title: cell line HCT116, library IHH026

status: Public on Apr 06 2011

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

institute: University of Cologne

description: genomic DNA hydrosheared in 8.5 kb fragments (std dev: 562 bp below median; 526 above median), 2x25bp paired-end (mate pair) sequences, library IHH026

library_source: genomic

data_processing:
For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.
Processed data for cell line HCT116 is available on Sample record GSM663567

source_name: Cell line was established from the primary colon carcinoma of an adult man

growth_protocol: standard growth conditions for cell lines

extract_protocol: Genomic DNA was hydrosheared, EcoP15I recognition sites were methylated and EcoP15I CAP adaptors were ligated to the ends of DNA fragments. The methylated DNA constructs were separated on agarose gel and 10 Kb sized fragments were selected for ligation resulting in circularized products where 5’ and 3’ ends of 10 Kb fragments were connected by an internal biotinylated adaptor with two flanking non-methylated EcoP15I CAP adaptors. Constructs were digested by methylation sensitive EcoP15I to release 5’ and 3’ paired-end tag (PET) constructs. Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Applied Biosystems SOLiD system.

tag: tumor type

value: primary carcinoma

value: colon


title: cell line HCT116, library IHH003

type: SRA

country: Germany

description:
genomic DNA hydrosheared in 9.7 kb fragments (std dev: 3,383 bp below median; 1,710 above median), 2x25bp paired-end (mate pair) sequences, library IHH003
Complete raw data not available for this record. csfasta files available as supplementary files.

molecule: genomic DNA

organism: Homo sapiens

tag: tissue


title: human leukemia 77

status: Public on Jan 13 2012

type: RNA

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

country: USA

institute: university of chicago

description: RMA expression value derived from Expression Console software; extended-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UC Microarray Core Facility.

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

data_processing: Raw data were processed with the Expression console (Affymetrix) for background correction and normalization log2 transformation. Data analysis and statistical evaluations were performed with customized R codes (version 2.10.1, http://www.r-project.org/).

label: biotin

molecule: total RNA

source_name: human leukemia

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNA was isolated with the miRNeasy Mini Kit (Qiagen), according to the manufacturers instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturers instructions.

tag: disease state

value: leukemia

tag: cell line

value: human leukemia cell line


title: human leukemia 55


title: human leukemia 16


title: control transgene

status: Public on Dec 10 2011

city: Boston

first: Taiowa

last: Montgomery

state: MA

address: 185 Cambridge Street, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description: Small RNA

library_source: transcriptomic

data_processing: Raw datasets are fastq files generated using Illumina software. The 5' adapter sequence ends with AAC for the control transgene library and CCC for the siRNA sensor transgene library. The sequence of the 3' adapter used during library preparation is 5'-CTGTAGGCACCATCAAT. Small RNA sequences can be parsed from between the adapter sequences. For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20. Sequences were not filtered for alignment to a genome. Tab-delimited files containing unique sequences and corresponding read counts were generated using custom Perl scripts.

organism: Caenorhabditis elegans

source_name: Whole worms, control transgene

growth_protocol: Animals were grown at 20˚C on E. coli strain OP50.

extract_protocol: Total RNA was isolated from synchronized animals, and small RNAs were size selected, tobacco acid pyrophosphatase (TAP)-treated to remove 5' di- and triphosphate groups, ligated to 5' and 3' adapters and subjected to RT-PCR.

tag: strain

value: mgSi3[pCMP2(ubl-1p::GFP::ubl-1-3'UTR Cbr-unc-119(+))] II; unc-119(ed3) IV

value: whole body

tag: developmental stage

value: young adult

tag: transgene

value: control


title: siRNA sensor transgene

description: Small RNA

data_processing: Raw datasets are fastq files generated using Illumina software. The 5' adapter sequence ends with AAC for the control transgene library and CCC for the siRNA sensor transgene library. The sequence of the 3' adapter used during library preparation is 5'-CTGTAGGCACCATCAAT. Small RNA sequences can be parsed from between the adapter sequences.  For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20. Sequences were not filtered for alignment to a genome. Tab-delimited files containing unique sequences and corresponding read counts were generated using custom Perl scripts.

source_name: Whole worms, siRNA sensor transgene

value: mgSi4[pCMP2(ubl-1p::GFP::siR-1-sensor-ubl-1-3'UTR Cbr-unc-119(+))] II; unc-119(ed3) IV

value: siRNA sensor


title: JMJD2B-depleted MCF-7 cells treated with E2, rep2

status: Public on Dec 31 2010

city: Toronto

first: Hitoshi

last: OKADA

state: Ontario

address: 620 University Ave Suite 7-706

department: Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Ontario Cancer Institute

description:
siJ2B E2(+)
HuGene1_102109H_HO11_#11

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) according to standard Affymetrix procedures.

scan_protocol: Array scanning was performed with the Affymetrix GeneChip Scanner 3000 according to the manufacturer's instructions (Affymetrix) at the microarray core facility.

data_processing:
Raw data were processed with Expression Console software. RMA expression values were derived. Subsequent analyses were performed using Partek software (version 6.5) default settings. Differentially expressed genes between E2-starved cells and E2-stimulated cells, and between JMJD2B-depleted cells and control cells, were identified. One-way ANOVA was performed with a 2-fold up-regulated or down-regulated gene expression cutoff. The p-value for ANOVA analysis was set as p<0.05 and further adjusted by FDR (Step Up, FDR<0.05).

Core-exon analysis.
Genome build: UCSC hg19.
Probe-group file: HuGene-1_0-st-v1.r4.pgf
Meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: MCF-7, JMJD2B depleted, E2

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: MCF-7 human breast cancer cells were obtained from the American Type Culture Collection (Manassas, VA). MCF-7 cells were cultured at 37°C in a humidified, 95% air/5% CO2 incubator in Eagle’s Minimum Essential Medium (ATCC #30-2003) supplemented with antibiotics, 10% fetal bovine serum (FBS) and 0.01 mg/mL bovine insulin. For steroid-free medium, phenol red-free DMEM (Gibco) and charcoal/dextran-treated FBS (HyClone, SH30068) were used.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: siRNA was used to knock down JMJD2B expression. MCF-7 cells were transfected with either control siRNA or JMJD2B siRNA, cultured in steroid-free medium for 72 hr, and stimulated with or without E2 for 4 hr.

tag: cell type

value: breast cancer

tag: gender

value: female

tag: sirna

tag: treatment

value: estradiol (E2)


title: steroid-depleted JMJD2B-depleted MCF-7 cells, rep1

description:
siJ2B E2(-)
HuGene1_102109H_HO7_#7

source_name: MCF-7, JMJD2B depleted, steroid depleted

value: steroid depletion


title: steroid-depleted JMJD2B-depleted MCF-7 cells, rep2

description:
siJ2B E2(-)
HuGene1_102109H_HO8_#8


title: human leukemia 67


title: JMJD2B-depleted MCF-7 cells treated with E2, rep3

description:
siJ2B E2(+)
HuGene1_102109H_HO12_#12


title: control MCF-7 cells treated with E2, rep3

description:
control E2(+)
HuGene1_102109H_HO6_#6

source_name: MCF-7, E2


title: steroid-depleted JMJD2B-depleted MCF-7 cells, rep3

description:
siJ2B E2(-)
HuGene1_102109H_HO9_#9


title: steroid-depleted control MCF-7 cells, rep3

description:
control E2(-)
HuGene1_102109H_HO3_#3

source_name: MCF-7, steroid depleted


title: negative3

status: Public on Nov 01 2010

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description: input DNA

data_processing: Sequencing reads were quality trimmed by clipping at 3 consecutive nucleotides with quality score less than 10. Reads shorter than 18 nucleotides were discarded and the remaining reads were mapped against the human reference genome (hg18 assembly, NCBI build 36) using SHRiMP package (Rumble et al, 2009)  with default settings, which allows mapping in SOLiD color space corresponding to dinucleotide encoding of the sequenced DNA. For analysis we used only uniquely placed reads, which were defined as reads having at least two additional mismatches in the second best hit compared to the best hit. The Cisgenome software package (Ji et al, 2008) was used for the identification of binding peaks from the ChIP-seq data. Two-sample analysis mode was used to compare samples with control input data. The parameters for peak discovery were set as follows: window size 100, step size 25, maximum gap 200, active single strand filtering with forward and reverse reads cutoff 4, minimum peak with 225 and minimum reads per window was set to obtain < 0.1 or 0.01 false positive rate (FDR).

source_name: cell line

extract_protocol: Immunoprecipitated chromatin was sheared for a second time for 6 minutes using Covaris sonicator (6 x 16 mm AFA fiber Tube, duty cycle: 20%, intensity: 5, cycles/burst: 200, frequency sweeping) to obtain suitable shorter fragments (75-125 bp). To exclude a shearing bias as a possible source of binding site ultrastructure, partial digestion using DNaseI was used as an alternative to shorten the fragments for one control ChIP-seq library and one input library. For DNaseI treatment, chromatin was resuspended in 45 µl of freshly prepared reaction buffer (10mM MnCl2, 0.1mM CaCl2, 10mM Tris, pH 7.5) and digested with 0.5mU of DNaseI for 5 minutes at room temperature. The reaction was stopped by adding EDTA to a final concentration of 50mM. Chromatin was immediately extracted using phenol/chloroform procedure and precipitated. After fragmentation, fragments were blunt-ended and phosophorylated at the 5'-prime end using the End-it Kit (Epicentre) according to the manufacturer’s instructions. Ligation of double stranded adapters compatible with SOLiD sequencing was performed using Quick ligation kit (New England Biolabs) with 750 mM P1 ds and P2 ds adaptor (Applied Biosystems), 11.7 µl of 2x Quick ligation buffer, 1 µl Quick Ligase in total volume of 23.4 µl. Samples were purified using Ampure beads (Agencourt) and run on a native 6% polyacrylamide gel. Fragments ranging from 140 to 180 bp were excised; the piece of gel containing DNA fragments was shredded and dispersed into 400 µl of Platinum PCR Supermix with 750 mM of each P1 and P2 PCR primer, 2,5 U of Pfu (Stratagene) and 5 U Taq (Bioline). Prior to ligation-mediated PCR the sample was incubated at 72˚C for 20 minutes in PCR mix to let the DNA diffuse out of the gel and to perform nick translation on non ligated 3'-ends of DNA fragments. After 17 cycles of amplification the library was purified using Ampure beads and was quality checked on 2100 Bioanalyzer (Agilent) for the absence of possible adapter dimers and heterodimers.


title: steroid-depleted control MCF-7 cells, rep1

description:
control E2(-)
HuGene1_102109H_HO1_#1


title: mRNA_RA_2

status: Public on Sep 10 2011

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

description: mRNA seq of Right atrial tissue

data_processing:
Basecalls performed using CASAVA version 1.3
For the poly-A enriched mRNA samples, reads were aligned to hg19 using tophat with the following parameters -r 0 --solexa1.3-quals -G hg19gene.gtf
For the miRNA-seq data, reads were aligned to miRBase Release 17 hairpins using bowtie with the -best option and allowing for 1 mismatch.  Aligned reads were then collapsed down to mature sequences.
genome build: hg19
processed data files format and content: Counts were obtained from the BAM files using custom scripts.

source_name: Right Atrial Tissue

extract_protocol: Total RNA was extracted using QIAGEN miRNeasy Mini Kits from 20 mg of atrial tissue samples.  Sequencing libraries were made following Illumina's mRNA protocol.  Briefly, RNA was purified by poly-A selection using oligo(dT) beads and chemically fragmented.  First and second strand cDNA synthesis was followed by end-repair and 3' adenylation.  5' and 3' Illumina adapters were ligated and size-selected using gel-purification and PCR amplification.   Using the same total RNA preparations, a smallRNA-sequencing library was constructed following Illumina's Alternative v1.5 smallRNA-seq protocol (Part # 15002615).  Briefly, 5' and 3' adapters were ligated onto the small RNAs and amplified.  The cDNA with adapters was size selected between 93-100 bp and 36 bp single-end sequencing was performed.

value: Right Atrial Heart


title: negative1

description: input DNA


title: JMJD2B-depleted MCF-7 cells treated with E2, rep1

description:
siJ2B E2(+)
HuGene1_102109H_HO10_#10


title: steroid-depleted control MCF-7 cells, rep2

description:
control E2(-)
HuGene1_102109H_HO2_#2


title: 20m.KCl.2

status: Public on Nov 10 2010

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

department: Biology

country: France

institute: CNRS

description: replicate:  2

hyb_protocol: Affy

scan_protocol: The Affy ATH1 chips have been processed and scanned according to the manufacturer protocol or as described by Krouk et al. PLoS Comput Biol 2009, 5(3):e1000326.  The Scanner is an Affymetrix GeneChip(R) scanner 3000 7G.

organism: Arabidopsis thaliana

source_name: 14 day old Roots

label_protocol: Affy

growth_protocol: arabidopsis are grown hydroponically for 14 days

extract_protocol: Plants have been extracted by Trizol reagent according to the manufacturer protocol.

treatment_protocol: High resolution NO3 treatments

value: 14 day old Roots

tag: time (minutes)

value: KCl


title: lateral_D

status: Public on Aug 24 2011

city: Oxford

first: T

middle: Grant

last: Belgard

address: Le Gros Clark Building, South Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

data_processing: Bam: Reads were processed with versions 1.4 and 1.6 of the Illumina pipeline.  The internal insert size and standard deviation was estimated for each library by empirically calculating the full width at half max (FWHM) for an internal insert size distribution constructed using uniquely mapping reads on the same chromosome from Illumina's Gerald pipeline.  The insert size was estimated to be the midpoint of the minimum and maximum insert sizes at half (or greater) the frequency of the most common insert size, and the standard deviation was calculated under a Gaussian assumption StdDev=FWHM/(2*sqrt(2ln2)).  Using this insert size and standard deviation, lanes were separately mapped with TopHat v1.0.13 to the mouse reference genome (mm9, downloaded from UCSC) plus all splice junctions from the UCSC Table Browser (cite) tables all_mrna (mouse mRNAs), intronEst (mouse spliced ESTs), and xenoMrna (mRNAs mapped from other species to mouse) with the following options: butterfly search, closure search, fill gaps, microexon search, min anchor length = 5, min isoform fraction = 0.0, max intron length = 500 kb.  In a second round of TopHat mapping (default options except min isoform fraction = 0.0), all novel junctions identified from any sample in the previous step were given to TopHat again (as raw junctions), so splice junctions could be measured across all samples in an unbiased manner.  Laminar samples were dissected from dorsal cortex (overlapping S1 and some motor cortex) and, separately, lateral cortex (partially overlapping S2 and insular cortex) from mice matched in number, strain, sex, litter distribution, and age to the original set of mice.  These additional eight adult male mice (56 days old; C57BL/6J strain) were also killed by cervical dislocation according to approved schedule one UK Home Office guidelines (Scientific Procedures Act, 1986).  These were treated exactly as described above, with the following exceptions: sample B was not split and RNA underwent two rounds of poly(A) selection.  Lanes with aberrant GC content were discarded and all reads were trimmed to correspond to two ends of 50 base pairs each.  A read fragment was discarded if any of the following conditions was met: either read failed Illuminaâs chastity filter, either read had eight or more bases (corresponding to tophatâs default minimum anchor length) with a Phred-scaled quality score less than three, either read mapped (bowtie v0.12.7 allowing up to two mismatches) to spliced or unspliced rRNAs, tRNAs or mitochondrial rRNAs as defined by Ensembl (release 62).  Fragment internal insert size and standard deviation were estimated with the FWHM technique.  Fragments were subsequently mapped on a lane-by-lane basis with tophat v1.2.0 (Trapnell et al., 2009) enabling microexon search, coverage search, butterfly search, and providing gene models corresponding to Ensembl (release 62).  All splice sites found in any lane (from original or replicate dorsal cortex samples, or lateral cortex samples) then combined for a final round of tophat mapping in which new splice site detection was disabled but all previously detected splice sites were provided.

molecule: polyA RNA

organism: Mus musculus

source_name: lateral cortex

extract_protocol: Total RNA >200 nt was extracted using the RNeasy Lipid Tissue Mini kit (QIAGEN), following the manufacturer's instructions and using the on-column DNase digest.  RNA quantity was assessed using a NanoDrop 1000 spectrophotometer (ThermoScientific), and RNA quality and integrity assessed using a BioAnalyzer (Agilent Laboratories).  Total RNA was prepared for paired-end deep sequencing on Illumina's Genome Analyzer II following the manufacturer's protocol.  Briefly, poly(A) RNA was enriched using Dynal oligo(dT) beads (Invitrogen) [enriched twice for the dorsal and lateral cortex samples; see publication for full details].  This was fragmented using the RNA fragmentation kit (Ambion).  First- and second-strand cDNA was synthesized with random hexamer primers (Invitrogen) and SuperScript II (Invitrogen).  Ends were repaired using T4 DNA polymerase and Klenow DNA polymerase.  A single adenosine and Illumina adapters were ligated using Klenow 3'-to-5' exo-nuclease.  Following gel purification of cDNA templates, the library was enriched with 15 rounds of PCR before being added to the flow cell for paired-end sequencing (51 nt from either end, of which 50 nt was used in mapping; except for two libraries in sample F where 76 nt were sequenced from either end, using 75 in mapping).  Paired-end library average internal insert sizes (standard deviations) were as follows: A 164 (27); B1 239 (29); B2 193 (28); C 184 (21); D 208 (22); E 172 (24); F 184 (28); DC2 A 287 (31); DC2 B 290 (28); DC2 C 291 (28); DC2 D 269 (30); DC2 E 284 (31); DC2 F 279 (21); LC A 281 (40); LC B 275 (32); LC C 282 (41); LC D 267 (29); LC E 268 (38); LC F 272 (34).

value: lateral cortex

tag: number of pooled mice

tag: Sex

value: male

tag: age

tag: laminar sample (see publication)

value: D


title: 9m.KCl.2

description: replicate:  2


title: control MCF-7 cells treated with E2, rep1

description:
control E2(+)
HuGene1_102109H_HO4_#4


title: 20m.KNO3.2

description: replicate:  2


title: 20m.KCl.1

description: replicate:  1


title: 9m.KNO3.2

description: replicate:  2


title: 20m.KNO3.1

description: replicate:  1


title: 9m.KNO3.1

description: replicate:  1


title: 9m.KCl.1

description: replicate:  1


title: control MCF-7 cells treated with E2, rep2

description:
control E2(+)
HuGene1_102109H_HO5_#5


title: To.1

description: replicate:  1


title: Patient 4

status: Public on Aug 30 2011

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

hyb_protocol: Array hybridization, washing, blocking, and Cy3 staining was performed according to the Illumina protocol.

scan_protocol: Arrays were scanned with an Illumina Bead Array Reader.

data_processing: Quantile normalization after Log2 transformation using BeadStudio V3.0.14 by Illumina

label: Biotin

source_name: Sarcoma, pre-treatment biopsy

label_protocol: Amplification and labeling was done using the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was isolated from tumor tissue using Qiagen RNeasy kit.

tag: histology

value: fibroblastic sarcoma

tag: response

value: Good-responder


title: To.2

description: replicate:  2

tag: tissue


title: human leukemia 1

tag: disease state

value: leukemia

value: human leukemia cell line


title: LG268, donor 2

status: Public on Sep 01 2010

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

country: Hungary

institute: UNIVERSITY OF DEBRECEN

hyb_protocol: 10 ug of fragmented biotinylated cRNA was hybridized for 16 hr at 45C on GeneChip HG133_plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
CHP file were generated by Affymetrix Expression Console, using RMA algorithm.
Details:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: differentiating monocyte-derived dendritic cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using 3` IVT Expression kit (Affymetrix).

growth_protocol: CD14+ monocyte were cultured in the presence of IL4 and GMCSF

extract_protocol: RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).

treatment_protocol: Cells were treated with various nuclear receptor agonists

tag: donor

value: monocyte-derived dendritic cells

tag: agent

tag: nuclear receptor agonist type

value: RXR agonist


title: GW3962, donor 3

value: LXR agonist


title: GW3962, donor 1


title: 9cisRA, donor 3

value: 9-cis retinoic acid

value: RAR and RXR agonist


title: GW3962, donor 2


title: N2_mixed_stage_small_RNA (Illumina)

status: Public on May 25 2010

city: Ann Arbor

first: Arun Prasad

last: Manoharan

state: MI

address: 210 washtenaw ave

department: Bioinformatics

institute: University of Michigan

description: 18-32 nt

data_processing: The raw Solexa sequence files were first processed with a custom written Perl script to remove the trailing Solexa adapter sequence. The processed sequences with length greater than or equal to 18 bp were then subjected to megaBLAST with the following parameters: -D 3 -W 12 -p 70 ( line output format =3,tile window size=12 and identity=70%). Alignments less than 18bp were removed and the reads were then filtered to pick out the alignment with the maximum no of matching bases. The sequences which aligned to more than 10 positions in the genome were filtered.

source_name: N2 mixed stage

growth_protocol: Worms were grown on 10 cm2 NGM plates seeded with OP50. For sperm isolation, we used the him-8(e1489) strain, which increases the percentage of XO males to ~37% of the population versus ~0.2% males in the N2 wild-type strain.  Male worms from the him-8(e1489) strain were further isolated from hermaphrodites by filtering through a 35 µm nylon mesh filter as described, resulting in >95% males in the final sample.  Isolated him-8(e1489) males were then subjected to 20,000 psi for 1 min, 3 times, to extrude and increase the yield of purified sperm. We used the fer-1(hc1) strain, which produces nonfunctional sperm at 25°C, to obtain purified unfertilized oocytes. The fer-1(hc1) worms grown at 25°C were disrupted briefly in a Waring blender to release more oocytes from the body cavity. Sample purity (>95%) was inspected by DAPI staining and microscopy.

extract_protocol: For each library, 18-32 nt small RNA was size selected from 50 µg of total RNA.  Small RNA was ligated to the 5' RNA adapter (5' GUU CAG AGU UCU ACA GUC CGA CGA UC 3') using T4 RNA ligase (Ambion) in the presence of RNaseOut (Invitrogen) overnight at 25°C. The ligated RNA was gel purified and ligated to the 3' RNA adapter (5' pUC GUA UGC CGU CUU CUG CUU GidT 3'(p = phosphate; idT = inverted deoxythymidine)) with T4 RNA ligase (Ambion) in the presence of RNaseOut (Invitrogen) overnight at 25°C. The ligated RNA was gel purified and converted to single-stranded cDNA using Superscript III reverse transcriptase (Invitrogen) and Illumina's small RNA RT-Primer (5' CAA GCA GAA GAC GGC ATA CGA 3'). The resulting cDNA was PCR-amplified with Taq DNA Polymerase (Roche) in 20 cycles using small RNA primer set (5' CAA GCA GAA GAC GGC ATA CGA 3',5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3''). PCR products were gel purified, quantified on the Agilent DNA 1000 chip and diluted to 10 nM for sequencing on the Illumina 1G.

treatment_protocol: RNA extraction was performed following the vendor’s protocol with the following modification: 3 times freeze/thaw/vortex and disruption with pellet pestle was included to increase worm lysis efficiency.

tag: phenotype

value: N2 (Bristol)

tag: stage

value: mixed stage


title: him-8_sperm_small_RNA (Illumina)

description: 18-32 nt

source_name: him-8 sperm

value: sperm


title: glp-4_young_adult_small_RNA (Illumina)

description: 18-32 nt

source_name: glp-4 young adult

value: young adult


title: eri-1_young_adult_small_RNA (Illumina)

description: 18-32 nt

source_name: eri-1 young adult


title: fer-1_oocyte_small_RNA (Illumina)

description: 18-32 nt

source_name: fer-1 oocyte

value: oocyte


title: control, donor 5

tag: cell type

value: vehicle

value: control


title: control, donor 4


title: RSG, donor 3

value: rosiglitazone

value: PPARg agonist


title: control, donor 6


title: AM580, donor 4

value: RAR agonist


title: AM580, donor 5


title: LG268, donor 3


title: N2_embryo_small_RNA (Illumina)

description: 18-32 nt

source_name: N2 embryos

value: embryo


title: GW1516, donor 2

value: PPARd agonist


title: GW1516, donor 1

value: monocyte-derived dendritic cells


title: LG268, donor 1

value: RXR agonist


title: 9cisRA, donor 2


title: control, donor 3


title: GW1516, donor 3


title: RSG, donor 1


title: RSG, donor 2


title: 9cisRA, donor 1


title: AM580, donor 6


title: control, donor 1


title: sample A2875 of patient 23840 (site 001)

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

institute: Miltenyi Biotec GmbH

description: Total RNA was obtained using the ABI TempusT whole blood collection system (Applied Biosystem, CA).

hyb_protocol: The hybridization procedure was performed according to the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent RISET 2.0 Oligo Microarrays 8x15K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37 °C) Agilent Gene Expression Wash Buffer 2 for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing: For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). An artificial common reference was computed from all samples included in the IOT dataset. Using this baseline, log2 ratios were calculated for each gene and sample. Additionally, p-values indicating the reliability of a observed difference between a sample and the common reference were calculated for each gene applying the universal error model implemented in the Rosetta Resolver software.

source_name: peripheral vein blood

label_protocol: Sample labeling was performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040). Briefly, 0.5 µg of each total RNA sample was used for the amplification and labeling step using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: IOT samples: Peripheral vein blood (4x 2.5 mL) was drawn directly into PAXgene Blood RNA tubes (QIAgen, Crawley UK). Whole-blood RNA was extracted using the PAXgene Blood RNA Kit, including treatment with DNAse I to prevent genomic DNA contamination (QIAgen). ITN samples: Total RNA was obtained using the ABI TempusT whole blood collection system (Applied Biosystem, CA) and frozen for future processing. Total RNA was purified using methods as described in Asare AL et al. BMC Genomics 2008; 9:474.

tag: HC

tag: ITN


title: sample A2371 of patient 001 (site 001) (replicate)

tag: CR


title: sample A2680 of patient 54342 (site 001)


title: sample A2505 of patient 026 (site 004) (replicate)


title: sample A2478 of patient 005 (site 004) (replicate)


title: sample A2665 of patient 41058 (site 001)


title: sample A2695 of patient 52714 (site 001)


title: sample A2935 of patient 147194 (site 001)


title: sample A2980 of patient 147266 (site 001)


title: sample A2499 of patient 022 (site 001)


title: sample A2920 of patient 53606 (site 001)


title: sample A2965 of patient 55798 (site 001)


title: sample A2890 of patient 51284 (site 001)


title: sample A2605 of patient 53580 (site 001)


title: sample A2379 of patient 004 (site 003)


title: sample A2590 of patient 53630 (site 001)


title: sample A2382 of patient 005 (site 004)


title: sample A2995 of patient 46286 (site 001)


title: sample A2650 of patient 54738 (site 001)


title: sample A2815 of patient 47834 (site 001)


title: sample A2635 of patient 51032 (site 001)


title: sample A2353 of patient 011 (site 001) (replicate)


title: sample A2710 of patient 14984 (site 001)


title: sample A2740 of patient 53714 (site 001)


title: sample A2800 of patient 42570 (site 001)


title: sample A2725 of patient 147367 (site 001)


title: sample A2518 of patient 024 (site 001) (replicate)


title: sample A2335 of patient 045 (site 004)


title: sample A2536 of patient 004 (site 003) (replicate)


title: sample A2575 of patient 42244 (site 001)


title: sample A2300 of patient 048 (site 004)


title: sample A2330 of patient 036 (site 004)


title: sample A2322 of patient 035 (site 001)


title: sample A2334 of patient 026 (site 004)


title: sample A2306 of patient 003 (site 003) (replicate)


title: sample A2493 of patient 052 (site 002)

tag: s-CNI


title: sample A2522 of patient 019 (site 004) (replicate)


title: sample A2199 of patient 001 (site 001)


title: sample A2521 of patient 004 (site 004) (replicate)


title: sample A2377 of patient 004 (site 004)


title: sample A2506 of patient 061 (site 002)


title: sample A2509 of patient 057 (site 002) (replicate)


title: sample A2211 of patient 011 (site 001)


title: sample A2513 of patient 012 (site 002) (replicate)


title: sample A2259 of patient 018 (site 004)


title: sample A2477 of patient 008 (site 002) (replicate)


title: sample A2197 of patient 029 (site 001)


title: sample A2488 of patient 016 (site 002)


title: sample A2299 of patient 047 (site 004)


title: sample A2298 of patient 046 (site 004)


title: sample A2268 of patient 054 (site 002)


title: sample A2252 of patient 003 (site 003)


title: sample A2220 of patient 024 (site 001)


title: sample A2490 of patient 026 (site 002) (replicate)


title: sample A2360 of patient 028 (site 002)


title: sample A2364 of patient 007 (site 004)


title: sample A2362 of patient 021 (site 004) (replicate)


title: sample A2266 of patient 048 (site 002)


title: sample A2491 of patient 050 (site 002) (replicate)


title: sample A2485 of patient 012 (site 002)


title: sample A2357 of patient 057 (site 002)


title: sample A2339 of patient 003 (site 001) (replicate)


title: sample A2294 of patient 011 (site 004) (replicate)


title: sample A2352 of patient 019 (site 001) (replicate)


title: sample A2296 of patient 043 (site 004)


title: sample A2286 of patient 021 (site 004)


title: sample A2303 of patient 026 (site 002) (replicate)


title: sample A2304 of patient 030 (site 002) (replicate)


title: sample A2336 of patient 006 (site 003)


title: sample A2333 of patient 019 (site 001)


title: sample A2337 of patient 030 (site 004) (replicate)


title: sample A2310 of patient 006 (site 004)


title: sample A2285 of patient 001 (site 004)


title: sample A2245 of patient 008 (site 001)


title: sample A2249 of patient 024 (site 002) (replicate)


title: sample A2244 of patient 007 (site 001)


title: sample A2242 of patient 011 (site 004)


title: sample A2243 of patient 014 (site 002)


title: sample A2288 of patient 030 (site 004)


title: sample A2274 of patient 007 (site 001) (replicate)


title: sample A2282 of patient 008 (site 002)


title: sample A2263 of patient 014 (site 001) (replicate)


title: sample A2313 of patient 014 (site 004) (replicate)


title: sample A2261 of patient 020 (site 004)


title: sample A2283 of patient 055 (site 002)


title: sample A2246 of patient 009 (site 001)


title: sample A2239 of patient 003 (site 001)


title: sample A2256 of patient 014 (site 004)


title: sample A2260 of patient 019 (site 004)


title: sample A2219 of patient 023 (site 001)


title: sample A2229 of patient 031 (site 004)


title: sample A2500 of patient 015 (site 001) (replicate)

tag: s-LP


title: sample A2206 of patient 050 (site 002)


title: sample A2201 of patient 026 (site 002)


title: sample A2205 of patient 030 (site 002)


title: sample A2351 of patient 065 (site 002) (replicate)


title: sample A2203 of patient 006 (site 002)


title: sample A2350 of patient 064 (site 002) (replicate)


title: sample A2194 of patient 025 (site 001)


title: sample A2326 of patient 071 (site 002)


title: sample A2373 of patient 003 (site 002) (replicate)

tag: Tol-DF


title: sample A2284 of patient 064 (site 002)


title: sample A2520 of patient 010 (site 004) (replicate)


title: sample A2381 of patient 069 (site 002)


title: sample A2517 of patient 039 (site 004)


title: sample A2275 of patient 015 (site 001)


title: sample A2213 of patient 014 (site 001)


title: sample A2257 of patient 016 (site 004)


title: sample A2305 of patient 065 (site 002)


title: sample A2215 of patient 004 (site 002)


title: sample A2386 of patient 037 (site 001)


title: sample A2511 of patient 005 (site 001)


title: sample A2240 of patient 004 (site 001)


title: sample A3014 of patient 005 (site 001) (replicate)


title: sample A3018 of patient 002 (site 002) (replicate)


title: sample A2502 of patient 015 (site 004)


title: sample A2210 of patient 024 (site 002)


title: sample A2327 of patient 072 (site 002)


title: sample A2388 of patient 039 (site 001)


title: sample A2207 of patient 038 (site 004)


title: sample A2328 of patient 075 (site 002)


title: sample A2359 of patient 067 (site 002)


title: sample A2365 of patient 006 (site 001) (replicate)


title: sample A2342 of patient 016 (site 001)


title: sample A2345 of patient 033 (site 004) (replicate)


title: sample A2302 of patient 001 (site 002) (replicate)


title: sample A2356 of patient 016 (site 001) (replicate)


title: sample A2307 of patient 002 (site 004)


title: sample A2332 of patient 034 (site 001)


title: sample A2295 of patient 033 (site 004)


title: sample A2281 of patient 002 (site 002) (replicate)


title: sample A2290 of patient 036 (site 001)


title: sample of patient EU3.049 (replicate)

description: RNA was extracted using the PAXgene Blood RNA Kit (QIAgen)

tag: IOT


title: sample A2273 of patient 006 (site 001)


title: sample of patient EU3.035 (replicate)


title: sample of patient EU3.049


title: sample A2279 of patient 033 (site 001)


title: sample A2277 of patient 017 (site 001)


title: sample of patient EU3.035


title: sample A2368 of patient 010 (site 004)


title: sample A2363 of patient 005 (site 003)


title: sample A2247 of patient 010 (site 001)


title: sample A2198 of patient 002 (site 002)


title: sample A2204 of patient 003 (site 002)


title: sample A2221 of patient 059 (site 002)


title: sample of patient EU3.017


title: sample of patient EU3.043


title: sample A2248 of patient 001 (site 002)


title: sample of patient EU3.020


title: sample of patient EU3.015a


title: sample of patient EU3.025


title: sample of patient EU3.010 (replicate)


title: sample of patient EU3.011


title: sample of patient EU3.010


title: sample of patient EU3.011 (replicate)


title: sample of patient EU3.007


title: sample of patient EU3.009 (replicate)


title: sample of patient EU3.074


title: sample of patient EU3.012a


title: sample of patient EU3.073


title: sample of patient EU3.013


title: sample of patient EU3.018


title: sample of patient EU3.016


title: sample of patient EU3.016 (replicate)


title: sample of patient EU3.023a


title: sample of patient EU3.027


title: sample of patient EU3.009


title: sample of patient EU3.027 (replicate)


title: sample of patient EU3.051


title: sample of patient EU3.037D


title: sample of patient EU3.029Da


title: sample of patient EU3.038D


title: sample of patient EU3.008


title: sample of patient EU3.045


title: sample of patient EU3.047


title: sample of patient EU1.003


title: sample of patient EU1.002


title: sample of patient EU3.051 (replicate)


title: sample of patient EU1.001


title: sample of patient EU3.066


title: sample of patient EU3.055


title: sample of patient EU3.060


title: sample of patient EU3.063


title: sample of patient EU3.052 (replicate)


title: sample of patient EU3.070


title: sample of patient EU3.075


title: sample of patient EU3.076


title: sample of patient EU3.071

tag: s-nCNI


title: sample of patient EU3.014


title: sample of patient EU3.030a


title: sample of patient EU3.068


title: sample of patient EU3.052


title: sample of patient EU3.031


title: sample of patient EU3.069


title: sample of patient EU3.059


title: sample of patient EU3.053


title: sample of patient EU3.061


title: sample of patient EU3.064


title: sample of patient EU3.064 (replicate)


title: sample of patient EU3.001


title: sample of patient EU3.054 (replicate)


title: sample of patient EU3.028


title: sample of patient EU3.026


title: sample of patient EU3.058


title: sample of patient EU3.054


title: sample of patient EU3.042 (replicate)


title: sample of patient EU3.050


title: sample of patient EU3.042


title: sample of patient EU3.041


title: sample of patient EU3.039 (replicate)


title: sample of patient EU3.041 (replicate)


title: sample of patient EU3.056


title: sample of patient EU3.038


title: sample of patient EU3.040


title: sample of patient EU3.039


title: sample of patient EU3.038 (replicate)


title: sample of patient EU3.037


title: sample of patient EU3.036


title: sample of patient EU3.034


title: sample of patient EU3.033


title: sample of patient EU3.032


title: sample of patient EU3.029


title: sample of patient EU3.024


title: sample of patient EU3.029 (replicate)


title: sample of patient EU3.022 (replicate)


title: sample of patient EU3.022


title: sample of patient EU3.021 (replicate)


title: sample of patient EU3.021


title: sample of patient EU3.006


title: sample of patient EU3.019


title: sample of patient EU3.006 (replicate)


title: sample of patient EU3.004


title: sample of patient EU3.003


title: sample of patient EU3.005 (replicate)


title: sample of patient EU3.005


title: sample of patient EU3.002


title: fer-1_oocyte_small_RNA (454)

description: 18-32 nt

data_processing: he barcoded 454 sequence files were first processed with a custom written Perl script to separate into individual sample reads and then to remove the ligated adapter sequences. The processed sequences with length greater than or equal to 18 bp were then subjected to megaBLAST with the following parameters: -D 3 -W 12 -p 70 ( line output format =3,tile window size=12 and identity=70%). Alignments less than 18bp were removed and the reads were then filtered to pick out the alignment with the maximum no of matching bases. The sequences which aligned to more than 10 positions in the genome were filtered.

extract_protocol: For each library, 18-32 nt small RNA was size selected from 50 µg of total RNA.  Small RNA was ligated to the 5' RNA adapter (5' GUU CAG AGU UCU ACA GUC CGA CGA UC 3') using T4 RNA ligase (Ambion) in the presence of RNaseOut (Invitrogen) overnight at 25°C. The ligated RNA was gel purified and ligated to the 3' RNA adapter (5' pUC GUA UGC CGU CUU CUG CUU GidT 3'(p = phosphate; idT = inverted deoxythymidine)) with T4 RNA ligase (Ambion) in the presence of RNaseOut (Invitrogen) overnight at 25°C. The ligated RNA was gel purified and converted to single-stranded cDNA using Superscript III reverse transcriptase (Invitrogen) and Illumina's small RNA RT-Primer (5' CAA GCA GAA GAC GGC ATA CGA 3'). The resulting cDNA was PCR-amplified with Taq DNA Polymerase (Roche) in 20 cycles using 454 fusion small RNA primer set (5' GCCTCCCTCGCGCCATCAGXXXXGTTCAGAGTTCTACAGTCCGA3',5' GCCTTGCCAGCCCGCTCAGXXXXCAAGCAGAAGACGGCATACGA 3' (XXXX: 4nt barcode)). PCR products were gel purified and sequenced on 454 GS FLX.


title: eri-1_young_adult_small_RNA (454)

description: 18-32 nt


title: glp-4_young_adult_small_RNA (454)

description: 18-32 nt


title: N2_young_adult_small_RNA (454)

description: 18-32 nt

source_name: N2 young adult


title: him-8_sperm_small_RNA (454)

description: 18-32 nt


title: sample of patient EU3.004 (replicate)


title: INPUT

status: Public on Mar 02 2010

data_processing: Sequencing reads were quality trimmed after 3 consecutive nucleotides with quality score less than 10. After quality trimming reads at least 18 nucleotides long were mapped against the human reference genome (hg18 assembly, NCBI build 36) using SHRiMP package [11]  with default settings which allows mapping in SOLiD color space corresponding to dinucleotide encoding of the sequenced DNA. For analysis we used only uniquely placed reads, which were defined as reads having at least two additional mismatches in the second best hit compared to the best hit.

extract_protocol: Chromatin was additionally sheared for 6 minutes using Covaris sonicator (6 x 16 mm AFA fiber Tube, duty cycle: 20%, intensity: 5, cycles/burst: 200, frequency sweeping) to obtain suitable shorter fragments (75-125 bp). After fragmentation, fragments were blunt-ended and phosophorylated at the 5'-prime end using the End-it Kit (Epicentre) according to the manufacturer’s instructions. Ligation of double stranded adapters compatible with SOLiD sequencing was performed using Quick ligation kit (New England Biolabs) with 750 mM P1 ds and P2 ds adaptor (Applied Biosystems), 11.7 µl of 2x Quick ligation buffer, 1 µl Quick Ligase (NEB) in total volume of 23.4 µl. Samples were purified using Ampure beads (Agencourt) and run on a native 6% polyacrylamide gel. Fragments ranging from 140 to 180 bp were excised; the piece of gel containing DNA fragments was shredded and dispersed into 400 µl of Platinum PCR Supermix with 750 mM of each P1 and P2 PCR primer, 2,5 U of Pfu (Stratagene) and 5 U Taq (Bioline). Prior to ligation-mediated PCR the sample was incubated at 72O C for 20 minutes in PCR mix to let the DNA diffuse out of the gel and to perform nick translation on non ligated 3'-ends of DNA fragments. After 17 cycles of amplification the library was purified using Ampure beads and was quality checked on 2100 Bioanalyzer (Agilent) for the absence of possible adapter dimers and heterodimers.

tag: cell line

value: HeLa


title: ALG2IP

status: Public on Apr 14 2010

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

institute: University Medical Center Groningen

description: Small RNA sequence data

data_processing: 3' adapter sequences were trimmed and inserts longer than 18 nt were mapped to the C. elegans genome (ce4).

source_name: small RNA from a HA::ALG-2 IP

extract_protocol: Nematode extracts were obtained by freezing about 2 ml of nematodes in IP buffer (10 mM Tris-HCl (pH 7.5), 100 mM KCl, 2 mM MgCl2, 0.05% (v/v) Tween-20, 15% (v/v) glycerol, 5 mM DTT and 1 tablet of complete mini–EDTAfree protease inhibitor cocktail (Roche) per 10 ml buffer) in liquid nitrogen, followed by grinding with mortar and pestle and homogenizing with 20 strokes in a tight fitting dounce. Debris were spun down twice five minutes in a tabletop centrifuge at 10,000 g at 4 C. For RNA immunoprecipitations, HA::ALG-2 were immunoprecipitated from nematode extract by incubation with anti-HA 3F10 affinity matrix (Roche) for 2 h at 4 C. Protein G–agarose (Roche) was used as the "empty-beads" control. After five washes with IP buffer, RNA from RNA-immunoprecipitates were isolated using Trizol LS (Invitrogen) according to the manufacturer's protocol. The small RNA fraction was enriched by excision of the 15 to 30 nt fraction from a polyacrylamide gel. For cDNA synthesis, the RNA molecules in this fraction were first poly A-tailed using poly(A)polymerase followed by ligation of synthetic RNA adapter to the 5' phosphate of the miRNAs. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in 454 sequencing.

tag: strain

tag: antibody


title: RDE1IP

description: Small RNA sequence data

source_name: small RNA from a HA::RDE-1 IP

extract_protocol: Nematode extracts were obtained by freezing about 2 ml of nematodes in IP buffer (10 mM Tris-HCl (pH 7.5), 100 mM KCl, 2 mM MgCl2, 0.05% (v/v) Tween-20, 15% (v/v) glycerol, 5 mM DTT and 1 tablet of complete mini–EDTAfree protease inhibitor cocktail (Roche) per 10 ml buffer) in liquid nitrogen, followed by grinding with mortar and pestle and homogenizing with 20 strokes in a tight fitting dounce. Debris were spun down twice five minutes in a tabletop centrifuge at 10,000 g at 4 C. For RNA immunoprecipitations, HA::RDE-1 were immunoprecipitated from nematode extract by incubation with anti-HA 3F10 affinity matrix (Roche) for 2 h at 4 C. Protein G–agarose (Roche) was used as the "empty-beads" control. After five washes with IP buffer, RNA from RNA-immunoprecipitates were isolated using Trizol LS (Invitrogen) according to the manufacturer's protocol. The small RNA fraction was enriched by excision of the 15 to 30 nt fraction from a polyacrylamide gel.  For cDNA synthesis, the RNA molecules in this fraction were first poly A-tailed using poly(A)polymerase followed by ligation of synthetic RNA adapter to the 5' phosphate of the miRNAs. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in 454 sequencing.


title: RNAi_rep2

status: Public on Apr 27 2010

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Jan09 and Grid: 014850_D_F_20090416) to obtain background corrected and spatially detrended Processed Signal intensities.

label_protocol: Agilent protocol

growth_protocol: Cells were maintained in DMEM supplemented with 10% FCS and grown at 37 ºC in a humidified incubator with 5% CO2. At approxiamtely 90% confluence, cells were passaged 1:10.

extract_protocol: Cells were harvested by trypsinization and RNA was extracted using Qiagen Rneasy kit following manufacturer's instructions.

treatment_protocol: Not applicable.


title: RNAi_rep1


title: 670.20 Segregant (A1)

status: Public on Jan 24 2010

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: 670.20 Segregant (A1)

hyb_protocol: reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-04 Scan Time : 14:44:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

organism: Saccharomyces bayanus

source_name: Reference

extract_protocol:
Extracted molecule : RNA
Extraction method : acid phenol extraction

treatment_protocol: Growth Condition : mixed

tag: species

value: S. bayanus

tag: strain name

value: mixed

source_name: 670.20 Segregant (A1)

treatment_protocol: Growth Condition : 25C YPD, midlog

value: 670.20 Segregant 1

tag: genotype

value: 670.20del:KanMX lys2

tag: sex/mating type

value: MATalpha


title: LMP_rep1


title: ALG1IP

description: Small RNA sequence data

source_name: small RNA from HA::ALG-1 IP

extract_protocol: Nematode extracts were obtained by freezing about 2 ml of nematodes in IP buffer (10 mM Tris-HCl (pH 7.5), 100 mM KCl, 2 mM MgCl2, 0.05% (v/v) Tween-20, 15% (v/v) glycerol, 5 mM DTT and 1 tablet of complete mini–EDTAfree protease inhibitor cocktail (Roche) per 10 ml buffer) in liquid nitrogen, followed by grinding with mortar and pestle and homogenizing with 20 strokes in a tight fitting dounce. Debris were spun down twice five minutes in a tabletop centrifuge at 10,000 g at 4 C. For RNA immunoprecipitations, HA::ALG-1 were immunoprecipitated from nematode extract by incubation with anti-HA 3F10 affinity matrix (Roche) for 2 h at 4 C. Protein G–agarose (Roche) was used as the "empty-beads" control. After five washes with IP buffer, RNA from RNA-immunoprecipitates were isolated using Trizol LS (Invitrogen) according to the manufacturer's protocol. The small RNA fraction was enriched by excision of the 15 to 30 nt fraction from a polyacrylamide gel. For cDNA synthesis, the RNA molecules in this fraction were first poly A-tailed using poly(A)polymerase followed by ligation of synthetic RNA adapter to the 5' phosphate of the miRNAs. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in 454 sequencing.


title: galactose Acy732 175 min

description: galactose Acy732 175 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 11:52:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sb common reference

label_protocol: reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf

source_name: galactose Acy732 175 min

treatment_protocol:
Time : 175 minutes
Growth Condition : 25C YNB + 2% galactose

value: prototroph 670.20del:KanMX


title: 555.11 Segregant 4 (A)

description: 555.11 Segregant 4 (A)

scan_protocol: Pixel Size : 5 Scan Date : 2008-07-23 Scan Time : 13:20:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 555.11 Segregant 4 (A)

value: 555.11 Segregant 4

value: 555.11del:KanMX lys2 his3

value: MATa


title: 670.20 Segregant (B1)

description: 670.20 Segregant (B1)

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-04 Scan Time : 14:53:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 670.20 Segregant (B1)

value: 670.20 Segregant 2


title: 670.20 Segregant (D1)

description: 670.20 Segregant (D1)

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-04 Scan Time : 14:18:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 670.20 Segregant (D1)

value: 670.20 Segregant 4

value: lys2 his3


title: 555.11 Segregant 2 (Alpha)

description: 555.11 Segregant 2 (Alpha)

scan_protocol: Pixel Size : 5 Scan Date : 2008-07-23 Scan Time : 12:38:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 555.11 Segregant 2 (Alpha)

value: 555.11 Segregant 2

value: prototroph


title: 670.20 Segregant (C1)

description: 670.20 Segregant (C1)

scan_protocol: Pixel Size : 5 Scan Date : 2008-08-04 Scan Time : 14:36:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 670.20 Segregant (C1)

value: 670.20 Segregant 3


title: 555.11 Segregant 1 (Alpha)

description: 555.11 Segregant 1 (Alpha)

scan_protocol: Pixel Size : 5 Scan Date : 2008-07-23 Scan Time : 12:54:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 555.11 Segregant 1 (Alpha)

value: 555.11 Segregant 1


title: LMP_rep2

value: HeLa


title: galactose Acy732 90 min

description: galactose Acy732 90 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 11:16:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: S. bayanus

source_name: galactose Acy732 90 min

treatment_protocol:
Time : 90 minutes
Growth Condition : 25C YNB + 2% galactose


title: galactose Acy732 110 min

description: galactose Acy732 110 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-12-19 Scan Time : 12:00:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: mixed

source_name: galactose Acy732 110 min

treatment_protocol:
Time : 110 minutes
Growth Condition : 25C YNB + 2% galactose


title: 555.11 Segregant 3 (A)

description: 555.11 Segregant 3 (A)

scan_protocol: Pixel Size : 5 Scan Date : 2008-07-23 Scan Time : 13:37:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 555.11 Segregant 3 (A)

value: 555.11 Segregant 3


title: BB11 Phosphate(bad)-lim-30c

description: norm same with Sb only

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-18 Scan Time : 12:46:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol: Growth Condition : 30C phosphate-limited, low potassium chemostat

source_name: Amy's mixed BB11 RNA


title: BB11 high potassium(DH)-lim-25c

description: norm same with Sb only

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-18 Scan Time : 13:24:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : 25C high potassium chemostat


title: sucrose 15 mins

description: sucrose 15 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 10:58:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sucrose 15 mins

treatment_protocol:
Time : 15 minutes
Growth Condition : 25C YNB + 2% sucrose


title: BB11 Glucose-lim-30c

description: BB11 Glucose-lim-30c

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-18 Scan Time : 12:29:56 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : 30C glucose-limited chemostat


title: 48hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 460 Pixel Size : 5 Laser on time : 27953 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 31.09 Scan Time : 13:50:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.25
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: time points mixture

treatment_protocol: Growth Condition : mixed timepoints

source_name: 48hrs in sporulation media

treatment_protocol:
Time : 48 hours
Growth Condition : 25C SPO++

value: MATa/alpha


title: BB11 low potassium(DH)-lim-25c

description: BB11 low potassium(DH)-lim-25c

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-18 Scan Time : 13:14:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : 25C low potassium chemostat


title: BB11 Phosphate-25c

description: BB11 Phosphate-25c

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-18 Scan Time : 12:38:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : 25C phosphate-limited chemostat


title: 46.5hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 539 Pixel Size : 5 Laser on time : 27933 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 31.12 Scan Time : 13:31:00 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 46.5hrs in sporulation media

treatment_protocol:
Time : 46.5 hours
Growth Condition : 25C SPO++


title: BB11 Glucose-lim-25c

description: BB11 Glucose-lim-25c

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-18 Scan Time : 13:33:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : 25C glucose-limited chemostat


title: sucrose 210 mins

description: sucrose 210 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 11:34:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sucrose 210 mins

treatment_protocol:
Time : 210 minutes
Growth Condition : 25C YNB + 2% sucrose

value: MATalpha


title: sucrose 60 mins

description: sucrose 60 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 11:16:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sb common reference

source_name: sucrose 60 mins

treatment_protocol:
Time : 60 minutes
Growth Condition : 25C YNB + 2% sucrose


title: BB11 Sulfur-lim-30c Vs RNA 5/13

description: not originally labeled a flip

scan_protocol: Pixel Size : 5 Scan Date : 2008-05-13 Scan Time : 09:29:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : 30C sulfur-limited chemostat

source_name: bb11 mixed reference

treatment_protocol: Growth Condition : mixed


title: glycerol 210 min

description: glycerol 210 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 12:19:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: glycerol 210 min

treatment_protocol:
Time : 210 minutes
Growth Condition : 25C YNB + 2% glycerol


title: 39hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 562 Pixel Size : 5 Laser on time : 27847 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 30.39 Scan Time : 12:04:29 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 39hrs in sporulation media

treatment_protocol:
Time : 39 hours
Growth Condition : 25C SPO++


title: glycerol 90 min

description: glycerol 90 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 12:10:25 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: glycerol 90 min

treatment_protocol:
Time : 90 minutes
Growth Condition : 25C YNB + 2% glycerol


title: galactose 210 mins

description: galactose 210 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-11 Scan Time : 11:39:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose 210 mins

treatment_protocol:
Time : 210 minutes
Growth Condition : 25C YNB + 2% galactose


title: glycerol 60 min

description: glycerol 60 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 12:02:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: glycerol 60 min

treatment_protocol:
Time : 60 minutes
Growth Condition : 25C YNB + 2% glycerol


title: 30.5hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 531 Pixel Size : 5 Laser on time : 27901 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 30.81 Scan Time : 12:58:25 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 30.5hrs in sporulation media

treatment_protocol:
Time : 30.5 hours
Growth Condition : 25C SPO++


title: 35hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 557 Pixel Size : 5 Laser on time : 27870 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 30.51 Scan Time : 12:28:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 35hrs in sporulation media

treatment_protocol:
Time : 35 hours
Growth Condition : 25C SPO++


title: galactose 15 mins

description: galactose 15 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-11 Scan Time : 11:12:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose 15 mins

treatment_protocol:
Time : 15 minutes
Growth Condition : 25C YNB + 2% galactose


title: galactose 60 mins

description: galactose 60 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-11 Scan Time : 11:21:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose 60 mins

treatment_protocol:
Time : 60 minutes
Growth Condition : 25C YNB + 2% galactose


title: 26.5hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 511 Pixel Size : 5 Laser on time : 27821 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 29.93 Scan Time : 11:38:37 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: time point mixture

treatment_protocol: Growth Condition : mixed timepoints

source_name: 26.5hrs in sporulation media

treatment_protocol:
Time : 26.5 hours
Growth Condition : 25C SPO++


title: sucrose 0 min

description: sucrose 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 10:49:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sucrose 0 min

treatment_protocol:
Time : 0 minutes
Growth Condition : 25C YNB + 2% sucrose


title: galactose 90 mins

description: galactose 90 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-11 Scan Time : 11:29:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: galactose 90 mins

treatment_protocol:
Time : 90 minutes
Growth Condition : 25C YNB + 2% galactose


title: 24hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 539 Pixel Size : 5 Laser on time : 27972 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 31.18 Scan Time : 14:10:20 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 24hrs in sporulation media

treatment_protocol:
Time : 24 hours
Growth Condition : 25C SPO++


title: 33hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 611 Pixel Size : 5 Laser on time : 27771 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 29.07 Scan Time : 10:48:38 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: time points mixture

source_name: 33hrs in sporulation media

treatment_protocol:
Time : 33 hours
Growth Condition : 25C SPO++


title: 37hrs time point sporulation of S.b. BB10

scan_protocol: Scan Power : 100 PMT Volts : 628 Pixel Size : 5 Laser on time : 27801 Laser Power : 10.00 Scan Date : 2007-12-21 Scan Temperature : 29.53 Scan Time : 11:18:58 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 37hrs in sporulation media

treatment_protocol:
Time : 37 hours
Growth Condition : 25C SPO++


title: Bleach Exposure (2, .25%, 30 min.)

description: Bleach Exposure (2, .25%, 30 min.)

scan_protocol: Scan Power : 100 PMT Volts : 541 Pixel Size : 5 Laser on time : 21789 Laser Power : 10.00 Scan Date : 2007-12-09 Scan Temperature : 30.36 Scan Time : 17:02:30 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 880, 3280
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Mixed Reference

treatment_protocol: Growth Condition : mixed

source_name: Exposed

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 0.25% Bleach (NaOCl)
Growth Condition : 25C YPD


title: Nickel Exposure (60 min.)

description: Nickel Exposure (60 min.)

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 5 Laser on time : 21004 Laser Power : 10.00 Scan Date : 2007-12-05 Scan Temperature : 28.86 Scan Time : 13:15:00 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 480, 2120
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 60 minutes
Compound Based Treatment : 1.5 mM NiCl2
Growth Condition : 25C YPD


title: galactose 0 min

description: galactose 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-11 Scan Time : 11:02:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: sb common reference

source_name: galactose 0 min

treatment_protocol:
Time : 0 minutes
Growth Condition : 25C YNB + 2% galactose


title: glycerol 15 min

description: glycerol 15 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-04-09 Scan Time : 11:43:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: glycerol 15 min

treatment_protocol:
Time : 15 minutes
Growth Condition : 25C YNB + 2% glycerol


title: Nickel Exposure (5 min.)

description: Nickel Exposure (5 min.)

scan_protocol: Scan Power : 100 PMT Volts : 580 Pixel Size : 5 Laser on time : 21137 Laser Power : 10.00 Scan Date : 2007-12-05 Scan Temperature : 30.75 Scan Time : 15:35:49 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 680, 4000
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 5 minutes
Compound Based Treatment : 1.5 mM NiCl2
Growth Condition : 25C YPD


title: Nickel Exposure (30 min.)

description: Nickel Exposure (30 min.)

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 5 Laser on time : 21101 Laser Power : 10.00 Scan Date : 2007-12-05 Scan Temperature : 30.48 Scan Time : 14:56:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 1.5 mM NiCl2
Growth Condition : 25C YPD


title: Nickel Exposure (0 min.)

description: Nickel Exposure (0 min.)

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 5 Laser on time : 21120 Laser Power : 10.00 Scan Date : 2007-12-05 Scan Temperature : 30.60 Scan Time : 15:18:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 480, 4360
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 1.5 mM NiCl2
Growth Condition : 25C YPD


title: rapamycin 10 mins

description: rapamycin 10 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 10:36:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: reference

source_name: rapamycin 10 mins

treatment_protocol:
Time : 10 minutes
Compound Based Treatment : 100 nM rapamycin
Growth Condition : 25C YPD


title: rapamycin 20 mins

description: rapamycin 20 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 10:55:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: rapamycin 20 mins

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 100 nM rapamycin
Growth Condition : 25C YPD


title: Nickel Exposure (20 min.)

description: Nickel Exposure (20 min.)

scan_protocol: Scan Power : 100 PMT Volts : 501 Pixel Size : 5 Laser on time : 21071 Laser Power : 10.00 Scan Date : 2007-12-05 Scan Temperature : 30.14 Scan Time : 14:25:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 1.5 mM NiCl2
Growth Condition : 25C YPD


title: Lead Exposure (60 min.)

description: Lead Exposure (60 min.)

scan_protocol: Scan Power : 100 PMT Volts : 525 Pixel Size : 5 Laser on time : 23739 Laser Power : 10.00 Scan Date : 2007-12-13 Scan Temperature : 31.18 Scan Time : 15:19:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1680, 4160
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 60 minutes
Compound Based Treatment : 2 mM PbCl2
Growth Condition : 25C YPD


title: rapamycin 0 min

description: rapamycin 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 10:19:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: rapamycin 0 min

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 100 nM rapamycin
Growth Condition : 25C YPD


title: Lead Exposure (30 min.)

description: Lead Exposure (30 min.)

scan_protocol: Scan Power : 100 PMT Volts : 511 Pixel Size : 5 Laser on time : 23017 Laser Power : 10.00 Scan Date : 2007-12-12 Scan Temperature : 31.03 Scan Time : 16:53:30 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1400, 4400
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 2 mM PbCl2
Growth Condition : 25C YPD


title: rapamycin 15 mins

description: rapamycin 15 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 10:46:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: rapamycin 15 mins

treatment_protocol:
Time : 15 minutes
Compound Based Treatment : 100 nM rapamycin
Growth Condition : 25C YPD


title: rapamycin 30 mins

description: rapamycin 30 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 11:03:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: rapamycin 30 mins

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 100 nM rapamycin
Growth Condition : 25C YPD


title: MG-132 30 mins

description: MG-132 30 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 12:05:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: MG-132 30 mins

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 100 uM MG132
Growth Condition : 25C YPD


title: Lead Exposure (20 min.)

description: Lead Exposure (20 min.)

scan_protocol: Scan Power : 100 PMT Volts : 484 Pixel Size : 5 Laser on time : 23758 Laser Power : 10.00 Scan Date : 2007-12-13 Scan Temperature : 31.21 Scan Time : 15:37:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1520, 4880
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol: Growth Condition : mixed

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 2 mM PbCl2
Growth Condition : 25C YPD


title: Bleach Exposure (2, .25%, 60 min.)

description: Bleach Exposure (2, .25%, 60 min.)

scan_protocol: Scan Power : 100 PMT Volts : 515 Pixel Size : 5 Laser on time : 23666 Laser Power : 10.00 Scan Date : 2007-12-13 Scan Temperature : 30.57 Scan Time : 14:06:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1520, 3160
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 60 minutes
Compound Based Treatment : 0.25% Bleach (NaOCl)
Growth Condition : 25C YPD


title: rapamycin 5 mins

description: rapamycin 5 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 10:27:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: rapamycin 5 mins

treatment_protocol:
Time : 5 minutes
Compound Based Treatment : 100 nM rapamycin
Growth Condition : 25C YPD


title: MG-132 20 mins

description: MG-132 20 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 11:57:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: MG-132 20 mins

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 100 uM MG132
Growth Condition : 25C YPD


title: 64hrs time point sporulation of S.b NRRL-Y11845

scan_protocol: Scan Power : 100 PMT Volts : 563 Pixel Size : 5 Laser on time : 17550 Laser Power : 7.72 Scan Date : 2007-10-26 Scan Temperature : 29.96 Scan Time : 12:14:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: asynchronous reference

treatment_protocol: Growth Condition : 25C YPD asynchronous

value: ACY7, prototroph MATa

source_name: 64hrs NRRL

treatment_protocol:
Time : 64 hours
Growth Condition : 25C SPO++


title: Lead Exposure (5 min.)

description: Lead Exposure (5 min.)

scan_protocol: Scan Power : 100 PMT Volts : 525 Pixel Size : 5 Laser on time : 23647 Laser Power : 10.00 Scan Date : 2007-12-13 Scan Temperature : 30.45 Scan Time : 13:47:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1680, 4880
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 5 minutes
Compound Based Treatment : 2 mM PbCl2
Growth Condition : 25C YPD


title: Lead Exposure (10 min.)

description: Lead Exposure (10 min.)

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 5 Laser on time : 22937 Laser Power : 10.00 Scan Date : 2007-12-12 Scan Temperature : 29.99 Scan Time : 15:30:51 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1360, 3960
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 10 minutes
Compound Based Treatment : 2 mM PbCl2
Growth Condition : 25C YPD


title: MG-132 15 mins

description: MG-132 15 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 11:48:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: MG-132 15 mins

treatment_protocol:
Time : 15 minutes
Compound Based Treatment : 100 uM MG132
Growth Condition : 25C YPD


title: MG-132 0 mins

description: MG-132 0 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 11:29:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: MG-132 0 mins

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 100 uM MG132
Growth Condition : 25C YPD


title: Lead Exposure (0 min.)

description: Lead Exposure (0 min.)

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 5 Laser on time : 25668 Laser Power : 10.00 Scan Date : 2007-12-16 Scan Temperature : 30.42 Scan Time : 16:01:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 2880
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

source_name: Mixed Reference

source_name: Exposed

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 2 mM PbCl2
Growth Condition : 25C YPD


title: zeocin 30 mins

description: zeocin 30 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 11:54:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: zeocin 30 mins

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 1 ug/mL zeocin
Growth Condition : 25C YPD


title: 40hrs time point sporulation of S.b NRRL-Y11845

scan_protocol: Scan Power : 100 PMT Volts : 685 Pixel Size : 5 Laser on time : 17672 Laser Power : 7.97 Scan Date : 2007-10-26 Scan Temperature : 30.94 Scan Time : 14:16:18 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 40hrs NRRL

treatment_protocol:
Time : 40 hours
Growth Condition : 25C SPO++


title: zeocin 20 mins

description: zeocin 20 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 11:46:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: reference

source_name: zeocin 20 mins

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 1 ug/mL zeocin
Growth Condition : 25C YPD


title: 24hrs time point sporulation of S.b NRRL-Y11845

scan_protocol: Scan Power : 100 PMT Volts : 606 Pixel Size : 5 Laser on time : 17631 Laser Power : 7.81 Scan Date : 2007-10-26 Scan Temperature : 30.63 Scan Time : 13:34:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 24hrs NRRL

treatment_protocol:
Time : 24 hours
Growth Condition : 25C SPO++


title: MG-132 10 mins

description: MG-132 10 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 11:39:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: MG-132 10 mins

treatment_protocol:
Time : 10 minutes
Compound Based Treatment : 100 uM MG132
Growth Condition : 25C YPD


title: 16hrs time point sporulation of S.b NRRL-Y11845

scan_protocol: Scan Power : 100 PMT Volts : 629 Pixel Size : 5 Laser on time : 17610 Laser Power : 7.78 Scan Date : 2007-10-26 Scan Temperature : 30.51 Scan Time : 13:14:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 16hrs NRRL-Y11845

treatment_protocol:
Time : 16 hours
Growth Condition : 25C SPO++


title: zeocin 15 mins

description: zeocin 15 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 11:37:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol: Growth Condition : mixed

source_name: zeocin 15 mins

treatment_protocol:
Time : 15 minutes
Compound Based Treatment : 1 ug/mL zeocin
Growth Condition : 25C YPD


title: 48hrs time point sporulation of S.b BB11

scan_protocol: Scan Power : 100 PMT Volts : 596 Pixel Size : 5 Laser on time : 17650 Laser Power : 7.93 Scan Date : 2007-10-26 Scan Temperature : 30.78 Scan Time : 13:53:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 48hrs BB11

treatment_protocol:
Time : 48 hours
Growth Condition : 25C SPO++


title: 40hrs time point sporulation of S.b

description: 40hrs time point sporulation of S.b

scan_protocol: Scan Power : 100 PMT Volts : 672 Pixel Size : 5 Laser on time : 17504 Laser Power : 7.67 Scan Date : 2007-10-26 Scan Temperature : 29.35 Scan Time : 11:28:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: zeocin 10 mins

description: zeocin 10 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 11:29:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: zeocin 10 mins

treatment_protocol:
Time : 10 minutes
Compound Based Treatment : 1 ug/mL zeocin
Growth Condition : 25C YPD


title: 16hrs time point sporulation of S.b

description: 16hrs time point sporulation of S.b

scan_protocol: Scan Power : 100 PMT Volts : 603 Pixel Size : 5 Laser on time : 17531 Laser Power : 7.72 Scan Date : 2007-10-26 Scan Temperature : 29.74 Scan Time : 11:54:52 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.2
Datafile type : GenePix Results 3
Image Origin : 0, 0
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol: Growth Condition : 25C YPD asynchronous


title: mms 20 min

description: mms 20 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 10:22:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: mms 20 mins

treatment_protocol:
Time : 20 minutes
Compound Based Treatment : 0.1% MMS
Growth Condition : 25C YPD


title: 64hrs time point sporulation of S.b BB11

scan_protocol: Scan Power : 100 PMT Volts : 627 Pixel Size : 5 Laser on time : 17696 Laser Power : 8.03 Scan Date : 2007-10-26 Scan Temperature : 30.97 Scan Time : 14:40:26 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: asynchronous reference

source_name: 64hrs BB11

treatment_protocol:
Time : 64 hours
Growth Condition : 25C SPO++


title: mms 30 min

description: mms 30 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 10:32:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: mms 30 mins

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 0.1% MMS
Growth Condition : 25C YPD


title: Ammonium Exposure (5 min.)(2)

description: Ammonium Exposure (5 min.)(2)

scan_protocol: Scan Power : 100 PMT Volts : 494 Pixel Size : 5 Laser on time : 23704 Laser Power : 10.00 Scan Date : 2007-12-13 Scan Temperature : 31.21 Scan Time : 14:44:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 880, 4080
Normalization: Channel 2 values were scaled such that the average ratio for each array was set at 1. This scaling factor was calculated using only features from S. bayanus (some arrays also contain S. cerevisiae features that were not used for this project) with >65% of pixels >1 standard deviations above background in both channels.

treatment_protocol:
Time : 5 minutes
Compound Based Treatment : 0.5 M NH4Cl
Growth Condition : 25C YPD


title: zeocin 5 mins

description: zeocin 5 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 11:21:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: zeocin 5 mins

treatment_protocol:
Time : 5 minutes
Compound Based Treatment : 1 ug/mL zeocin
Growth Condition : 25C YPD


title: zeocin 0 mins

description: zeocin 0 mins

scan_protocol: Pixel Size : 5 Scan Date : 2008-02-29 Scan Time : 11:12:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: zeocin 0 mins

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 1 ug/mL zeocin
Growth Condition : 25C YPD


title: 24hrs time point sporulation of S.b

description: 24hrs time point sporulation of S.b

scan_protocol: Scan Power : 100 PMT Volts : 632 Pixel Size : 5 Laser on time : 17570 Laser Power : 7.74 Scan Date : 2007-10-26 Scan Temperature : 30.17 Scan Time : 12:33:46 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: time point cell cycle of S.B -5 300 min

description: time point cell cycle of S.B -5 300 min

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 5 Laser on time : 13941 Laser Power : 5.34 Scan Date : 2007-08-08 Scan Temperature : 29.84 Scan Time : 11:21:14 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 300 mins after alpha-factor release

treatment_protocol:
Compound Based Treatment : pronase after alpha factor arrest
Growth Condition : 25C YPD
Time : 300 minutes


title: mms 15 min

description: mms 15 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 10:13:25 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: mms 15 mins

treatment_protocol:
Time : 15 minutes
Compound Based Treatment : 0.1% MMS
Growth Condition : 25C YPD


title: time point cell cycle of S.B -4 290 min

description: time point cell cycle of S.B -4 290 min

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 5 Laser on time : 13914 Laser Power : 5.34 Scan Date : 2007-08-08 Scan Temperature : 29.47 Scan Time : 10:54:32 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 290 mins after alpha-factor release

treatment_protocol:
Compound Based Treatment : pronase after alpha factor arrest
Growth Condition : 25C YPD
Time : 290 minutes


title: time point cell cycle of S.B -3 280 min

description: time point cell cycle of S.B -3 280 min

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 5 Laser on time : 13895 Laser Power : 5.32 Scan Date : 2007-08-08 Scan Temperature : 29.07 Scan Time : 10:35:50 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [116465] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 280 mins after alpha-factor release

treatment_protocol:
Compound Based Treatment : pronase after alpha factor arrest
Growth Condition : 25C YPD
Time : 280 minutes


title: mms 0 min

description: mms 0 min

scan_protocol: Pixel Size : 5 Scan Date : 2008-03-06 Scan Time : 09:47:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: reference

source_name: mms 0 mins

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 0.1% MMS
Growth Condition : 25C YPD