title: 10-day seedling of Columbia wild type (rep1)

label_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

value: Columbia wild type


title: 10-day seedling of Columbia wild type (rep2)

status: Public on Feb 14 2012

type: RNA

city: Saskatoon

first: Ed

last: Tsang

address: 110 Gymnasium Place

department: Plant Bioinformatics Institute

country: Canada

institute: National Research Council of Canada

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

scan_protocol: scanned at 5 μm resolution using a GenePix 4000B microarray scanner

data_processing: Quantile normalization was performed in all replicate arrays, and RMA (Robust Multichip Average) analysis was performed to generate gene expression values

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol: Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions.

tag: age

value: 10 day

tag: tissue

value: seedling

tag: cultivar


title: 10-day seedling of Columbia wild type (rep3)


title: Tumor ID 23

status: Public on Feb 16 2012

type: genomic

city: New York

first: FANG

last: FANG

state: NY

address: 1275 York Avenue

department: The Human Oncology and Pathogenesis Program

country: USA

institute: Memorial Sloan-Kettering Cancer Center

description: mskcc bank number s3

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: data was normalized and analyzed using partek software and R packages. Specifically centered logit transformation was used for data normalization.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: glioma

label_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

extract_protocol: The genomic DNA was extracted from snap-frozen sections from the breast cancer patients by using a DNeasy Tissue kit (Qiagen)

tag: tissue type

value: frozen tissue for primary tumor

tag: cell type

value: glioma

tag: status

value: CIMP-


title: Tumor ID 1

description: mskcc bank number s7


title: 7-day seedling of sahh1 mutant (rep2)

value: 7 day

value: sahh1 mutant


title: 7-day seedling of sahh1 mutant (rep3)


title: 10-day seedling of sahh1 mutant (rep3)


title: Tumor ID 19

description: mskcc bank number s6


title: 7-day seedling of sahh1 mutant (rep4)


title: 7-day seedling of sahh1 mutant (rep1)


title: 10-day seedling of sahh1 mutant (rep1)


title: 7-day seedling of Columbia wild type (rep2)


title: Tumor ID 6

description: mskcc bank number s11


title: 7-day seedling of Columbia wild type (rep3)


title: 7-day seedling of Columbia wild type (rep4)


title: 10-day seedling of sahh1 mutant (rep4)


title: Tumor ID 21

description: mskcc bank number s1

value: CIMP+


title: 4-day seedling of Columbia wild type (rep2)

value: 4 day


title: 4-day seedling of sahh1 mutant (rep4)


title: 4-day seedling of Columbia wild type (rep4)


title: 7-day seedling of Columbia wild type (rep1)


title: 4-day seedling of sahh1 mutant (rep3)


title: 1 day seedling of sahh1 mutant (rep1)

value: 1 day


title: 4-day seedling of Columbia wild type (rep1)


title: 4-day seedling of sahh1 mutant (rep2)


title: 4-day seedling of Columbia wild type (rep3)


title: 4-day seedling of sahh1 mutant (rep1)


title: 1 day seedling of Columbia wild type (rep2)


title: 1 day seedling of sahh1 mutant (rep3)


title: 1 day seedling of sahh1 mutant (rep4)


title: 10-day seedling of Columbia wild type (rep4)


title: 1 day seedling of Columbia wild type


title: 1 day seedling of sahh1 mutant (rep2)


title: 1 day seedling of Columbia wild type (rep3)


title: Diseased individual (ulcerative colitis) of twinpair #10

status: Public on Jan 18 2012

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description:
corresponds to sample UC8 in table 1
Gene expression data from whole biopsies, primary mucosal tissue

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 2.0 Plus Array (Affymetrix GeneChipHybridization Oven 640). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using GCRMA (R Bioconductor, gcrma package).

label: biotin

source_name: primary mucosal tissue,  colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: RNA extracted using RNEasy (Qiagen) according to the manufacturers guidelines

tag: twin pair

tag: individual

value: diseased

value: colon, mucosal tissue

tag: mean age

value: 31.5 years old


title: Diseased individual (ulcerative colitis) of twinpair #12

description:
corresponds to sample UC9 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Diseased individual (ulcerative colitis) of twinpair #7

description:
corresponds to sample UC5 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: 1 day seedling of Columbia wild type (rep4)


title: Diseased individual (ulcerative colitis) of twinpair #8

description:
corresponds to sample UC6 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Diseased individual (ulcerative colitis) of twinpair #4

description:
corresponds to sample UC3 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Healthy individual of twinpair #10

description:
corresponds to sample Hu8 in table 1
Gene expression data from whole biopsies, primary mucosal tissue

value: healthy


title: Healthy individual of twinpair #7

description:
corresponds to sample Hu5 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Healthy individual of twinpair #1

description:
corresponds to sample Hu1 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: NGP neuroblastoma cell transfected with INHBA, biological rep 7

status: Public on Dec 29 2011

first: Dimitris

last: Anastassiou

address: 1328 S. W. Mudd Building, MC 4712

institute: Columbia University

description: Gene expression profile of peritumoral mouse stromal cells adjacent to NGP neuroblastoma tumor transfected with INHBA

hyb_protocol: 15E-6 g of biotinylated cRNA were hybridized to HG-U133A 2.0 gene chip.

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: The CEL files were normalized and summarized into probe-set values using RMA normalization.

organism: Mus musculus

source_name: NGP neuroblastoma cells containing FUW-Luciferase plasmid, co-transfected with INHBA- pReceiver-Lv105

label_protocol: cRNA was labeled and fragmented using Affymetrix GeneChip 3'IVT express kit according to Affymetrix protocol

growth_protocol: An inoculum of 106 NGP-FUW tumor cells expressing either INHBA, FST or control NGP cells suspended in 0.1 mL of phosphate-buffered saline (PBS) were injected to the mouse's left kidney. Mice were sacrificed when estimated tumor weight reached 1.5 g and tumors were collected.

extract_protocol: Total RNA was isolated from tumors by guanidine thiocyanate method using Qiagen miRNeasy mini kit

treatment_protocol: NGP neuroblastoma cells containing FUW-Luciferase plasmid were stably co-transfected with either FST-pReceiver-Lv105 or INHBA- pReceiver-Lv105.

value: peritumoral mouse stromal cells adjacent to NGP neuroblastoma tumor cells

tag: transfection

value: INHBA


title: NGP neuroblastoma cell transfected with INHBA, biological rep 4


title: Diseased individual (ulcerative colitis) of twinpair #1

description:
corresponds to sample UC1 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: NGP neuroblastoma cell transfected with INHBA, biological rep 5


title: Healthy individual of twinpair #9

description:
corresponds to sample Hu7 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Healthy individual of twinpair #8

description:
corresponds to sample Hu6 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Diseased individual (ulcerative colitis) of twinpair #9

description:
corresponds to sample UC7 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Healthy individual of twinpair #4

description:
corresponds to sample Hu3 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: Healthy individual of twinpair #6

description:
corresponds to sample Hu4 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: NGP neuroblastoma cell transfected with INHBA, biological rep 3


title: NGP neuroblastoma transfected with FST, biological rep 5

description: Gene expression profile of peritumoral mouse stromal cells adjacent to NGP neuroblastoma tumor transfected with FST

source_name: NGP neuroblastoma cells containing FUW-Luciferase plasmid, co-transfected with FST-pReceiver-Lv105

value: FST


title: Diseased individual (ulcerative colitis) of twinpair #6

description:
corresponds to sample UC4 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: 252665511343-4

status: Public on Jan 05 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 1650.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile interslide normalization.

source_name: Plasma cell lymphoma

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Chomzynski, total RNA extraction

value: Lymph node

tag: amount in (µg)

tag: origin

value: Plasma cell lymphoma

tag: genotype

tag: strain

value: Black 6

tag: developmental stage

value: Mature B cell

tag: disease

value: Lymphoma

tag: rin number


title: Healthy individual of twinpair #12

description:
corresponds to sample Hu9 in table 1
Gene expression data from whole biopsies, primary mucosal tissue


title: NGP neuroblastoma cell transfected with INHBA, biological rep 1


title: NGP neuroblastoma cell transfected with INHBA, biological rep 2


title: NGP neuroblastoma transfected with FST, biological rep 2


title: NGP neuroblastoma biological control rep 3

description: Gene expression profile of peritumoral mouse stromal cells adjacent to NGP neuroblastoma tumor

source_name: NGP neuroblastoma cells containing FUW-Luciferase plasmid

value: Control


title: NGP neuroblastoma transfected with FST, biological rep 4


title: NGP neuroblastoma biological control rep 2


title: NGP neuroblastoma transfected with FST, biological rep 3


title: NGP neuroblastoma transfected with FST, biological rep 6


description: Gene expression profile of NGP neuroblastoma tumor cells transfected with INHBA

value: NGP neuroblastoma tumor cells


description: Gene expression profile of NGP neuroblastoma tumor cells transfected with FST


title: NGP neuroblastoma cell transfected with INHBA, biological rep 6


title: NGP neuroblastoma biological control rep 4

description: Gene expression profile of NGP neuroblastoma tumor cells


title: NGP neuroblastoma transfected with FST, biological rep 1


title: NGP neuroblastoma cell transfected with INHBA, biological rep 7


title: NGP neuroblastoma biological control rep 1


title: NGP neuroblastoma biological control rep 5


title: P. pacificus : Dauer-Exit (12hrs) vs Mix-Stage, Biological replicate 3

status: Public on Sep 03 2011

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 3 of 3.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent P. pacificus oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the “normexp” method (Ritchie et al., 2007). The arrays were lowess normalized individually (“normalizeWithinArrays option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Pristionchus pacificus

source_name: P. pacificus dauer-exit-12hours

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Mixed stage worms were grown on 10 cm NGM plates seeded with 10-15 young adults, and harvested on day 5 for RNA extraction. Dauer larvae were grown in liquid culture in S-medium at 22 C and were harvested on day 12. For dauer-exit time-course, about 200 purified dauers were seeded onto 10cm NGM plates spotted with 2ml of OP50 and allowed to recover at 20C. These worms were washed off at the 12hour time-point and used for RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

source_name: P. pacificus mix-stage

value: mix-stage


title: P. pacificus : Dauer-Exit (12hrs) vs Mix-Stage, Biological replicate 2

description: Biological replicate 2 of 3.


title: AL Chip#24

status: Public on Oct 13 2011

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: 24_HGU133 plus 2.0_Irma_030310.CEL

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: AL

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

value: skin

value: Patient P10

tag: condition

value: AL

tag: eczema severity


title: ANL Chip#23

description: 23_HGU133 plus 2.0_Irma_030310.CEL

source_name: ANL

label_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

tag: tissue

value: ANL


title: P. pacificus : Dauers vs Mix-Stage, Biological replicate 4

description: Biological replicate 4 of 4.

source_name: P. pacificus dauers

value: dauers


title: trigeminal nerve BDIV male

status: Public on Jul 01 2011

city: Essen

first: Andrea

last: Kindler-Röhrborn

address: Hufeland Str. 55

department: Patholpgy & Neuropathology

institute: University of Essen

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation with BeadStudio 3.0

organism: Rattus norvegicus

source_name: trigeminal nerve BDIV male

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

extract_protocol: RNA was extracted with Trizol reagent according to the manufacturers instructions. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: BDIV

tag: gender

value: male

tag: age

value: 85 days

tag: treatment

value: untreated

value: trigeminal nerve


title: P. pacificus : Dauers vs Mix-Stage, Biological replicate 2

description: Biological replicate 2 of 4.


title: P. pacificus : Dauer-Exit (12hrs) vs Mix-Stage, Biological replicate 1

description: Biological replicate 1 of 3.


title: P. pacificus : Dauers vs Mix-Stage, Biological replicate 1

description: Biological replicate 1 of 4.


title: trigeminal nerve BDIX female

source_name: trigeminal nerve BDIX female

value: BDIX

value: female


title: D2-Gpnmb+ control rep7 (OHN)

status: Public on Apr 15 2011

city: Mount Desert

first: Gareth

middle: Rhys

last: Howell

address: 600 Main Street

institute: The Jackson Laboratory

description: ONH R113441

hyb_protocol: Hybridization and post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChipTM  Scanner 3000 laser confocal slide scanner

data_processing: The images were quantified using GeneChipTM Operating Software (GCOS) v1.2.  Probe level data were imported into the R statistical software environment (http://www.r-project.org) and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package

source_name: ONH no glaucoma

label_protocol: Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA). 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA).

growth_protocol: All mice were housed in a 14 h light to 10 h dark cycle

extract_protocol: For tissue harvesting, mice were anesthetized and the left eye was dissected free, and the cornea and lens removed. The optic nerve was cut close to the back of the eye. The optic nerve head was excised using a sharpened 1mm glass capillary centered over the optic nerve and immediately placed in RNAlater® (Qiagen). A small portion of central retina as well as a small portion of choroid and sclera are included in this tissue. This tissue is substantially enriched for the glial lamina. The retina (containing no optic nerve head) was then dissected free from the back of the eye and placed in a separate vial containing RNAlater (Ambion, Austin TX) and stored at 4oC until required. The process was repeated for the right eye. Dissection of each eye was completed in ≤5 minutes (10 minutes per mouse)

tag: glaucoma

value: control

tag: phenotype

value: no glaucoma

tag: radiation

value: No radiation treatment

value: Female

tag: age (mos)


title: D2-Gpnmb+ control rep8 (OHN)

description: ONH L113442

value: optic nerve head

value: 10.5 months


title: P. pacificus : Dauers vs Mix-Stage, Biological replicate 3

description: Biological replicate 3 of 4.

value: mix-stage


title: trigeminal nerve BDIV female

source_name: trigeminal nerve BDIV female


title: trigeminal nerve BDIX.BDIV-Mss4a male

source_name: trigeminal nerve BDIX.BDIV-Mss4a male


title: D2-Gpnmb+ control rep5 (OHN)

description: ONH R113417


title: D2-Gpnmb+ control rep10 (OHN)

description: ONH L113446


title: D2-Gpnmb+ control rep9 (OHN)

description: ONH R113445


title: D2-Gpnmb+ control rep2 (OHN)

description: ONH L113415


title: D2-Gpnmb+ control rep4 (OHN)

description: ONH L113417


title: 201B7 iPSC

status: Public on Sep 10 2011

city: Tokyo

first: Takuya

last: Yagi

address: 35-Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University

hyb_protocol: Following fragmentation, all arrays were hybridized at 45C for 16 hr.

scan_protocol: GeneChips were scanned using an AFX GC3000 G7 scanner.

data_processing: The gene expression raw data were extracted using the AFFX Gene Chip Operation System. Quality control was performed on the basis of Affymetrix quality control metrics. The data were analyzed with the Gene Spring GX 11.0 (Agilent).

source_name: undifferentiated 201B7 iPSC

label_protocol: Approximately 150 ng of RNA from each sample was labeled using GeneChip 3’IVT Express (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: iPSC were cultured in hES medium containing bFGF.

extract_protocol: Total RNA samples were isolated using RNeasy kit.

treatment_protocol: Cells were washed with PBS and Rneasy kit was used to isolate total RNA.

tag: cell line

value: 201B7 iPSC

tag: cell type

value: iPSC cell line


title: trigeminal nerve BDIX.BDIV-Mss4a female

source_name: trigeminal nerve BDIX.BDIV-Mss4a female


title: D2-Gpnmb+ control rep6 (OHN)

description: ONH L113441

tag: strain


title: trigeminal nerve BDIX male

source_name: trigeminal nerve BDIX male


title: D2-Gpnmb+ control rep1 (OHN)

description: ONH R113413


title: D2-Gpnmb+ control rep3 (OHN)

description: ONH R113415


title: SDQ3891_LEM2_SP646_MXEMB extraction1_array1 channel_1

status: Public on Mar 09 2011

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: SDQ3891 LEM2;target name: LEM-2;host: Rabbit;antigen: MVDVEKMSDA ELRAELNVRG ANVGPVTGTT RSLYEKKLKK LLSGGAKTPA RPTVAKPAPK PTPKSAPAPK SPKSPPARRS IPRAAATAAN STINSTFNRS ; clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3891 LEM2;short description: Rabbit antisera against the amino-terminal 100 amino acids of LEM-2 produced at SDI.;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User?s Guide.

data_processing: ChIP-chip normalization standard MA2C:JL:2 protocol. ChIP-chip_normalization_standard_MA2C_v2. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means that the INPUT or IP values for any probes which have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In a single experiment, median within the sliding window defined by 2x bandwidth parameter is assigned as MA2C score at the center of each probe. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by 2x bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190

label: Cy3 dye

organism: Caenorhabditis elegans

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vKI3. Antibody was incubated with protein A/G beads at 4 oC for at least 1 hr and then washed by extraction buffer. For each reaction, 0.5-2 mg of protein extract was taken and sarkosyl was added to 1% final concentration. Before immunoprecipitation, 10% of extract was taken. The extract was mixed with the antibody-beads complex and incubated overnight at 4C. After washing beads, immune complexes were eluted from beads twice with 150uL elution buffer (1% SDS in TE with 250 mM NaCl) for 15minutes at 65C. Samples were treated with RNase A at room temperature for ? 1 hr then proteinase K at 55C for ? 1 hr. Samples were transferred to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/
Worm_LM-PCR_Amplification_for_ChIP-chip_vKI3. DNA was incubated with End Repair Enzyme mix (Epicentre, Madison) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends. The DNA fragments were ligated with T-over-hanged linker and then amplified by PCR with the longer linker oligonucleotide as a primer.

tag: developmental stage

value: Mixed Embryo

tag: genotype

tag: Sex

value: mixed Male and Hermaphrodite population

label: Cy5 dye

tag: Strain

tag: Developmental Stage

tag: Genotype


title: JL00006_ZFP1_RB774_MXEMB extraction1_array1 channel_1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: JL00006 ZFP1;target name: ZFP-1;host: Rabbit;antigen: ISQNGTSSTS QSNRLNLPSF MEQLLERQWD QGSSLLMANA HFDVAQLLSC LFQLKSENFR LEENLSGLRK RRDHLFALNS RLAEVNTLDV SKRQRSDGLL LQQQIAHHLD PTSIVPKAEV HKQEPLSAPT SVPLPANHSS SLFEDIKAPK ATYSRKTPSN IPLTVPLSTA ATALTTTTAA SSGAPVNSNI QNHRATPSTA GAPMAATPIM TAVTSANELA ALSPERAQAL LNMYRMPLDA NVAAQLSMIT NFPGQVNPSL FSRLLAVNMM NGGLQPNGQP LSALPPPTSA TPNGK; clonal: Polyclonal;purified: Affinity;company: Covance;catalog: Jason Lieb lab;short description: A rabbit polyclonal antibody raised against amino acids 573-867 of AAK26137/WP:CE25003/F54F2.2a. Antibody was affinity purified against the same region of ZFP-1 as used for immunization.;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

growth_protocol: Worm_embryo_growth_and_harvest_v3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_vMBJ5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody (10 ug) was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 25 ul packed volume of protein A sepharose (GE Healthcare), and washed with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9. Amplification was carried out using 25-30 cycles.

value: wild type


title: No or early 2 rep10 (OHN)

description: ONH L120252

source_name: ONH no or early glaucoma

value: glaucoma

value: no or early glaucoma


title: No or early 2 rep4 (OHN)

description: ONH R113655

tag: tissue


title: No or early 2 rep7 (OHN)

description: ONH L115862

tag: gender


title: No or early 1 rep5 (OHN)

description: ONH L115831


title: No or early 1 rep2 (OHN)

description: ONH R112847


title: delta-gng1_cellulose_DD_rep2

status: Public on Mar 02 2011

city: Vienna

first: Doris

last: Tisch

state: Vienna

address: Gumpendorferstraße 1a

department: Chemical Engineering

country: Austria

institute: Technical University of Vienna

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichoderma reesei

source_name: T. reesei grown on cellulose in darkness

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

growth_protocol: Trichoderma reesei strains QM9414 (ATCC 26921) and the phlp1, gnb1 and gng1 deleted strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1 % microcrystalline cellulose as carbon source in constant light (LL) or constant darkness (DD) for 72 hours.

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with RevertAid-H- First Strand cDNA Synthesis Kit (Fermentas) and Random Hexamer Primer.

treatment_protocol: Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.

tag: background strain

tag: genotype/variation

value: delta-gng1, reduced growth rate

tag: condition

value: darkness


title: No or early 2 rep1 (OHN)

description: ONH L112848

tag: glaucoma

tag: phenotype


title: delta-gng1_cellulose_LL_rep2

source_name: T. reesei grown on cellulose in light

value: light


title: delta-gng1_cellulose_DD_rep1


title: No or early 2 rep9 (OHN)

description: ONH L120227

tag: radiation

tag: age (mos)


title: No or early 1 rep8 (OHN)

description: ONH L120253


title: No or early 2 rep3 (OHN)

description: ONH L113655


title: No or early 2 rep5 (OHN)

description: ONH R115825


title: No or early 2 rep6 (OHN)

description: ONH L115836


title: delta-gnb1_cellulose_DD_rep2

value: delta-gnb1, reduced growth rate


title: No or early 1 rep7 (OHN)

description: ONH L120243


title: No or early 1 rep10 (OHN)

description: ONH L120275


title: No or early 1 rep4 (OHN)

description: ONH L115809


title: delta-gnb1_cellulose_LL_rep2


title: delta-gng1_cellulose_LL_rep1


title: QM9414_cellulose_DD_rep2

description: QM9414_DD_replicate 2

growth_protocol: Trichoderma reesei strain QM9414 (ATCC 26921) was grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1 % microcrystalline cellulose as carbon source in constant light (LL) or constant darkness (DD) for 72 hours.

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Random Hexamer Primer.

value: wildtype


title: delta-gnb1_cellulose_LL_rep1


title: No or early 1 rep1 (OHN)

description: ONH R112840

value: female

tag: age


title: delta-phlp1_cellulose_LL_rep2

value: delta-phlp1, reduced growth rate, responsive to light


title: delta-phlp1_cellulose_DD_rep1


title: delta-gnb1_cellulose_DD_rep1


title: QM9414_cellulose_DD_rep1

description: QM9414_DD_replicate 1


title: No or early 1 rep9 (OHN)

description: ONH L120273

value: No radiation treatment

tag: strain

value: Female


title: delta-phlp1_cellulose_LL_rep1


title: QM9414_cellulose_LL_rep1

description: QM9414_LL_replicate 1


title: No or early 2 rep8 (OHN)

description: ONH R115871

value: optic nerve head

value: 10.5 months


title: No or early 2 rep2 (OHN)

description: ONH L113654


title: delta-phlp1_cellulose_DD_rep2


title: QM9414_cellulose_LL_rep2

description: QM9414_LL_replicate 2


title: No or early 1 rep3 (OHN)

description: ONH R113656


title: No or early 1 rep6 (OHN)

description: ONH L120231


title: chromium transformed cell line (large colony) #3

status: Public on Sep 14 2010

first: Hong

last: Sun

address: 341 East 25 Street

department: Medicine

institute: NYU School of Medicine

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 1.0 ST Arrays and scanned at the NYU Cancer Institute Genomics Facility.

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

data_processing:
Data analysis was performed using GeneSpring v11 (Agilent Technologies)
HuGene-1_0-st-v1_CORE.mps

source_name: chromated transformed cell line (largel colony)

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: Cell lines were derived from individual colonies grown in soft agar, and then expanded and maitained in monolayer.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). The isolated T.RNA was subjected to a colum purification using Rneasy Plus Micro Kit (Qiagen)

treatment_protocol: Cells were exposed to 0.5 _M potassium chromate for 30 days, followed by 3-week anchorage-independent growth in soft agar.

tag: cell line

tag: cell type

value: chromated transformed cell (large colony)

tag: treatment

value: potassium chromate


title: Stat3Fl/Fl_C

status: Public on Oct 20 2010

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

institute: MFPL

description: Gene expression data from Stat3Fl/Fl (Floxed)  livers

hyb_protocol: According to standard Affymetrix protocol.

data_processing: RMA

source_name: total liver tissue_Stat3Fl/Fl

extract_protocol: Trizol followed by RNeasy Mini kit (Qiagen)

value: liver

tag: genotype

value: 2 weeks


title: chromium transformed cell line (large colony) #2


title: Stat3Δhc Mdr2-/-_B

description: Gene expression data from Stat3Δhc  Mdr2-/- knockout livers

scan_protocol: According to standard Affymetrix protocol.

source_name: total liver tissue_Stat3Fl/FlMdr2-/-

value: Stat3Δhc Mdr2-/-


title: Stat3Fl/FlMdr2-/-_B

description: Gene expression data from Stat3Fl/Fl  Mdr2-/- knockout livers

source_name: total liver tissue_Stat3Dhc Mdr2-/-

label_protocol: According to standard Affymetrix protocol.


title: Stat3Fl/FlMdr2-/-_C


title: Stat3Fl/Fl_B


title: Stat3Fl/Fl_A


title: Stat3Δhc_C

description: Gene expression data from Stat3Δhc  knockout livers

source_name: total liver tissue_Stat3Dhc


title: control cell line #3

source_name: Control cell line

value: Control cell


title: parental Beas-2B cells

source_name: Parental BEAS-2B cells

value: Parental cell


title: Stat3Δhc Mdr2-/-_A


title: control cell line #2


title: Stat3Δhc_A


title: control cell line #1


title: chromium transformed cell line (large colony) #1


title: chromium transformed cell line (small colony) #1

source_name: chromated transformed cell line (small colony)

value: chromated transformed cell (small colony)


title: Stat3Δhc Mdr2-/-_C


title: chromium transformed cell line (small colony) #2


title: chromium transformed cell line (small colony) #3


title: Stat3Δhc_B


title: Stat3Fl/FlMdr2-/-_A


title: H3K9me3_(new_lot).14-16_hr_OR_embryo extraction5_array1

status: Public on Aug 10 2010

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me3 (new lot); target name: H3K9me3; host: Rabbit; antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K9; clonal: Polyclonal; purified: Affinity; company: Abcam; catalog: ab8898; reference: http://www.abcam.com/Histone-H3-tri-methyl-K9-antibody-ChIP-Grade-ab8898.html; short description: rabbit polyclonal to Histone H3 tri methyl K9 ChIP grade;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing:
M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

input: GSM575467_pirrota_835_E_late1_Input_DNA_14cyc.606.CEL

organism: Drosophila melanogaster

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Oregon-R

tag: developmental stage

value: Embryo 14-16hr OR

value: wild type


title: NonDiaVHexane_rep4

status: Public on May 20 2010

city: Gainesville

first: Greg

last: Ragland

state: FL

department: Entomology and Nematology

institute: University of Florida

description:
Biological Replicate 4
Each pool hybed 3 times, each in a separate phenotypic comparison
ED = early diapause
ND = non diapause
LD = late diapause
HEX = heaxane treated

hyb_protocol: 825 ng of Cy 3 labeled and 825ng of Cy 5 labeled aRNA was fragmented and hybridized with rotation at 65°C for 17 hours

scan_protocol: The arrays were washed according to the manufacturer's protocol and then scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Data were extracted using Feature Extraction 9.5 software (Agilent Technologies, Inc.) including correction to internal Agilent control probes. Raw data files are not background corrected and normalized, except for correction to internal Agilent probes.

organism: Sarcophaga crassipalpis

source_name: HEX

label_protocol: cDNA was synthesized from 500 ng of total RNA using the Agilent Low RNA Input Linear Amplification Kit® according to the manufacturer's protocol. cDNA was used as a template for in vitro transcription (IVT) in the presence of T7 RNA Polymerase and cyanine labeled CTP's.  The amplified, labeled aRNA was purified using the Qiagen RNeasy Mini Kit®.

growth_protocol: Breeding adults and larvae reared in short-day conditions (10h light and 14h dark at 25C for adults and 20C for larvae) to induce diapause, producing diapausing pupae. Diapausing pupae sampled at 20 and 50 days to produce early and late diapausers, respectively. An additional pool of late diapausing pupae were treated topically with 5µl of hexane to pharmacologically stimulate diapause termination and were sampled 24h later. The diapause status of individuals in the three diapause groups were confirmed morphologically by a lack of adult developmental landmarks, such as the expansion of the imaginal antennae. Breeding adults and larvae reared in long-day conditions (15h light and 9h dark at 25C for adults and 20C for larvae) to produce direct developing, non-diapause pupae.

extract_protocol: Pools of four individuals each were homogenized in tri-reagent and total RNA was extracted from each individual using the Ambion RiboPure® Kit

tag: pool

source_name: ND


title: LateDiaVHexane_rep1

description:
Biological Replicate 1
Each pool hybed 3 times, each in a separate phenotypic comparison
ED = early diapause
ND = non diapause
LD = late diapause
HEX = heaxane treated

source_name: LD


title: LateDiaVHexane_rep4


title: LateDiaVHexane_rep3

description:
Biological Replicate 3
Each pool hybed 3 times, each in a separate phenotypic comparison
ED = early diapause
ND = non diapause
LD = late diapause
HEX = heaxane treated


title: NonDiaVHexane_rep2

description:
Biological Replicate 2
Each pool hybed 3 times, each in a separate phenotypic comparison
ED = early diapause
ND = non diapause
LD = late diapause
HEX = heaxane treated


title: NonDiaVLateDia_rep1


title: NonDiaVLateDia_rep2


title: EarlyDiaVHexane_rep2

source_name: ED


title: EarlyDiaVHexane_rep3


title: EarlyDiaVHexane_rep1


title: LateDiaVHexane_rep2


title: EarlyDiaVLateDia_rep3


title: NonDiaVLateDia_rep3


title: NonDiaVHexane_rep3


title: EarlyDiaVLateDia_rep4


title: NonDiaVHexane_rep1


title: EarlyDiaVHexane_rep4


title: EarlyDiaVNonDia_rep4


title: NonDiaVLateDia_rep4


title: EarlyDiaVNonDia_rep1


title: EarlyDiaVNonDia_rep2


title: EarlyDiaVNonDia_rep3


title: EarlyDiaVLateDia_rep1


title: EarlyDiaVLateDia_rep2


title: Monocytes

status: Public on Mar 01 2010

city: Belfast

first: Christina

middle: L

last: O'Neill

state: Northern Ireland

address: Centre for Vision & Vascular Science   Institute of Clinical Sciences A Grosvenor Road Royal Victoria Hospital

department: Centre for Vision and Vascular Science

country: United Kingdom

institute: Queens University Belfast

description: Replicate 1

hyb_protocol: Standard Illumina hybridisation protocol

data_processing: Data normalised using lumi package generated on 'R' bioconductor for quantile normalisation

source_name: Human peripheral blood

label_protocol: Standard Illumina labelling procedure

growth_protocol: Monocytes were isolated from PB by incubating MNCs with CD14+ magnetic microbeads. Freshly sorted CD14+ cells were used for total RNA extraction.

extract_protocol: Total RNA was extrcted using RNAqueous kit (Ambion) according to manufacturers kit

tag: tissue

value: Human peripheral blood

value: Freshly sorted CD14+ monocytes


title: OEC peripheral blood C

description: Replicate C

growth_protocol: OECs were isolated from the MNC layer of cord or peripheral blood using Histopaque 1077. Cells were seeded at a density of 1x107 on collagen coated wells and maintained in EGM-2 MEDIUM FOR 14-28 days until small colonies of OECs formed. Cells were expanded in culture and early passage OECs were used for total RNA extraction.

value: early passage OECs


title: OEC peripheral blood B

description: Replicate B


title: HDMECs

description: Replicate 1

source_name: Human dermis

growth_protocol: DMECs were purchased from PromoCell Gmbh (Heidelberg, Germany) as frozen aliquots containing 1-2 x106 cells. Cells were maintained in endothelial cell growth medium MV (PromoCell) containing  5% FCS. Cells at P3 were used for total RNA extraction.

value: Human dermis

value: early passage HDMECs


title: eEPC peripheral blood C

description: Replicate C

growth_protocol: eEPCs were isolated from the mononuclear cell (MNC) layer of cord or peripheral blood by density gradient centrifugation using Histopaque 1077. Cells were seeded at a density of 2x106 on fibronectin coaded 5cm petris and maintained in EGM-2MV medium (Lonza) supplemented with 10% fetal bovine serum for 7 days.

value: 7 day old eEPCs


title: OEC peripheral blood A

description: Replicate A


title: eEPC peripheral blood A

description: Replicate A


title: OEC cord blood

description: Replicate 1

source_name: Human umbilical cord

value: Human umbilical cord


title: eEPC peripheral blood B

description: Replicate B


title: eEPC cord blood

description: Replicate 1


title: Adult Male replicate 1

status: Public on Feb 11 2010

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

description:
Biological replicate 1 of 6 Male Adult
Print batch: 8/8/05

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chamber, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon Genepix 6.0

data_processing: The probes with fluorescence intensities under 50 were filtered out. For each developmental stage, the genes with hybridization intensities above 50 in more than 50% of arrays were used for further analysis. The expression ratios (ratios of the sample to reference fluorescence intensities) were quantile normalized in the statistical environment R 2.8.0 using the affy package (www.rproject.org) and used for the analyses.

organism: Taeniopygia guttata

source_name: Adult Male

label_protocol: 1 ug of aRNA was primed with 3 ul of 100 uM random hexamer primers at 70C for 10 min, then reversed transcribed at 46C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 uM dATP, dCTP, dGTP, 60uM dTTP and 40uM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; 0.5ug total RNA was amplified using Agilent's Low RNA input linear amplification kit

treatment_protocol: Whole telencephalon isolated from an individual bird more than ninety days post-hatch

value: Telencephalon

value: Adult

tag: gender

value: Male

source_name: universal SoNG reference

treatment_protocol: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: telencephalon

value: Male and Female


title: Adult Male replicate 3

description:
Biological replicate 3 of 6 Male Adult
Print batch: 3/28/06


title: Adult Female replicate 4

description:
Biological replicate 4 of 6 Female Adult
Print batch: 8/8/05

source_name: Adult Female

value: Female


title: Adult Male replicate 4

description:
Biological replicate 4 of 6 Male Adult
Print batch: 8/8/05


title: Adult Female replicate 6

description:
Biological replicate 6 of 6 Female Adult
Print batch: 3/28/06


title: Adult Female replicate 2

description:
Biological replicate 2 of 6 Female Adult
Print batch: 3/28/06


title: Day 45 Female replicate 1

description:
Biological replicate 1 of 6 Female Post-hatch Day 45
Print batch: 3/28/06

source_name: Day 45 Female

treatment_protocol: Whole telencephalon isolated from an individual bird forty five days post-hatch

value: Post-hatch Day 45


title: Adult Male replicate 2

description:
Biological replicate 2 of 6 Male Adult
Print batch: 3/28/06


title: Adult Male replicate 5

description:
Biological replicate 5 of 6 Male Adult
Print batch: 8/8/05


title: Day 45 Male replicate 6

description:
Biological replicate 6 of 6 Male Post-hatch Day 45
Print batch: 3/28/06

source_name: Day 45 Male


title: Day 45 Female replicate 5

description:
Biological replicate 5 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Day 45 Female replicate 2

description:
Biological replicate 2 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Day 45 Male replicate 3

description:
Biological replicate 3 of 6 Male Post-hatch Day 45
Print batch: 8/8/05


title: Adult Female replicate 3

description:
Biological replicate 3 of 6 Female Adult
Print batch: 3/28/06


title: Adult Female replicate 1

description:
Biological replicate 1 of 6 Female Adult
Print batch: 3/28/06


title: Day 45 Female replicate 4

description:
Biological replicate 4 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Day 45 Male replicate 1

description:
Biological replicate 1 of 6 Male Post-hatch Day 45
Print batch: 3/28/06


title: Day 45 Male replicate 2

description:
Biological replicate 2 of 6 Male Post-hatch Day 45
Print batch: 3/28/06


title: Day 45 Female replicate 6

description:
Biological replicate 6 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Adult Male replicate 6

description:
Biological replicate 6 of 6 Male Adult
Print batch: 3/28/06


title: Day 45 Male replicate 5

description:
Biological replicate 5 of 6 Male Post-hatch Day 45
Print batch: 3/28/06


title: Day 45 Female replicate 3

description:
Biological replicate 3 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Day 45 Male replicate 4

description:
Biological replicate 4 of 6 Male Post-hatch Day 45
Print batch: 8/8/05


title: Day 25 Male replicate 6

description:
Biological replicate 6 of 6 Male Post-hatch Day 25
Print batch: 3/28/06

source_name: Day 25 Male

treatment_protocol: Whole telencephalon isolated from an individual bird twenty five days post-hatch

value: Post-hatch Day 25


title: Adult Female replicate 5

description:
Biological replicate 5 of 6 Female Adult
Print batch: 8/8/05


title: Day 25 Male replicate 5

description:
Biological replicate 5 of 6 Male Post-hatch Day 25
Print batch: 3/28/06


title: Day 25 Male replicate 3

description:
Biological replicate 3 of 6 Male Post-hatch Day 25
Print batch: 3/28/06


title: Day 25 Male replicate 1

description:
Biological replicate 1 of 6 Male Post-hatch Day 25
Print batch: 8/8/05


title: Day 1 Male replicate 6

description:
Biological replicate 6 of 6 Male Post-hatch Day 1
Print batch: 8/8/05

source_name: Day 1 Male

treatment_protocol: Whole telencephalon isolated from an individual bird one day post-hatch

value: Post-hatch Day 1


title: Day 1 Female replicate 5

description:
Biological replicate 5 of 6 Female Post-hatch Day 1
Print batch: 8/8/05

source_name: Day 1 Female


title: Day 25 Male replicate 4

description:
Biological replicate 4 of 6 Male Post-hatch Day 25
Print batch: 8/8/05


title: Day 1 Male replicate 2

description:
Biological replicate 2 of 6 Male Post-hatch Day 1
Print batch: 3/28/06


title: Day 1 Female replicate 1

description:
Biological replicate 1 of 6 Female Post-hatch Day 1
Print batch: 3/28/06


title: Day 25 Female replicate 3

description:
Biological replicate 3 of 6 Female Post-hatch Day 25
Print batch: 3/28/06

source_name: Day 25 Female


title: Day 1 Male replicate 4

description:
Biological replicate 4 of 6 Male Post-hatch Day 1
Print batch: 8/8/05


title: Day 1 Female replicate 4

description:
Biological replicate 4 of 6 Female Post-hatch Day 1
Print batch: 3/28/06


title: Day 25 Female replicate 6

description:
Biological replicate 6 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Day 1 Male replicate 3

description:
Biological replicate 3 of 6 Male Post-hatch Day 1
Print batch: 3/28/06


title: Day 25 Female replicate 2

description:
Biological replicate 2 of 6 Female Post-hatch Day 25
Print batch: 8/8/05


title: Day 1 Female replicate 2

description:
Biological replicate 2 of 6 Female Post-hatch Day 1
Print batch: 8/8/05


title: Day 25 Female replicate 5

description:
Biological replicate 5 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Day 1 Male replicate 5

description:
Biological replicate 5 of 6 Male Post-hatch Day 1
Print batch: 3/28/06


title: Day 1 Female replicate 3

description:
Biological replicate 3 of 6 Female Post-hatch Day 1
Print batch: 3/28/06


title: Day 25 Female replicate 4

description:
Biological replicate 4 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Day 1 Male replicate 1

description:
Biological replicate 1 of 6 Male Post-hatch Day 1
Print batch: 3/28/06


title: Day 1 Female replicate 6

description:
Biological replicate 6 of 6 Female Post-hatch Day 1
Print batch: 3/28/06


title: Day 25 Female replicate 1

description:
Biological replicate 1 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Spring STI replicate 6

status: Public on Dec 16 2009

description:
Biological replicate 6 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chamber, and incubated O/N at 42ûC. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon GenePix 6.0.

data_processing: Data were background-subtracted and values < 0.5 were set to 0.5. Spots with -100 flags were filtered out before print-tip loess normalization. A scale between-array normalization was performed, then arrays with the reference in the Cy5 channel were inverted by multiplying by -1 to make all log ratios test/reference.

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 46C for 16 h in the presence of 400 U SuperScript III RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; 0.5µg total RNA was amplified using Agilent's Low RNA input linear amplification kit

tag: season

value: male and female

organism: Melospiza melodia

source_name: SE

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the spring (mid to late June, 2005; the breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live caged male song sparrow decoy and recorded male conspecific songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.

value: Spring

value: Simulated Territorial Intrusion

value: diencephalon

value: male


title: Day 25 Male replicate 2

description:
Biological replicate 2 of 6 Male Post-hatch Day 25
Print batch: 8/8/05


title: Spring STI replicate 5

description:
Biological replicate 5 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Spring Control replicate 7

description:
Biological replicate 7 of 7. male song sparrow captured in the spring after a control territorial intrusion by a heterospecific male
print batch: 4/2/2007

source_name: SC

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the spring (mid to late June, 2005; the breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a control territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live  caged male white-crowned sparrow decoy and recorded white-crowned sparrow songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.

value: Control


title: Spring Control replicate 6

description:
Biological replicate 6 of 7. male song sparrow captured in the spring after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Spring STI replicate 8

description:
Biological replicate 8 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 4/2/2007


title: Spring STI replicate 7

description:
Biological replicate 7 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Spring Control replicate 5

description:
Biological replicate 5 of 7. male song sparrow captured in the spring after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Autumn STI replicate 8

description:
Biological replicate 8 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 4/2/2007

source_name: AE

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the autumn (mid November, 2005 to late January, 2006; the non-breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live caged male song sparrow decoy and recorded male conspecific songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.

value: Autumn


title: Autumn STI replicate 7

description:
Biological replicate 7 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Autumn Control replicate 7

description:
Biological replicate 7 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006

source_name: AC

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the autumn (mid November, 2005 to late January, 2006; the non-breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a control territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live  caged male white-crowned sparrow decoy and recorded white-crowned sparrow songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.


title: Autumn STI replicate 6

description:
Biological replicate 6 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Autumn Control replicate 6

description:
Biological replicate 6 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Spring Control replicate 4

description:
Biological replicate 4 of 7. male song sparrow captured in the spring after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Spring STI replicate 2

description:
Biological replicate 2 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Autumn Control replicate 8

description:
Biological replicate 8 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 4/2/2007


title: Autumn STI replicate 5

description:
Biological replicate 5 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Autumn Control replicate 5

description:
Biological replicate 5 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Autumn STI replicate 4

description:
Biological replicate 4 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 4/2/2007


title: Spring STI replicate 1

description:
Biological replicate 1 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Spring Control replicate 2

description:
Biological replicate 2 of 7. male song sparrow captured in the spring after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Autumn STI replicate 3

description:
Biological replicate 3 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Autumn Control replicate 2

description:
Biological replicate 2 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Autumn Control replicate 3

description:
Biological replicate 3 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Autumn STI replicate 1

description:
Biological replicate 1 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Spring Control replicate 3

description:
Biological replicate 3 of 7. male song sparrow captured in the spring after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Spring STI replicate 3

description:
Biological replicate 3 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Autumn STI replicate 2

description:
Biological replicate 2 of 8. male song sparrow captured in the autumn after a simulated territorial intrusion by a conspecific male.
print batch: 5/31/2006


title: Spring Control replicate 1

description:
Biological replicate 1 of 7. male song sparrow captured in the spring after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Spring STI replicate 4

description:
Biological replicate 4 of 8. male song sparrow captured in the spring after a simulated territorial intrusion by a conspecific male.
print batch: 4/2/2007


title: Liposarcoma_telomerase_8

status: Public on Nov 02 2009

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

institute: The University of Glasgow

hyb_protocol: 100ul of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65C rotating at 10 rpm and washed as as per manufacturor's instructions for one colour arrays (Agilent Technologies).

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing: Normalised to the 75th percentile with intensities below 0.01 being set to 0.01. Data filtered to contain only those probes with Present, Marginal or Unknown status in 22 of 26 samples.

source_name: Liposarcoma, Fresh Frozen

label_protocol: 800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.

growth_protocol: Bone marrow hMSC were cultured in DMEM-LG plus Glutamax supplemented with 17% Hyclone FBS (Thermo Fisher Scientific, Waltham, MA) at 5% CO2.

extract_protocol: Frozen Liposarcoma tissue was disrupted using a Hybaid Ribolyser at a setting of 5.5 for 5 x 10 second pulses with 30 second pauses in between and RNA was extracted using the RNeasy Lipid kit (Qiagen Inc, Hilden, Germany) as per manufacturers’ instructions. Primary hMSC aspirates were isolated by centrifugation at 700 g for 15 min at 4 °C over a Ficoll-Hypaque gradient (Sigma) and total RNA was extracted using Nucleospin II RNA extraction kit (Macherey-Nagel) as per manufacutor's instructions.

value: Liposarcoma, Fresh Frozen


title: Autumn Control replicate 4

description:
Biological replicate 4 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 4/2/2007


title: Liposarcoma_telomerase_2


title: Autumn Control replicate 1

description:
Biological replicate 1 of 8. male song sparrow captured in the autumn after a control territorial intrusion by a heterospecific male
print batch: 5/31/2006


title: Liposarcoma_telomerase_5


title: Liposarcoma_telomerase_3


title: Liposarcoma_telomerase_6


title: Liposarcoma_telomerase_4


title: Liposarcoma_ALT_1


title: Liposarcoma_telomerase_1


title: hMSC_3_2 II

source_name: Bone marrow aspirate purified hMSCs

value: Bone marrow aspirate purified hMSCs


title: Liposarcoma_ALT_7


title: Liposarcoma_ALT_4


title: Liposarcoma_ALT_8


title: Liposarcoma_ALT_2_1


title: Liposarcoma_ALT_2_2


title: Liposarcoma_ALT_6


title: Liposarcoma_ALT_9


title: Liposarcoma_ALT_3


title: Liposarcoma_telomerase_7


title: hMSC_4_1 II


title: hMSC_1_2 II


title: hMSC_4_2 II


title: hMSC_1_1 II


title: hMSC_3_1 II


title: hMSC_2_2 II


title: hMSC_2_1 II


title: Liposarcoma_ALT_5


title: IMR90_normal_2

data_processing: Normalised to the 75th percentile with intensities below 0.01 being set to 0.01. Data filtered to contain only those probes with Present, Marginal or Unknown status in 26 of 28 samples.

source_name: normal lung fibroblasts

growth_protocol: SKLU, WI38-SV40, WI38 and IMR90 were cultured in MEM (10% FBS and 1% L-glutamine) and A2780  were cultured in RPMI 1640 (10% FBS and 1% L-glutamine) at 5% CO2. Bone marrow hMSC were cultured in DMEM-LG plus Glutamax supplemented with 17% Hyclone FBS (Thermo Fisher Scientific, Waltham, MA) at 5% CO2.

extract_protocol: Immortalised cell lines and normal cell strains were rinsed in PE, trypsanised and total RNA was extracted using Nucleospin II RNA extraction kit (Macherey-Nagel) as per manufacutor's instructions. Primary hMSC aspirates were isolated by centrifugation at 700 g for 15 min at 4 °C over a Ficoll-Hypaque gradient (Sigma).

value: normal lung fibroblasts


title: IMR90_normal_1


title: WI38_normal_2


title: hMSC_3_2 I


title: hMSC_4_1 I


title: WI38_normal_1


title: hMSC_3_1 I


title: HT1080_telomerase_1

source_name: fibrosarcoma

value: fibrosarcoma


title: hMSC_4_2 I


title: hMSC_2_2 I


title: hMSC_1_2 I


title: 5637_telomerase_2

source_name: Bladder Carcinoma

value: Bladder Carcinoma


title: C33A_telomerase_2

source_name: cervical carcinoma

value: cervical carcinoma


title: hMSC_1_1 I


title: SKLU_ALT_2

source_name: lung adenocarcinoma

value: lung adenocarcinoma


title: C33A_telomerase_1


title: SUSM1_ALT_1

source_name: liver fibroblasts

value: liver fibroblasts


title: hMSC_2_1 I


title: HT1080_telomerase_2


title: SKLU_ALT_1


title: WI38-SV40_ALT_1

source_name: SV40 immortalised lung fibroblasts

value: SV40 immortalised lung fibroblasts


title: A2780_telomerase_1

source_name: ovarian carcinoma

value: ovarian carcinoma


title: SUSM1_ALT_2


title: 5637_telomerase_1


title: KMST6_ALT_1

source_name: lung fibroblasts

value: lung fibroblasts


title: KMST6_ALT_2


title: A2780_telomerase_2


title: WI38-SV40_ALT_2


title: phenol-adapted strain, phenol, biological replicate 2

status: Public on Aug 31 2009

city: Tianjin

first: Bing-Zhi

last: Li

address: Weijin Road 92#

country: China

institute: Tianjin University

description: Transcriptional response to phenol.

hyb_protocol: The biotin-labeled cRNA was hybridized to the GeneChip® Yeast Genome 2.0 Array from Affymetrix (California, US) after dilution and fragmentation according to Affymetrix’s protocol.

scan_protocol: Microarrays were scanned with the Genechip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operation System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Saccharomyces cerevisiae

source_name: phenol-adapted strain, 20 minutes after phenol addition

label_protocol: Total RNA labeling was conducted according to the Affymetrix GeneChip Expression analysis technical manual (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Strains were incubated in 400 ml high-sugar YPD medium (10 g/L yeast extract, 20 g/L peptone, 100 g/L glucose) in a 2-liter conical flask with an initial OD600 of 0.35.

extract_protocol: Total RNA was isolated according to the hot phenol method.

treatment_protocol: Cultures for microarray analysis were collected 20 minutes after the addition of the inhibitor (furfural, phenol, or acedic acid) or medium, which was added at mid-exponential phase.

tag: inhibitor

value: phenol


title: Normal Chip#6

status: Public on Nov 01 2009

description: Normal Chip#6.CEL

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor). Each platform was preprocess separately, then merged. An extra quantile normalization was needed to normalized across platforms (matrix of additionally-normalized data is available as GSE16161 supplementary file, GSE16161_QuantNormAcrossPlatform.txt).

source_name: Normal, ma, Patient 6

label_protocol: Affymetrix protocol

extract_protocol: Qiagen RNeasy Kit protocol

value: skin biopsy

tag: individual

value: Patient 6

tag: condition

value: Normal


title: Normal Chip#3

description: Normal Chip#3.CEL

source_name: Normal, ma, Patient 3

value: Patient 3


title: Normal Chip#5

description: Normal Chip#5.CEL

source_name: Normal, ma, Patient 5

value: Patient 5


title: phenol-adapted strain, no inhibitor, biological replicate 2

description: Gene expression at exponential phase.

source_name: phenol-adapted strain, without inhibitor addition


title: Normal Chip#8

description: Normal Chip#8.CEL

source_name: Normal, ma, Patient 8

value: Patient 8


title: Normal Chip#4

description: Normal Chip#4.CEL

source_name: Normal, ma, Patient 4

value: Patient 4


title: Normal Chip#2

description: Normal Chip#2.CEL

source_name: Normal, ma, Patient 2

value: Patient 2


title: Normal Chip#7

description: Normal Chip#7.CEL

source_name: Normal, ma, Patient 7

value: Patient 7


title: phenol-adapted strain, no inhibitor, biological replicate 1

description: Gene expression at exponential phase.


title: phenol-adapted strain, phenol, biological replicate 1

description: Transcriptional response to phenol.


title: Normal Chip#1

description: Normal Chip#1.CEL

source_name: Normal, ma, Patient 1

value: Patient 1


title: AD2R369M

status: Public on Jan 12 2009

city: Montreal

first: Olivier

middle: Charles

last: Maes

state: Quebec

address: 3999 Cote Ste Catherine

department: Bloomfield Centre for Research in Aging

institute: Lady Davis Institute for Medical Research

description: peripheral blood mononuclear cell

hyb_protocol: Nadon, Mohr, and Becker, National Institute on Aging microarray facility--resources for gerontology research. Journals of Gerontology Series A-Biological Sciences & Medical Sciences, 2005. 60(4): p. 413-5, PMID: 15933377, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15933377

scan_protocol: Hybridization intensities were measured by a Storm PhosphorImager (Molecular Dynamics)

data_processing: Array-Pro Analyzer 4.5 software (Media Cybernetics). Data acquisition was made using the option net intensity.

label: alpha 32P dCTP

source_name: peripheral blood

label_protocol: 3 µg of total RNA was processed into radioactive cDNA targets

extract_protocol: Lacelle et al., J Gerontol A Biol Sci Med Sci, 2002. 57(7): p. B285-7, PMID: 12084799, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=12084799

tag: Sporadic Alzheimer's Disease, Male


title: SAGE_Breast_carcinoma_CL_ZR75_1_estrogen

status: Public on Mar 20 2009

type: SAGE

anchor: NlaIII

city: Bethesda

first: Cancer Genome Anatomy Project

last: CGAP

state: MD

department: Cancer Genome Anatomy Project

institute: National Cancer Institute

description:
CGAP_Numeric_library_ID: 176
Tagging_enzyme: BsmF I
Library_producer: Kornelia Polyak
Laboratory: Kornelia Polyak, Dana-Farber Cancer Institute
References: P. Seth et al., Oncogene 21, 836-43 (2002) [PUBMED=11850811]

source_name: mammary gland, carcinoma, cell line, non-normalized, short SAGE, SAGE

tag: organ/tissue

value: mammary gland

tag: tissue preparation

value: cell line

tag: sex

value: female

value: breast carcinoma cell line

tag: other information

value: ZR75-1 estrogen receptor positive, estrogen dependent human breast cancer cell line, estrogen deprived for a week, cells were collected 16 hours following addition of fresh medium containing 10 nM estrogen.


title: NEC951M

description: peripheral blood mononuclear cell

tag: Normal elderly control, Male


title: ADR874M

description: peripheral blood mononuclear cell


title: AD1018M

description: peripheral blood mononuclear cell


title: SAGE_Breast_carcinoma_CL_ZR75_1_tamoxifen

description:
CGAP_Numeric_library_ID: 177
Tagging_enzyme: BsmF I
Library_producer: Kornelia Polyak
Laboratory: Kornelia Polyak, Dana-Farber Cancer Institute
References: P. Seth et al., Oncogene 21, 836-43 (2002) [PUBMED=11850811]

tag: cell type

value: ZR75-1 estrogen receptor positive, estrogen dependent human breast cancer cell line, estrogen deprived for a week, cells were collected 16 hours following addition of fresh medium containing 10 uM 4-OH-tamoxifen.


title: NEC1025F

description: peripheral blood mononuclear cell

tag: Normal elderly control, Female


title: SAGE_Breast_carcinoma_CL_ZR75_1_untreated

description:
CGAP_Numeric_library_ID: 178
Tagging_enzyme: BsmF I
Library_producer: Kornelia Polyak
Laboratory: Kornelia Polyak, Dana-Farber Cancer Institute
References: P. Seth et al., Oncogene 21, 836-43 (2002) [PUBMED=11850811]

value: ZR75-1 human estrogen receptor positive, estrogen dependent breast cancer cell line, estrogen deprived for 1 week, cells collected 16 hours following change to fresh medium (no estrogen added).


title: AD961F

description: peripheral blood mononuclear cell

tag: Sporadic Alzheimer's Disease, Female


title: NECR325F

description: peripheral blood mononuclear cell


title: NEC1014F

description: peripheral blood mononuclear cell


title: NECR593F

description: peripheral blood mononuclear cell


title: NEC3R447F

description: peripheral blood mononuclear cell


title: Sample 11273, Slide 32024_F

status: Public on Jun 13 2007

city: Raleigh

first: Erin

last: Kennerly

state: NC

institute: NCSU

description:
Whole Blood was collected in EDTA tubes and immediately mixed and stored in RNAlater.
All protocols were followed according to manufacturer's instructions.

hyb_protocol: Arrays were hybridized overnight following Illumina's Ref-8 hybridization protocol

scan_protocol: Arrays were scanned using Illumina's Beadstation Scanner on the Default settings

data_processing: Raw values were extracted from Array images using Illumina's BeadStudio Software Version 1.5.0.34. Normalized VALUEs represent median standardized log base 2 signal intensities.

organism: Canis rufus

source_name: Whole Blood

label_protocol: Total RNA was biotin labeled using Ambion's Illumina RNA Amplification Kit

extract_protocol: Whole Blood stored in RNALater was extracted using Ambion's RiboPure Blood RNA extraction KitWhole Blood stored in RNALater was extracted using Ambion's RiboPure Blood RNA extraction Kit

tag: Sample 11273, Slide 32024_F, Male, captive


title: Sample 11270, Slide 32024_D

tag: Sample 11270, Slide 32024_D, Female, Free Range


title: Sample 10406, Slide 32022_E

tag: Sample 10406, Slide 32022_E, Male, Captive


title: Sample 11274, Slide 32024_C

tag: Sample 11274, Slide 32024_C, Female, Captive


title: Sample 11136, Slide 32022_F

tag: Sample 11136, Slide 32022_F, Male, Free Range


title: Sample 11270, Slide 32022_G

tag: Sample 11270, Slide 32022_G, Female, Free Range


title: Sample 11310, Slide 32022_H

source_name: Whole blood

tag: Sample 11310, Slide 32022_H, Male, Free Range


title: Sample 11105, Slide 32022_C

tag: Sample 11105, Slide 32022_C, Male, Free Range


title: Sample 11105, Slide 32024_G

tag: Sample 11105, Slide 32024_G, Male, Free Range


title: Sample 11275, Slide 32021_H

description:
Whole blood was collected in EDTA tubes and immediately mixed and stored with RNAlater.
All protocols were followed according to manufacturer's instructions.

tag: Sample 11275, Slide 32021_H, Female, Captive


title: Sample 11206, Slide 32022_B

tag: Sample 11206, Slide 32022_B, Male, Free Range


title: Sample 10537, Slide 32022_D

tag: Sample 10537, Slide 32022_D, Male, Captive


title: Sample 11148, Slide 32021_G

tag: Sample 11148, Slide 32021_G, Female, Free Range


title: Sample 10632, Slide 32024_H

tag: Sample 10632, Slide 32024_H, Male, Captive


title: Sample 11206, Slide 32024_E

tag: Sample 11206, Slide 32024_E, Male, Free Range


title: Sample 11275, Slide 32024_B

tag: Sample 11275, Slide 32024_B, Female, Captive


title: Sample 20288, Slide 32021_C

organism: Canis latrans

tag: Sample 20288, Slide 32021_C, Female, Free Range, Coyote


title: Sample 10406, Slide 32021_D

tag: Sample 10406, Slide 32021_D, Male, Captive


title: Sample 10537, Slide 32021_B

tag: Sample 10537, Slide 32021_B, Male, Captive


title: Sample 11148, Slide 32024_A

tag: Sample 11148, Slide 32024_A, Female, Free Range


title: Sample 11310, Slide 32021_A

tag: Sample 11310, Slide 32021_A, Male, Free Range


title: Sample 11136, Slide 32021_F

tag: Sample 11136, Slide 32021_F, Male, Free Range


title: Sample 111080, Slide 32021_E

tag: Sample 111080, Slide 32021_E, Male, Free Range


title: Sample 11274, Slide 32022_A

tag: Sample 11274, Slide 32022_A, Female, captive


title: Sample 20288, Slide 32020_F

description:
Whole Blood was collected in EDTA tubes and immediately mixed and stored in RNAlater.
All protocols were followed according to manufacturer's instructions

data_processing: Raw Values were extracted from Array image files using Illumina's BeadStudio Software version 1.5.0.34. Normalized VALUEs represent median standardized log base 2 signal intensities.

tag: Sample 20288, Slide 32020_F, Female, Free Range, Coyote


title: Sample 11270, Slide 32020_B

tag: Sample 11270, Slide 32020_B, Female, Free Range


title: Sample 11273, Slide 32020_C

tag: Sample 11273, Slide 32020_C, Male, Captive


title: Sample 11148, Slide 32020_H

tag: Sample 11148, Slide 32020_H, Female, Free Range


title: Sample 11310, Slide 32020_E

tag: Sample 11310, Slide 32020_E, Male, Free Range


title: Sample 11136, Slide 32013_G

description:
Whole Blood was collected in EDTA Tubes and immediately mixed and stored in RNAlater.
All protocols were followed according to manufacturer's instructions.

data_processing: Raw Values were extracted from Array images using Illumina's BeadStudio Software Version 1.5.0.34. Normalized VALUEs represent median standardized log base 2 signal intensities.

tag: Sample 11136, Slide 32013_G, Male, Free Range


title: Sample 111080, Slide 32020_G

tag: Sample 111080, Slide 32020_G, Male, Free Range


title: Sample 11206, Slide 32013_H

tag: Sample 11206, SLide 32013_H, Male, Free Range


title: Sample 11275, Slide 32020_A

source_name: Whole

tag: Sample 11275, Slide 32020_A, Female, Captive


title: Sample 11148, Slide 32013_E

tag: Sample 11148, Slide 32013_E, Female, Free Range


title: Sample 10632, Slide 32020_D

tag: Sample 10632, Slide 32020_D, Male, Captive


title: Sample 11274, Slide 32013_D

tag: Sample 11274, Slide 32013_D, Female, Captive


title: Sample 10406, Slide 32013_C

tag: Sample 10406, Slide 32013_C, Male, Captive


title: Sample 11273, Slide 32011_H

description:
Whole blood was collected in EDTA tubes and immediately mixed and stored in RNAlater.
All protocols were followed according to manufacturer's instructions

data_processing: Raw values were extracted from Array image using Illumina's BeadStudio Software version 1.5.0.34. Normalized VALUEs represent median standardized log base 2 signal intensities.

tag: Sample 11273, Slide 32011_H, Male, Captive


title: Sample 111080, Slide 32011_D

tag: Sample 111080, Slide 32011_D, Male, Free Range


title: Sample 11206, Slide 32011_C

tag: Sample 11206, Slide 32011_C, Male, Free Range


title: Sample 11273, Slide 32013_A

tag: Sample 11273, Slide 32013_A, Male, Captive


title: Sample 20288, Slide 32013_B

tag: Sample 20288, Slide 32013_B, Female, Free Range, Coyote


title: Sample 11275, Slide 32011_F

tag: Sample 11275, Slide 32011_F, Female, Captive


title: Sample 11105, Slide 32011_B

tag: Sample 11105, Slide 32011_B, Male, Free Range


title: Sample 11274, Slide 32011_E

tag: Sample 11274, Slide 32011_E, Female, Captive


title: Sample 11270, Slide 32010_H

description:
All samples were collected in EDTA tubes, immediated mixed and stored with RNAlater.
All protocols followed manufacturer's recommendations

data_processing: Raw Intensity Values were extracted using Illumina BeadStudio Software Version 1.5.0.34. Normalized VALUEs represent median standardized log base 2 signal intensities.

tag: Sample 11270, Slide 32010_H, Female, Free Range


title: Sample 11105, Slide 32013_F

tag: Sample 11105, Slide 32013_F, Male, Free Range


title: LIN54 S phase Replicate 2

status: Public on Apr 17 2007

city: Beijing

first: Xiaopeng

last: Zhu

address: 15 Datun Street

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-LIN54 antibody, replicate 2 out of 3

hyb_protocol: Affymetrix fluidics protocol EukGE-WS2v4_450

scan_protocol: Scanning was carried out on an Affymetrix scanner GCS3000.  The scan protocol was contained in a .cif file for chip type Hs_PromPR_v02.

data_processing:
Affymetrix GCOS processed image files to generate .CEL files.
MAT (Model-based Analysis for Tiling Arrays) analysis algorithm used to detect regions enriched by chromatin immunoprecipitation (ChIP) on Affymetrix Human Promoter Array 1.0R (ChIP-chip).

source_name: LIN54 ChIP from S-phase T98G cells

label_protocol:
The chromatin immunprecipitated DNA (ChIP) or 2 ng of whole genomic DNA (Input) were amplified by ligation-mediated PCR, digested with Dnase I to give fragments of ~50 bp.
The DNA fragments were end-labelled with biotin in a TdT-catalyzed reaction.

growth_protocol: Human T98G cells grown till 70% confluency in DMEM supplemeted with 10 % fetal calf serum

extract_protocol: Chromatin was prepared from formalin-fixated cells exactly as described in Rayman, Takahashi et al. (2002) Genes Dev 16, 933-947

treatment_protocol: Cells were incubated in serum-free medium for 3 days to induce G0 arrest, then serum was added for 24 h to induce S-phase.

tag: human glioblastoma cell line T98G CRL-1690


title: LIN54 S phase Replicate 1

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-LIN54 antibody, replicate 1 out of 3


title: LIN54 S phase Replicate 3

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-LIN54 antibody, replicate 3 out of 3


title: LIN9 S phase Replicate 3

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-LIN9 antibody, replicate 3 out of 3

source_name: LIN9 ChIP from S-phase T98G cells


title: LIN9 S phase Replicate 1

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-LIN9 antibody, replicate 1 out of 3


title: LIN9 S phase Replicate 2

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-LIN9 antibody, replicate 2 out of 3


title: Sample 11310, Slide 32010_D

description:
Blood collected in wild and immediately mixed and stored in RNAlater.
All procedures were followed according to manufacturer's protocols

data_processing: Raw data extracted using Illumina Beadstudio version 1.5.0.34. Normalized VALUEs represent median standardized log base 2 signal intensities.

tag: Sample 11310, Slide 32010_D, Male, Free Range


title: Sample 10537, Slide 32010_G

description:
Sample collected and immediately stored in RNAlater.
Followed All manufacturers protocols

data_processing: Raw Intensity Values were obtained using Illumina's BeadStudio Software version 1.5.0.34. Normalized VALUEs represent median standardized log base 2 signal intensities.

tag: Sample 10537, Slide 32010_G, Male, Captive


title: E2F4 S phase Replicate 3

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-E2F4 antibody, replicate 3 out of 3

source_name: E2F4 ChIP from S-phase T98G cells


title: Sample 20288, Slide 32010_F

description:
Sample collected in wild, mixed and stored with RNA later.
Followed All manufacturers protocols

tag: Sample 20288, Slide 32010_F, Female, Free Range, Coyote


title: p130 S phase Replicate 3

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-p130 antibody, replicate 3 out of 3

source_name: p130 ChIP from S-phase T98G cells


title: p130 S phase Replicate 2

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-p130 antibody, replicate 2 out of 3


title: E2F4 S phase Replicate 2

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-E2F4 antibody, replicate 2 out of 3

data_processing:
Affymetrix GCOS processed image files to generate .CEL files.

MAT (Model-based Analysis for Tiling Arrays) analysis algorithm used to detect regions enriched by chromatin immunoprecipitation (ChIP) on Affymetrix Human Promoter Array 1.0R (ChIP-chip).


title: p130 S phase Replicate 1

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-p130 antibody, replicate 1 out of 3


title: E2F4 S phase Replicate 1

description: Chromatin from S-phase synchronized T98G cells immunoprecipitated with anti-E2F4 antibody, replicate 1 out of 3


title: Genome Input S phase Replicate 3

description: Input chromatin from S-phase T98G cells, replicate 3 out of 3

source_name: Input chromatin from S-phase T98G cells


title: LIN54 G0 phase Replicate 2

description: Chromatin from G0-arrested T98G cells immunoprecipitated with anti-LIN54 antibody, replicate 2 out of 3

source_name: LIN54 ChIP from G0 arrested T98G cells

growth_protocol: Human T98G cells grown till confluency in DMEM supplemeted with 10 % fetal calf serum

treatment_protocol: Cells were incubated in serum-free medium for 3 days to induce G0 arrest


title: LIN54 G0 phase Replicate 3

description: Chromatin from G0-arrested T98G cells immunoprecipitated with anti-LIN54 antibody, replicate 3 out of 3


title: Genome Input S phase Replicate 1

description: Input chromatin from S-phase T98G cells, replicate 1 out of 3


title: Genome Input S phase Replicate 2

description: Input chromatin from S-phase T98G cells, replicate 2 out of 3


title: LIN54 G0 phase Replicate 1

description: Chromatin from G0-arrested T98G cells immunoprecipitated with anti-LIN54 antibody, replicate 1 out of 3


title: LIN9 G0 phase Replicate 2

description: Chromatin from G0-arrested T98G cells immunoprecipitated with anti-LIN9 antibody, replicate 2 out of 3

source_name: LIN9 ChIP from G0 arrested T98G cells


title: Sample 10632, Slide 32011_A

description:
Whole blood was collected in EDTA tubes and immediately mixed and stored in RNAlater.
All protocols were followed according to manufacturer's instructions

tag: Sample 10632, Slide 32011, Male, Captive


title: LIN9 G0 phase Replicate 3

description: Chromatin from G0-arrested T98G cells immunoprecipitated with anti-LIN9 antibody, replicate 3 out of 3


title: E2F4 G0 phase Replicate 2

description: Chromatin from G0-arrested T98G cells immunoprecipitated with anti-E2F4 antibody, replicate 2 out of 3

source_name: E2F4 ChIP from G0 arrested T98G cells