recommendations (Invitrogen)

treatment_protocol: Once reaching stationary phase (measured by colony forming unit counts) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: sample

value: Whole cell

tag: genotype

tag: growth phase

value: Stationary


title: IgG Control 1

tag: cell line

tag: antibody

tag: treatment

tag: time


title: Stationary 2308, biological rep 1

description: Gene expression data from stationary phase wildtype 2308 cells

value: Wildtype


title: IgG 2Gy 6h 1

value: IgG

value: 2 Gy

value: 6 h


title: NM_6

tag: age

tag: cancer history

value: No

value: BRCA2 G6085T

tag: culture medium

value: OSE

tag: passage

tag: class

value: NM


title: Stationary abcR1abcR1, biological rep 2


title: Stationary 2308, biological rep 2


title: IgG Control 3


title: Subject 5L

tag: rna integrity score

tag: rna yield (ug)


title: Subject 6L

tag: sample id

tag: stress (0-low, 1-high)


title: Subject 7L

tag: sex (0-male 1-female)

tag: smoking status (0-non smoker, 1-former smoker, 2-current smoker)


title: Brain from Gaighatta Female rep 1

city: N. Dartmouth

first: Robert

last: Drew

address: 285 Old Westport Road

institute: University of Massachusetts Dartmouth

description: Gene expression data from brain of wild Gaighatta zebrafish strain

hyb_protocol: Affymetrix Zebrafish Genome Arrays (~14,900 transcripts) were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 rpm), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.  This was followed by another round of SAPE.   All microarray procedures were performed at the Genomics Core Facility of the Center for Reproductive Biology at Washington State University (Pullman, WA).

scan_protocol: All microarrays were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: CEL files containing raw data were then processed and analyzed using R software and Bioconductor packages. Microarray hybridization data were examined for physical anomalies on the chip by pseudochip and residual error visualizations. Quality assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport.  The arrays were then pre-processed using the Robust Multi-array Average (RMA) procedure using the affy package. Next, unexpressed and low variability genes were removed by unbiased filtering.  Affymetrix present-marginal-absent (PMA) calls were determined using a P-value cut off for absent of greater than 0.04 and present less than 0.04; marginal calls were treated as absent. Unexpressed genes were then defined as having a signal less than the expression value at which 99% of genes were called as absent across all samples.  A filter on interquartile range was also applied to remove genes with low variability.  Genes with an interquartile range of less than 0.5 across all chips in the experiment were excluded, reducing the dataset further to 7,958 genes.  Signal intensities were also examined at the probe level to identify single feature polymorphisms (SFPs), differences at the probe level due to genetic polymorphisms rather than expression differences, which may also impact computed expression values.  Briefly, in R using previously described methods, the RMA normalized expression estimate for each probe set was subtracted from background corrected and normalized expression levels at individual probes within the probe set.  Normalized residuals were analyzed using significance analysis of microarrays (SAM) within the siggenes package to detect features with a significant effect for strain (FDR adjusted  < 0.01). A total of 3,199 genes with significant SFPs were then removed from the analysis.

organism: Danio rerio

source_name: Brain from wild Gaighatta strain, Univ. of Idaho

label_protocol: For each array, 10 ug of total RNA were converted to cDNA.  Biotinylated cRNA was then produced in vitro using the GeneChip expression 3′ amplification one-cycle target labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Prior to the experiment, all zebrafish were reared in a recirculating zebrafish facility at the University of Idaho, designed by Aquaneering Inc. (San Diego, CA).  Fish were feed twice daily with a combination of commercial flake food and Artemia nauplii.  Temperature of the facility was maintained at 28ºC with a constant 14 h light: 10 h dark cycle.  These rearing conditions were maintained during the behavior assays.

extract_protocol: Total RNA was then extracted using the TRIzol method following manufacturer’s protocol (Invitrogen).

treatment_protocol: Sixteen adult fish (4 to 6 months old) from each strain were randomly assigned to 1-L aquaria (22 cm long, 15 cm high, 5 cm wide), one fish per aquarium.  The aquaria were delimited into six 2-cm vertical zones using thin twine tied across the front of the entire row of aquaria.  Fish were then observed using a high-throughput behavioral assay to quantity fear-related behaviors.  Following behavioral observations, fish were removed from the individual tanks and temporily placed in one of sixteen 3-L group tanks.  On the sampling day, each fish was anesthetized in 170 mg L−1 tricaine methanesulfonate (MS222, Western Chemical Inc., Ferndale, WA), briefly blotted on a paper towel, and rapidly measured for standard length and body mass.  The brain was then quickly removed and homogenized in TRIzol (Invitrogen, Carlsbad, CA).  Brains from all individuals in a tank were homogenized together, for a total of two biological replicate pools per sex per strain (16 microarrays total).

tag: strain

value: Gaighatta

tag: tissue

value: Brain

tag: rearing history

value: Wild

value: Adult

tag: Sex

value: Female


title: Subject 4L


title: Brain from Nadia Male rep 1

description: Gene expression data from brain of wild Nadia zebrafish strain

source_name: Brain from wild Nadia strain, Univ. of Idaho

value: Nadia

value: Male


title: Subject 8L


title: Subject 2L


title: Brain from Gaighatta Male rep 1


title: Subject 1L

tag: sex (0-female 1-male)


title: Brain from Gaighatta Female rep 2


title: Brain from Nadia Male rep 2


title: M PER417-003, Drought-treated plants, biological rep3

city: Yokohama

first: Tetsuya

last: Sakurai

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description: Gene expression data from drought-stress-treated M PER417-003 plants

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacture's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent microarray (GPL14139) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Percentile normalization (50 percentile) was performed for each chip.

organism: Manihot esculenta subsp. peruviana

source_name: Drought-treated M PER417-003 plants

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

growth_protocol: After cutting of shoots from the cassava plants, the shoots were grown in  a glass bottle containing MS medium supplemented with 2% sucrose and 0.3% gelrite for 4 weeks (16 hours light / 8 hours dark).

extract_protocol: The total RNA was extracted from the plants before or after drought treatment using RNeasy Plant Mini kit (QIAGEN) according to manufacture’s instruction.

treatment_protocol: The plantlets were subjected to drought treatment by removing the plantlets from the gelrite plate, placing on a plastic plate and keeping them for  1 hour under 40-80 μmol photons m-2 sec-1 at 30ºC in 50% of relative humidity. Then total RNA was prepared from the shoots and used for the microarray hybridization.

value: Stem and leaves

value: 30 day-old plantlets  after cutting

tag: treatment

value: drought

tag: cultivar


title: Brain from Gaighatta Male rep 2

tag: age


title: Brain from Nadia Female rep 1


title: Brain from SH Male rep 2

description: Gene expression data from brain of domesticated SH zebrafish strain

source_name: Brain from domesticated SH strain, Univ. of Idaho

value: SH

value: Domesticated


title: Brain from Nadia Female rep 2


title: Brain from SH Male rep 1


title: Brain from TM1 Male rep 2

description: Gene expression data from brain of domesticated TM1 zebrafish strain

source_name: Brain from domesticated TM1 strain, Univ of Idaho


title: Brain from SH Female rep 2


title: Brain from SH Female rep 1


title: Brain from TM1 Female rep 1


title: Brain from TM1 Male rep 1