title: PBMCs-Type 1 Diabetes-IDDM32_T1D_4MO

source_name: PBMCs from Type 1 Diabetes patient and the timepoint 4 months after diagnosis.

value: White

value: Insulin


title: 101049

status: Public on Sep 12 2007

type: RNA

city: San Diego

first: Jack

last: Yu

state: CA

address: 3210 Merryfield Row

country: USA

institute: Veridex, LLC

description: acute myeloid leukemia

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: blood from 65 year old male

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from cell samples using the Trizol Kit.

tag: acute myeloid leukemia

tag: Sex

value: M

tag: Age

tag: Diagnosis

value: AML-SECONDARY

tag: Response

value: Complete Response

tag: Unfavorable Karyotype

value: YES

tag: Baseline WBC

tag: Overall Survival (Days) :564


title: 101077

description: acute myeloid leukemia

source_name: blood from 75 year old female

value: F

value: Stable Disease

value: NO

tag: Overall Survival (Days) :574


title: 100209

description: acute myeloid leukemia

source_name: blood from 73 year old male

value: Progressive Disease

value: Other

tag: Overall Survival (Days) :209


title: 101095

description: acute myeloid leukemia

source_name: blood from 82 year old male

tag: Overall Survival (Days) :108


title: 100213

description: acute myeloid leukemia

source_name: blood from 81 year old female

tag: Overall Survival (Days) :257


title: 100210

description: acute myeloid leukemia

source_name: blood from 68 year old male

tag: Overall Survival (Days) :654


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 2 of 38

status: Public on Sep 14 2007

type: genomic

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Chromatin immunoprecipitation was performed using monoclonal antibodiesd. DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

hyb_protocol: NimbleGen human whole genome array

scan_protocol: GenePix 4000B

data_processing:
The raw data is provided directly from NimbleScan version 1.2
normalization done by QSPLINE

label: Samples were labeled by Cy3

molecule: genomic DNA

source_name: Histone H3K27me3 associated genomic DNA in Human H1 ES cells

label_protocol: Immunoprecipitated total genomic DNA bound by Histone H3K27me3 was labeled Cy3

extract_protocol: Genomic DNA bound by Histone H3K27me3 extracted via immunoprecipitation

tag: Histone H3K27me3 associated genomic DNA were immunoprecipitated by H3K27me3 antibody from H1 human ES cells.

label: Samples were labeled by Cy5

label_protocol: Genomic DNA extracted via immunoprecipitation

extract_protocol: Genomic DNA was extracted via immunoprecipitation

tag: Total Genomic DNA from Human H1 ES cells used as input for the the immunoprecipitation


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 1 of 38

data_processing: normalization done by QSPLINE

source_name: Histone H3K4me3 associated genomic DNA in Human H1 ES cells

label_protocol: Immunoprecipitated total genomic DNA bound by Histone H3K4me3 was labeled Cy3

extract_protocol: Genomic DNA bound by Histone H3K4me3 extracted via immunoprecipitation

tag: Histone H3K4me3 associated genomic DNA were immunoprecipitated by H3K4me3 antibody from H1 human ES cells.

source_name: Total Genomic DNA from Human H1 ES cells


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 2 of 38


title: 101038

description: acute myeloid leukemia

tag: Overall Survival (Days) :151


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 1 of 38


title: 101043

description: acute myeloid leukemia

source_name: blood from 76 year old female

tag: acute myeloid leukemia

tag: Overall Survival (Days) :200


title: 100104

description: acute myeloid leukemia

source_name: blood from 63 year old female

tag: Sex

tag: Age

value: AML-DE NOVO

tag: Overall Survival (Days) :728


title: 101046

description: acute myeloid leukemia

source_name: blood from 66 year old female

tag: Diagnosis

tag: Response

tag: Unfavorable Karyotype

tag: Overall Survival (Days) :53


title: 100208

description: acute myeloid leukemia

source_name: blood from 76 year old male

tag: Baseline WBC

tag: Overall Survival (Days) :29


title: 101109

description: acute myeloid leukemia

tag: Overall Survival (Days) :656


title: 100604

description: acute myeloid leukemia

source_name: blood from 63 year old male

tag: Overall Survival (Days) :64


title: 100121

description: acute myeloid leukemia

source_name: blood from 72 year old male

tag: Overall Survival (Days) :252


title: 100109

description: acute myeloid leukemia

tag: Overall Survival (Days) :68


title: 101075

description: acute myeloid leukemia

source_name: blood from 71 year old male

value: Hematological Improvement

tag: Overall Survival (Days) :659


title: 101114

description: acute myeloid leukemia

tag: Overall Survival (Days) :69


title: 100205

description: acute myeloid leukemia

source_name: blood from 74 year old male

tag: acute myeloid leukemia

tag: Overall Survival (Days) :754


title: 101057

description: acute myeloid leukemia

source_name: blood from 85 year old male

tag: Sex

tag: Overall Survival (Days) :386


title: 100338

description: This sample has two chips, therefore the values represent the average of the features from both chips.

source_name: blood from 78 year old male

tag: Age

tag: Overall Survival (Days) :8


title: 100302

description: acute myeloid leukemia

source_name: blood from 73 year old female

tag: Overall Survival (Days) :48

tag: Response

tag: Diagnosis


title: 100322

description: acute myeloid leukemia

source_name: blood from 73 year old male

tag: Unfavorable Karyotype

tag: Baseline WBC

tag: Overall Survival (Days) :237


title: 100110

description: acute myeloid leukemia

source_name: blood from 74 year old female

tag: Overall Survival (Days) :983


title: 100341

description: acute myeloid leukemia

source_name: blood from 67 year old male

tag: Overall Survival (Days) :433


title: 101102

description: acute myeloid leukemia

source_name: blood from 69 year old male

tag: Overall Survival (Days) :76


title: 100307

source_name: blood from 68 year old male

tag: Overall Survival (Days) :179


title: 101008

description: acute myeloid leukemia

source_name: blood from 82 year old male

tag: Overall Survival (Days) :548


title: 100333

source_name: blood from 65 year old male

tag: acute myeloid leukemia

tag: Overall Survival (Days) :364


title: 100330

source_name: blood from 67 year old female

tag: Sex

tag: Overall Survival (Days) :153


title: 101021

description: acute myeloid leukemia

source_name: blood from 69 year old female

tag: Age

tag: Overall Survival (Days) :991


title: 100339

description: acute myeloid leukemia

source_name: blood from 75 year old male

tag: Overall Survival (Days) :25


title: 100336

description: acute myeloid leukemia

source_name: blood from 80 year old male

tag: Overall Survival (Days) :67

tag: Response


title: breast tumor - I490

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

description: aCGH data from ER+ breast tumor

hyb_protocol: The test and reference probes were combined with 35 ╡g of Cot-1 DNA in 1.5mL tube and ethanol precipitated. Following centrifugation (30 min at 14000 rpm), the probes were re-suspended in 5 ╡l of water, 10 ╡l 20% SDS and 35 ╡l of Master Mix #1, heated to 73║C for 10 minutes and incubated for 60 minutes at 37║C to block repetitive elements on the probe. Hybridization was performed for 48 hours at 37║C. After hybridization, the slides were washed with PN solution at room temperature followed by a 15 min wash with wash solution (50% Formamide, 2X SSC, pH 7). DAPI was applied to the slides for Image analysis using a custom built CCD camera system

data_processing: Data analysis was carried out using UCSF Spot software. SPROC software was used to automatically filter the data to reject data points based on low DAPI intensity, low correlation between Cy3 and Cy5 and low reference/DAPI signal intensity. Observations with standard deviation of replicates grater then 0.2 were declared missing.

source_name: Cryobanked tumor Pat_ID  I490

label_protocol: 400-600 ng of reference and test genomic DNA was labeled with Cy5 and Cy3 respectively (using the BioPrime kit from Invitrogen). The DNA was denatured in the presence of random primer at 100 ║C for 10 minutes. Labeling occurred with the addition of Cy5 to the reference DNA and Cy3 to the test DNA and Klenow. Incubation took place overnight at 37║C in a thermalcycler. The unincorporated nucleotides were removed using a MicroSpin G-25 Columns (Amersham).

extract_protocol: DNA was purified from frozen tumor powders using High Pure PCR Preparation Kit (Roche Diagnostics; Indianapolis, Indiana

tag: ER Status

value: ER+

tag: PR Status

value: PR+

tag: ErBB2 amplification

tag: age

tag: grade

tag: stage

tag: node

source_name: Normal Blood

tag: Normal


title: breast tumor - I501

description: aCGH data from ER+ breast tumor

scan_protocol: Image analysis using a custom built CCD camera system

source_name: Cryobanked tumor Pat_ID  I501


title: breast tumor - I486

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I486


title: 100319

description: acute myeloid leukemia

source_name: blood from 71 year old male

tag: acute myeloid leukemia

tag: Baseline WBC

tag: Overall Survival (Days) :233

tag: Unfavorable Karyotype

tag: Diagnosis


title: breast tumor - I518

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I518


title: breast tumor - I476

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I476

value: PR-

tag: grade:


title: 100324

source_name: blood from 85 year old male

tag: Sex

tag: Age

tag: Overall Survival (Days) :248


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 3 of 38

source_name: Histone H3K4me3 associated genomic DNA in Human H1 ES cells

tag: Histone H3K4me3 associated genomic DNA were immunoprecipitated by H3K4me3 antibody from H1 human ES cells.

tag: Total Genomic DNA from Human H1 ES cells used as input for the the immunoprecipitation


title: breast tumor - I472

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I472

tag: ER Status

tag: PR Status

tag: ErBB2 amplification

value: x


title: breast tumor - I470

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I470

tag: age

tag: grade

tag: stage


title: breast tumor - I434

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I434

tag: node

tag: Normal


title: breast tumor - I427

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I427


title: breast tumor - I403

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I403


title: breast tumor - I456

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I456


title: breast tumor - I412

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I412


title: breast tumor - I397

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I397


title: breast tumor - I370

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I370


title: breast tumor - I354

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I354

source_name: Normal Blood


title: breast tumor - I362

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I362


title: breast tumor - I449

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I449


title: breast tumor - I419

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I419


title: breast tumor - I317

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I317


title: breast tumor - I353

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I353


title: breast tumor - I263

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I263


title: breast tumor - I335

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I335


title: breast tumor - I312

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I312


title: breast tumor - I251

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I251


title: breast tumor - I281

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I281


title: breast tumor - I255

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I255


title: breast tumor - I272

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I272


title: breast tumor - I308

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I308


title: breast tumor - I289

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I289


title: breast tumor - I309

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I309

tag: stage:

tag: node:


title: breast tumor - I252

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I252


title: breast tumor - I261

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I261

source_name: Normal Blood


title: BM 48h Ctrl 3

city: Canberra

first: Lina

last: Tze

state: ACT

country: Australia

institute: John Curtin School of Medical Research

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

organism: Mus musculus

source_name: Rag2-GFP, HEL-Ig BM cells

label_protocol: Ambion cDNA synthesis with T7 oligo dT primer (Array Script).  Labeling with biotin-11-CTP and biotin-16-UTP.

growth_protocol: 5 day culture in RPMI + 10% FBS, Pen/Strep, L-glut, 2-ME, 16ng/mL IL-7

extract_protocol: Qiagen RNeasy protocol

treatment_protocol: HEL treated samples were washed after 5 days, replaced with new media with no IL-7, but 1ug/mL HEL.  Control samples were treated the same except no HEL in the media.  HEL Mlo samples were sorted for IgMa low, IgDneg.  HEL 48h samples were sorted for B220+ IgMahi, GFP+ cells after 48h in HEL.  BM 48h Ctrl samples were sorted for B220+ IgMahi GFPneg after 48h in culture with no HEL.

tag: Strain C57BL/14


title: BM 48h Ctrl 2

tag: Strain C57BL/13


title: breast tumor - I247

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I247


title: breast tumor - I246

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I246

value: nv


title: breast tumor - I245

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I245


title: breast tumor - I242

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I242


title: breast tumor - s1748

description: Gene expression data from ER+ N0 breast cancer from young cohort

hyb_protocol: Affymetrix Comm Hyb Setup 21 & Affymetrix Comm Wash Stain 21  (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

scan_protocol: GeneChip HT Scanner protocol v2.2.09  (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

data_processing: RMA normalization with affy package in Bioconductor R

source_name: TISSUE_ID s1748

label_protocol: Affymetrix Gene Expression TP 21 (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

extract_protocol: Qiagen RNAesy purification from formamide extracted samples

tag: estrogen receptor (ER)+

tag: progesterone receptor (PR)+


title: breast tumor - s0395

source_name: TISSUE_ID s0395

tag: progesterone receptor (PR)-


title: BM 48h Ctrl 1

tag: Strain C57BL/12


title: HEL 48h 3

tag: Strain C57BL/11


title: breast tumor - s0166

description: Gene expression data from ER+ N0 breast cancer from old cohort

source_name: TISSUE_ID s0166


title: HEL 48h 2

tag: Strain C57BL/10


title: breast tumor - s1777

source_name: TISSUE_ID s1777


title: HEL 48h 1

tag: Strain C57BL/9


title: breast tumor - s0372

source_name: TISSUE_ID s0372


title: breast tumor - I500

source_name: Pat_ID I500


title: breast tumor - I218

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I218

tag: ER Status

tag: PR Status

tag: ErBB2 amplification


title: breast tumor - I224

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I224

tag: age

tag: grade:

tag: stage


title: breast tumor - I203

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I203

tag: grade

tag: node

tag: Normal


title: breast tumor - I195

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I195


title: HEL Mlo 2

data_processing: MAS 4

source_name: HEL-Ig BM cells

tag: Strain C57BL/7


title: breast tumor - I240

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I240

source_name: Normal Blood


title: breast tumor - I427

source_name: Pat_ID I427

tag: estrogen receptor (ER)+

value: N+


title: breast tumor - I503

source_name: Pat_ID I503


title: breast tumor - I370

source_name: Pat_ID I370


title: HEL Mlo 3

tag: Strain C57BL/8


title: breast tumor - I189

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I189


title: breast tumor - I188

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I188


title: breast tumor - I181

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I181


title: breast tumor - I312

source_name: Pat_ID I312

tag: progesterone receptor (PR)-


title: breast tumor - I180

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I180


title: breast tumor - I272

source_name: Pat_ID I272

tag: progesterone receptor (PR)+


title: breast tumor - I179

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I179


title: breast tumor - I289

source_name: Pat_ID I289


title: breast tumor - I171

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I171


title: breast tumor - I282

source_name: Pat_ID I282


title: embryonic hearts, vehicle control treatment, T12h, biological replicate 2

first: Jing

last: Chen

address: 777 Highland Ave

department: pharmaceutical Sciences

institute: University of Wisconsin - Madison

description: Gene expression data of zebrafish embryonic hearts extracted from 84 hpf old embryos at 12 h post 1h-TCDD dosing

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned in an Aglient Gene Array Scanner

data_processing: All .cel images were pre-processed with the GC-RMA function in the ArrayAssist Express Version 4.0 software.  The output signal intensity for each probeset ID was log2 transformed.

organism: Danio rerio

source_name: Zebrafish embryonic heart at the age of 84hpf old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All zebrafish embryos were kept at 27ºC in egg water with a 14-h/ 10-h light/dark cycle until the designated age for experiment.

extract_protocol: Zebrafish embryonic heart extraction: 200 cmlc2::GFP transgenic embryos were collected in a 1.5 ml Eppendorf tube with 1 ml L-15/10%FBS media and passed through a 19.5 gauge needle connected to a 10 ml syringe 60 times,  thus internal organs were separated from the body by shear force.  Fluorescent hearts that specifically expressing GFP were identified and picked up under a fluorescence dissecting scope.

treatment_protocol: For Retinoic Acid treatment, 72 hpf old zebrafish embryos were treated with 1μM all-trans retinoic acid in 0.1% DMSO or 0.1% DMSO continously until the timepoint for heart extraction.  For TCDD treatment, 72 hpf old zebrafish embryos were treated with 1ng/μl TCDD in 0.1% DMSO or 0.1% DMSO as a vehicle control for 1 h.

tag: Genotype

value: cmlc2::GFP transgenic zebrafish


title: embryonic hearts, vehicle control treatment, T12h, biological replicate 3


title: embryonic hearts, TCDD treatment, T12h, biological replicate 3


title: breast tumor - I227

source_name: Pat_ID I227


title: breast tumor - I317

source_name: Pat_ID I317


title: breast tumor - I222

source_name: Pat_ID I222


title: breast tumor - I261

source_name: Pat_ID I261


title: breast tumor - I263

source_name: Pat_ID I263


title: embryonic hearts, TCDD treatment, T12h, biological replicate 2


title: breast tumor - I162

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I162

source_name: Normal Blood


title: HEL Mlo 1

source_name: HEL-Ig BM cells

tag: Strain C57BL/6


title: embryonic hearts, vehicle control treatment, T 4h, biological replicate3

description: Gene expression data of zebrafish embryonic hearts extracted from 76 hpf old embryos at 4 h post 1h-TCDD dosing

source_name: Zebrafish embryonic heart at the age of 76hpf old


title: breast tumor - I242

source_name: Pat_ID I242


title: breast tumor - I218

source_name: Pat_ID I218

value: N?


title: embryonic hearts, TCDD treatment, T12h, biological replicate 1


title: embryonic hearts, vehicle control treatment, T 4h, biological replicate1


title: breast tumor - I227

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I227


title: breast tumor - I189

source_name: Pat_ID I189


title: embryonic hearts, vehicle control treatment, T12h, biological replicate 1


title: embryonic hearts, vehicle control treatment, T 4h, biological replicate2


title: breast tumor - I151

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I151


title: breast tumor - I139

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I139


title: breast tumor - I131

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I131


title: breast tumor - I152

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I152


title: breast tumor - I153

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I153


title: breast tumor - I153

source_name: Pat_ID I153


title: breast tumor - I151

source_name: Pat_ID I151


title: breast tumor - I139

source_name: Pat_ID I139


title: breast tumor - I130

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I130


title: breast tumor - I180

source_name: Pat_ID I180


title: embryonic hearts, TCDD treatment, T 4h, biological replicate2


title: breast tumor - I129

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I129

source_name: Normal Blood


title: breast tumor - I108

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I108


title: breast tumor - I131

source_name: Pat_ID I131


title: breast tumor - I130

source_name: Pat_ID I130


title: breast tumor - I099

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I099


title: embryonic hearts, TCDD treatment, T 4h, biological replicate3

source_name: Zebrafish embryonic heart at the age of 76hpf old


title: embryonic hearts, TCDD treatment, T 4h, biological replicate1


title: embryonic hearts, vehicle control treatment, T 2h, biological replicate1

description: Gene expression data of zebrafish embryonic hearts extracted from 74 hpf old embryos at 2 h post 1h-TCDD dosing

source_name: Zebrafish embryonic heart at the age of 74hpf old


title: breast tumor - I088

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I088


title: embryonic hearts, vehicle control treatment, T 2h, biological replicate3


title: embryonic hearts, TCDD treatment, T 2h, biological replicate 3


title: breast tumor - I108

source_name: Pat_ID I108


title: breast tumor - I101

source_name: Pat_ID I101


title: embryonic hearts, vehicle control treatment, T 2h, biological replicate2


title: embryonic hearts, TCDD treatment, T 2h, biological replicate 1


title: embryonic hearts, vehicle control treatment, T1h, biological replicate 3

description: Gene expression data of zebrafish embryonic hearts extracted from 73 hpf old embryos at 1 h post 1h-TCDD dosing


title: embryonic hearts, vehicle control treatment, T1h, biological replicate 2

source_name: Zebrafish embryonic heart at the age of 73hpf old


title: breast tumor - I055

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I055


title: breast tumor - I129

source_name: Pat_ID I129


title: breast tumor - I099

source_name: Pat_ID I099


title: breast tumor - I101

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I101


title: embryonic hearts, vehicle control treatment, T1h, biological replicate 1


title: breast tumor - I090

source_name: Pat_ID I090


title: breast tumor - I083

source_name: Pat_ID I083


title: breast tumor - I046

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I046

source_name: Normal Blood


title: breast tumor - I050

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I050


title: breast tumor - I028

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I028


title: breast tumor - I035

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I035


title: embryonic hearts, TCDD treatment, T 2h, biological replicate 2


title: embryonic hearts, TCDD treatment, T1h, biological replicate 3


title: breast tumor - I019

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I019


title: breast tumor - I097

source_name: Pat_ID I097


title: embryonic hearts, TCDD treatment, T1h, biological replicate 2


title: embryonic hearts, DMSO treatment, T12h, biological replicate3

description: Gene expression data of zebrafish embryonic hearts extracted from 84 hpf old embryos at 12 h post RA dosing

source_name: Zebrafish embryonic heart at the age of 84hpf old


title: breast tumor - I050

source_name: Pat_ID I050


title: breast tumor - I055

source_name: Pat_ID I055


title: breast tumor - I046

source_name: Pat_ID I046


title: embryonic hearts, TCDD treatment, T1h, biological replicate 1

source_name: Zebrafish embryonic heart at the age of 73hpf old


title: embryonic hearts, DMSO treatment, T12h, biological replicate2


title: breast tumor - I019

source_name: Pat_ID I019


title: breast tumor - I011

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I011


title: embryonic hearts, DMSO treatment, T12h, biological replicate1


title: breast tumor- I007

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I007


title: breast tumor- I005

description: aCGH data from ER+ breast tumor

source_name: Cyrobanked tumor Pat_ID I005


title: breast tumor - I007

source_name: Pat_ID I007


title: breast tumor - I005

source_name: Pat_ID I005


title: breast tumor - b0484

source_name: TISSUE_ID b0484


title: embryonic hearts, RA treatment, T12h, biological replicate2


title: embryonic hearts, DMSO treatment, T4h, biological replicate3

description: Gene expression data of zebrafish embryonic hearts extracted from 76 hpf old embryos at 4 h post RA dosing

source_name: Zebrafish embryonic heart at the age of 76hpf old


title: embryonic hearts, RA treatment, T4h, biological replicate3


title: breast tumor-b0472

source_name: TISSUE_ID b0472


title: breast tumor-b0417

source_name: TISSUE_ID b0417


title: embryonic hearts, RA treatment, T12h, biological replicate1


title: embryonic hearts, RA treatment, T4h, biological replicate2


title: breast tumor-b0335

source_name: TISSUE_ID b0335


title: Array2609_TUN_BiolRep2_TechRep2

city: Tallahassee

first: Andre

middle: Southernman Teixeira

last: Irsigler

state: FL

address: Chieftan Way

department: Biology

institute: Florida State University

hyb_protocol: the microarray slides were incubated for 45 min in 50 ml of a pre-hybridization buffer 5X SSC, 0.1% (w/v) SDS and 1% (w/v) of BSA (all from Sigma), washed sequentially in ultra-pure water and iso(2)-Propanol (Fisher, Waltham, MA), and air-dried. Slides were then incubated with Cy3- and Cy5-labeled cDNA (20 μl) from treated and control samples for 20 h at 42°C in a water bath protected from light. The hybridization buffer consisted of 0.5% SDS (w/v), 5X SSC, 5X Denhardt’s, 50% (v/v) formamide, 0.5 μg/μl denatured calf thymus DNA (all from Sigma) and 0.5 μg/μl polyA RNA (Amersham Biosciences). Following incubation, slides were washed sequentially in three steps in the following solutions: (1) 1X SSC, 0.2% (w/v) SDS, (2) 0.1X SSC, 0.2% (w/v) SDS, and (3) 0.1X SSC

scan_protocol: Microarray slides were scanned at the Cy3 (530 nm) and Cy5 (650 nm) wavelengths with a ScanArray 4000 laser fluorescent scanner (Packard Bioscience, Perkin Elmer, Wellesley, MA), at a laser power of 100% and photomultiplier tube (PMT) gain of 75%

data_processing: The image analysis and calculation of mean background-subtracted intensity of the spots were performed using QuantArray software version 2.2 (PerkinElmer). Normalization based on the LOWESS algorithm [42] and data analysis were performed using Genespring software version 7.2 (Agilent Technologies, Santa Clara, CA)

organism: Glycine max

source_name: RNA from soybean leaves submmited to DMSO control

label_protocol: 10 μg of total RNA were reverse-transcribed with the SuperScriptTM Indirect cDNA Labeling System (Invitrogen) in the presence of cyanine-3-dUTP (Cy3-dUTP) or cyanine-5-dUTP (Cy5-dUTP; Amersham Biosciences, Piscataway, NJ) according to the manufacturer’s instructions. RNA samples from each biological replicate were labeled twice, once with each dye

extract_protocol: Total RNA was extracted from frozen leaves with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions from the manufacturer, and further purified through silica columns

tag: aerial portions of three-week-old soybean plants excised below the cotyledons and directly treated with respective solutions

source_name: RNA from soybean leaves submmited to TUN treatment


title: breast tumor-b0463

source_name: TISSUE_ID b0463


title: embryonic hearts, DMSO treatment, T4h, biological replicate2


title: breast tumor-b0307

source_name: TISSUE_ID b0307


title: breast tumor - I016

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I016

tag: ER Status

source_name: Normal Blood


title: Array2609_TUN_BiolRep2_TechRep1


title: embryonic hearts, RA treatment, T12h, biological replicate3

source_name: Zebrafish embryonic heart at the age of 84hpf old


title: Array2248_TUN_BiolRep1_TechRep2


title: breast tumor-b0473

source_name: TISSUE_ID b0473


title: embryonic hearts, RA treatment, T4h, biological replicate1


title: embryonic hearts, DMSO treatment, T2h, biological replicate2

description: Gene expression data of zebrafish embryonic hearts extracted from 74 hpf old embryos at 2 h post RA dosing

source_name: Zebrafish embryonic heart at the age of 74hpf old


title: embryonic hearts, DMSO treatment, T4h, biological replicate1


title: embryonic hearts, DMSO treatment, T2h, biological replicate3


title: Array2248_TUN_BiolRep1_TechRep1


title: HT29 E+Gb

city: Bologna

first: rossella

last: solmi

address: Via Belmeloro 8

country: Italy

institute: University of Bologna

description:
Comparison of untreated and treated human colon cancer cell line global gene expression was performed using hybridization of the microarray Ocimum Pan Human 40K array A, an oligonucleotide-based array on a glass slide containing 20,000 gene-specific probes (50 mer) (Ocimum Biosolutions, Hyderabad, India).
Gene expression measurements were performed by a process of RNA extraction, reverse transcription and labeling of cDNA. In this process reference (i.e. untreated) and investigated (i.e treated) cDNA are labeled with different dyes and then co-hybridized on slides containing cDNA fragments. The slides are then scanned with a laser system, and two false color images are generated for each hybridization with cDNA from the investigated and reference sample.

hyb_protocol: In one reaction mRNA is reverse transcrbed into florescently labeled cDNA. CyDye-labeled cDNA was purified by G-50 columns (CyScribe GFX Pirification kit no.27-9606-02, Amersham Bioscence, Europe, Freiburg, Germany).We added respectively 130 µL of preheated hybridization buffer to Cy3- or Cy5-fluorescently labeled reference, and proceeded to investigate cDNA. For hybridization we used the microarray "Gene Frame" as a cover slip to prevent reagent loss due to evaporation during incubation at 37°C overnight. In a set of hybridization (n=5) Caco-2 untreated cells were labeled with Cy3-dUTP fluorochrome and the reference Caco-2 treated cells with Cy5-dUTP fluorochrome respectively. In a second set of hybridization (n=5) HT-29 untreated cells were labeled with Cy3-dUTP fluorochrome when compared with EGF, Gefitinib and EGF plus Gefitinib and EGF plus Cetuximab HT-29 treated cells (labeled with Cy5-dUTP fluorochrome) and labeled with Cy5-dUTP fluorochrome when compared with Cetuximab and (labeled with Cy3-dUTP fluorochrome). Washing was performed three times for 10 min with 1 x saline sodium citrate (SSC), 0.1% sodium dodecyl sulfate (SDS) at 42 °C, and three times for 5 min with 0.1 x SSC at room temperature. Slides were dried by centrifugation for 2 min at 2000 rpm.

scan_protocol: A GenePix 4000a DNA microarray scanner (Axon, Union City, CA, USA) was used to scan the slides under dried conditions.

data_processing:
All statistical analyses on microarray data were performed using R software v2.5.0  [http://www.r-project.org/] and the Bioconductor software package [http://www.bioconductor.org/biocLite.R]. The microarray data were initially background-corrected using a normal plus exponential convolution model, normalized both within arrays using a method that normalizes the M-values for a each single microarray using robustly fitted regression splines  for each print-tip group and uses empirical Bayesian approach to shrink the individual print-tip curves towards a common value, and subsequently between arrays using a method which ensures that the A-values (average intensities) have the same empirical distribution across arrays, leaving the M-values (log-ratios) unchanged.
After the normalization step the probes were pre-filtered on the basis of empty spots and negative control intensity distribution over all the arrays. A threshold of log intensity = 6.2 was chosen. On this basis 16,443 out of 20,160 probes that showed a mean intensity  >  6.2  in at least one sample were considered for further analysis.
Hierarchical agglomerative clustering was performed on the correlation distance between samples.
A separate channel analysis was applied to the dataset; a mixed linear model was fitted to data after estimating the correlation between the two channels for the same spot.
A moderated t statistic was computed using an empirical Bayes method to shrink the probe-wise sample variances towards a common value and to augment the degrees of freedom for individual variances34. The Benjamini Hochberg method for multiple tests was used to obtain an adjusted p value.

source_name: Total RNA from colon cancer untreated cells labeled with Cyanine-3 (green)

label_protocol: 30 μg of total RNA was used for each sample. cDNA was synthesized using a CyScribe First-Strande cDNA Labeling Kit Cat.no RPN6200(Amersham Biosciences,  that provides reagents for praparation of Cy3  labeled cDNA probes.

extract_protocol: RNA was extracted from the cells using Total NucleoSpin RNA II kit(machery-Nagel, Germany Tech-Bio).

tag: HT-29 cell lines untreated

source_name: Total RNA from  HT-29 EGFplusGefitinib treated cells labeled with Cyanine-5(red)

label_protocol: 30 μg of total RNA was used for each sample. cDNA was synthesized using a CyScribe First-Strande cDNA Labeling Kit Cat.no RPN6200(Amersham Biosciences,  that provides reagents for praparation of Cy5 labeled cDNA probes.

tag: HT-29 EGFplusGefitinib treated


title: Array2250_PEG_BiolRep2_TechRep2

source_name: RNA from soybean leaves submmited to water control

source_name: RNA from soybean leaves submmited to PEG treatment


title: HT29 E+Cx

source_name: Total RNA from  HT-29 EGFplusCetuximab treated cells labeled with Cyanine-5(red)

tag: HT-29 EGFplusCetuximab treated


title: HT29 Gb

source_name: Total RNA from  HT-29 Gefitinib treated cells labeled with Cyanine-5(red)

tag: HT-29 Gefitinib treated


title: HT29 Cx

source_name: Total RNA from colon cancer Cetuximab treated cells labeled with Cyanine-3(green)

tag: HT-29 cetuximab 10nM treated

source_name: Total RNA from HT-29 untreated cells labeled with Cyanine-5(red)

tag: HT-29 untreated


title: embryonic hearts, RA treatment, T2h, biological replicate3


title: embryonic hearts, DMSO treatment, T1h, biological replicate1

description: Gene expression data of zebrafish embryonic hearts extracted from 73 hpf old embryos at 1 h post RA dosing

source_name: Zebrafish embryonic heart at the age of 73hpf old


title: embryonic hearts, RA treatment, T1h, biological replicate3


title: embryonic hearts, DMSO treatment, T2h, biological replicate1


title: Array2244_PEG_BiolRep1_TechRep2


title: LCM 800 biological rep5

status: Public on Sep 11 2007

city: Chicago

first: Jian

last: Zhou

state: IL

address: 5841 S Maryland Ave

department: functional Genomics Facility

institute: University of Chicago

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Genechip Scanner 3000.

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

organism: Rattus norvegicus

source_name: rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: regular rat diet

extract_protocol: LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.

treatment_protocol: no treatment; kidneys were immediately frozen after dissection

tag: Lewis-hsd rat

tag: Age

value: 18 weeks


title: breast tumor - I083

description: aCGH data from ER+ breast tumor

source_name: Cryobanked tumor Pat_ID  I083

tag: PR Status

tag: ErBB2 amplification

tag: age

tag: grade

tag: stage

tag: node

tag: Normal


title: Array2250_PEG_BiolRep2_TechRep1

tag: aerial portions of three-week-old soybean plants excised below the cotyledons and directly treated with respective solutions


title: Array2244_PEG_BiolRep1_TechRep1


title: embryonic hearts, DMSO treatment, T1h, biological replicate3

tag: Genotype


title: LCM 800 biological rep1


title: embryonic hearts, RA treatment, T2h, biological replicate2


title: iron biological rep4

source_name: untreated rat kidney glomeruli

extract_protocol: Paired kidneys from both normal and anti-Thy1.1 rats were collected.  Following a mid-line incision, the aorta was cannulated and one kidney perfused with iron oxide particles (NDT vol 9 p304).  The renal artery of the contra-lateral kidney was clamped to prevent its perfusion by iron oxide. Iron oxide containing glomeruli from the perfused kidney were isolated by a combined sieving technique and magnetic purification; this technique resulted in a glomerular purity of >99% by phase contrast microscopy. Total RNA from glomeruli was extracted using Trizol (Invitrogen, Carlsbad, CA) as per the manufacturer's instructions with only minor modifications.  The quality of all RNA samples was assured by evaluation on an Agilent Technologies 2100 Bioanalyzer (Palo Alto, CA).


title: LCM 800 biological rep2


title: embryonic hearts, DMSO treatment, T1h, biological replicate2


title: Caco-2 E

data_processing:
All statistical analyses on microarray data were performed using R software v2.5.0  [http://www.r-project.org/] and the Bioconductor software package [http://www.bioconductor.org/biocLite.R]. The microarray data were initially background-corrected using a normal plus exponential convolution model, normalized both within arrays using a method that normalizes the M-values for a each single microarray using robustly fitted regression splines  for each print-tip group and uses empirical Bayesian approach to shrink the individual print-tip curves towards a common value, and subsequently between arrays using a method which ensures that the A-values (average intensities) have the same empirical distribution across arrays, leaving the M-values (log-ratios) unchanged.
After the normalization step the probes were pre-filtered on the basis of empty spots and negative control intensity distribution over all the arrays. A threshold of log intensity = 6.2 was chosen. On this basis 16,443 out of 20,160 probes that showed a mean intensity  >  6.2  in at least one sample were considered for further analysis.

label_protocol: 30 μg of total RNA was used for each sample. cDNA was synthesized using a CyScribe First-Strande cDNA Labeling Kit Cat.no RPN6200(Amersham Biosciences,  that provides reagents for praparation of Cy3 labeled cDNA probes.

extract_protocol: RNA was extracted from the cells using Total NucleoSpin RNA II kit(machery-Nagel, Germany Tech-Bio)

tag: Caco-2 cell lines untreated

source_name: Total RNA from Caco-2 EGF treated cells labeled with Cyanine-5(red)

label_protocol: 30 μg of total RNA was used for each sample. cDNA was synthesized using a CyScribe First-Strande cDNA Labeling Kit Cat.no RPN6200(Amersham Biosciences),  that provides reagents for praparation of Cy5 labeled cDNA probes.

tag: Caco-2 EGF treated


title: embryonic hearts, RA treatment, T1h, biological replicate2


title: Caco-2 Gb

source_name: Total RNA from Caco-2 Gefitinib treated cells labeled with Cyanine-5(red)

tag: Caco-2 Gefitinib treated


title: Array2457_AZC_BiolRep2_TechRep2

source_name: RNA from soybean leaves submmited to AZC treatment


title: HT29 E

tag: HT-29 cell lines untreated

source_name: Total RNA from HT-29  EGF treated cells labeled with Cyanine-5(red)

tag: HT-29 EGF treated


title: Array2108_AZC_BiolRep1_TechRep1

tag: aerial portions of three-week-old soybean plants excised below the cotyledons and directly treated with respectives solutions


title: LCM 20 biological rep4

tag: Lewis-hsd rat


title: Caco-2 E+Cx

source_name: Total RNA from Caco-2  EGFplusCetuximab treated cells labeled with Cyanine-5(red)

tag: Caco-2 EGFplusCetuximab treated


title: Caco-2 E+Gb

source_name: Total RNA from colon cancer untreated cells labeled with Cyanine-3 (green)

source_name: Total RNA from Caco-2 EGFplusGefitinib treated cells labeled with Cyanine-5(red)

tag: Caco-2 EGFplusGefitinib treated


title: Array2457_AZC_BiolRep2_TechRep1

source_name: RNA from soybean leaves submmited to water control


title: iron biological rep3

tag: Age


title: embryonic hearts, RA treatment, T2h, biological replicate1

source_name: Zebrafish embryonic heart at the age of 74hpf old


title: embryonic hearts, RA treatment, T1h, biological replicate1


title: iron biological rep2


title: iron biological rep1


title: Caco-2 Cx

tag: Caco-2 cetuximab 10nM treated

source_name: Total RNA from Caco-2 untreated cells labeled with Cyanine-5(red)

tag: Caco-2 untreated


title: 600 nM alpha factor 60min

city: Rehovot

first: Ofer

last: Sarig

address: Weizmann Institute of Science

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: S.cerevisiae a-type cells were compared before and after (60 minutes) addition of alpha factor (600nM).

hyb_protocol: Arrays were purchased from the Microarray Centre, University Health Network, Ontario, where PCR products are printed. For each hybridization, cDNA samples were labeled with Cy3 and Cy5 and combined with blockers: 5?g Herring sperm (Promega), 5?g tRNA (Gibco) and 17.5?g Poly A (Poly A oligos were synthesized with mixed length of 40, 50 and 60 Adenine residues). The labeled cDNAs were concentrated to 40?l using Microcon (Millipore) and 40?l of hybridization x2 solution (10x SSC, 50% formamide and 0.2% SDS) was added. Microarrays containing all yeast ORFs were pre-hybridized by incubating at 42ºC for 45 minutes in a solution containing 1% BSA, 25% formamide, 5x SSC and 0.1% SDS. The slides were washed in sterile water and dried by centrifugation (3 minutes, 2000 rpm).  The labeled samples were boiled for 5 minutes, centrifuged for 1 minute, hybridized on the slide and placed in a hybridization chamber (Corning) for overnight incubation at 42ºC. The slides were then washed for 5 minutes at 42ºC with a solution containing 2x SSC and 0.1% SDS. Additional wash was performed at room temperature with a solution containing 0.1x SSC and 0.1% SDS, followed by three additional washes at room temperature in 0.1x SSC solution.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience) and image intensity data were extracted and analyzed with QuantArray analysis software.

data_processing: For each array, bad spots were omitted from the analysis. For each spot, the Quantarray program outputs the level of signal intensity and background fluorescence. As a first step, we re-defined the spot intensity by subtracting the spot-specific background. For each channel (Cy3 or Cy5) we then calculated the value of background signal, defined by the mean (intensity-background) of the controlled spots printed with 3x SSC buffer. All intensity values below this background level were reset to this background level. The data for each spot was then transformed into a log2-ratios. The data was normalized by subtracting from each log2ratio the median. Values of duplicates were averaged.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae a-type cells 60 minutes after addition of alpha factor (600nM)

label_protocol: The cDNA from alpha-factor treated and untreated cells was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

growth_protocol: Cells were grown on YPD to log phase at 30oC prior to addition of alpha-factor

extract_protocol: 5 O.D. units of cells were collected, pelleted and immediately frozen. Total RNA was obtained using RNeasy yeast RNA purification kit (Qiagen).

tag: Strain

value: W303-1a, bar1delta, haploid

source_name: S. cerevisiae grown in YPD at 30oC

label_protocol: cDNA was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

tag: For reference we used the same culture prior to addition of alpha-factor, in which cells were grown to log phase in YPD at 30oC.


title: Array2108_AZC_BiolRep1_TechRep2


title: 600 nM alpha factor 90min

description: S.cerevisiae a-type cells were compared before and after (90 minutes) addition of alpha factor (600nM).

source_name: S.cerevisiae a-type cells 90 minutes after addition of alpha factor (600nM)


title: 60 nM alpha factor 30min

description: S.cerevisiae a-type cells were compared before and after (30 minutes) addition of alpha factor (60nM).

source_name: S.cerevisiae a-type cells 30 minutes after addition of alpha factor (60nM)


title: 60 nM alpha factor 60min

description: S.cerevisiae a-type cells were compared before and after (60 minutes) addition of alpha factor (60nM).

source_name: S.cerevisiae a-type cells 60 minutes after addition of alpha factor (60nM)


title: 60 nM alpha factor 90min

description: S.cerevisiae a-type cells were compared before and after (90 minutes) addition of alpha factor (60nM).

source_name: S.cerevisiae a-type cells 90 minutes after addition of alpha factor (60nM)


title: 600 nM alpha factor 5min

description: S.cerevisiae a-type cells were compared before and after (5 minutes) addition of alpha factor (600nM).

source_name: S.cerevisiae a-type cells 5 minutes after addition of alpha factor (600nM)


title: LCM 800 biological rep3

source_name: rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication


title: 60 nM alpha factor 15min

description: S.cerevisiae a-type cells were compared before and after (15 minutes) addition of alpha factor (60nM).

source_name: S.cerevisiae a-type cells 15 minutes after addition of alpha factor (60nM)


title: 60 nM alpha factor 5min

description: S.cerevisiae a-type cells were compared before and after (5 minutes) addition of alpha factor (60nM).

source_name: S.cerevisiae a-type cells 5 minutes after addition of alpha factor (60nM)


title: LCM 20 biological rep3


title: 0.6 nM alpha factor 60min

description: S.cerevisiae a-type cells were compared before and after (60 minutes) addition of alpha factor (0.6nM).

source_name: S.cerevisiae a-type cells 60 minutes after addition of alpha factor (0.6nM)


title: 6 nM alpha factor 30min

description: S.cerevisiae a-type cells were compared before and after (30 minutes) addition of alpha factor (6nM).

source_name: S.cerevisiae a-type cells 30 minutes after addition of alpha factor (6nM)


title: 6 nM alpha factor 15min

description: S.cerevisiae a-type cells were compared before and after (15 minutes) addition of alpha factor (6nM).

source_name: S.cerevisiae a-type cells 15 minutes after addition of alpha factor (6nM)


title: LCM 20 biological rep1


title: 6 nM alpha factor 90min

description: S.cerevisiae a-type cells were compared before and after (90 minutes) addition of alpha factor (6nM).

source_name: S.cerevisiae a-type cells 90 minutes after addition of alpha factor (6nM)


title: 6 nM alpha factor 60min

description: S.cerevisiae a-type cells were compared before and after (60 minutes) addition of alpha factor (6nM).

source_name: S.cerevisiae a-type cells 60 minutes after addition of alpha factor (6nM)


title: 0.6 nM alpha factor 15min

description: S.cerevisiae a-type cells were compared before and after (15 minutes) addition of alpha factor (0.6nM).

source_name: S.cerevisiae a-type cells 15 minutes after addition of alpha factor (0.6nM)


title: 0.6 nM alpha factor 90min

description: S.cerevisiae a-type cells were compared before and after (90 minutes) addition of alpha factor (0.6nM).

source_name: S.cerevisiae a-type cells 90 minutes after addition of alpha factor (0.6nM)


title: 6 nM alpha factor 5min

description: S.cerevisiae a-type cells were compared before and after (5 minutes) addition of alpha factor (6nM).

source_name: S.cerevisiae a-type cells 5 minutes after addition of alpha factor (6nM)


title: 600 nM alpha factor 120min

description: S.cerevisiae a-type cells were compared before and after (120 minutes) addition of alpha factor (600nM).

source_name: S.cerevisiae a-type cells 120 minutes after addition of alpha factor (600nM)

source_name: S. cerevisiae grown in YPD at 30oC


title: LCM 800 biological rep4

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: bone_marrow_03

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description: MDC vs control genomic DNA

hyb_protocol: Hybridization: 1. Add the following components in the order indicated to reaction tubes containing 150 l of purified Cy5- and Cy3-labeled sample mixture: 50µl Cot-1 DNA (1.0 mg/ml) (Invitrogen 15279-011), 50µl Agilent 10x Blocking Reagent, 250µl Agilent

scan_protocol: Scanned on Agilent Array scanner G2505B following manufacturers recommendations, scan resolution: 10µm. Images were quantified using Feature Extraction Software (version A.7.5.1, June 2004) (Agilent Technologies).

data_processing: Linear&LOWESS normalized log10 ratios (red/green) (standard settings of Feature Extraction Software), converted to log2 ratios (test/reference) afterwards

source_name: bone marrow

label_protocol: Labelling: 1.) Digestion of genomic DNA: Mix the following components on ice in the order stated: 15µl Nuclease free water, 5µl 10x Buffer C (Promega), 2.5µl Alu I (10u/ul)( Promega P/N R6281), 2.5µl Rsa I (10U/ul) (Promega P/N R6371). Dilute 2-5 ug genom

extract_protocol: For DNA isolation archieved bone marrow cells were washed in PBS and DNA was isolated with QIAmp DNA Blood Midi Kit (Qiagen, Hilden, Germany) according to the protocol of the manufacturer.

tag: WHO classification

value: 5q- syndrome, bm blasts (%):1, sex/age at diagnosis (years):female/49, karyotype:46,XX,del(5)(q12q33)[17]/46,XX[3], % del5q (FISH):35, % del5q (karyogram)85

source_name: human genomic female DNA: Promega G1521

tag: control

value: pooled female DANN


title: LCM 20 biological rep2


title: 0.6 nM alpha factor 30min

description: S.cerevisiae a-type cells were compared before and after (30 minutes) addition of alpha factor (0.6nM).

source_name: S.cerevisiae a-type cells 30 minutes after addition of alpha factor (0.6nM)


title: bone_marrow_02

description: MDC vs control genomic DNA

value: 5q- syndrome, bm blasts (%):1, sex/age at diagnosis (years):female/70, karyotype:46,XX,del(5)(q13q33)[17]/46,XX[3], % del5q (FISH):57, % del5q (karyogram)85


title: bone_marrow_09

description: MDC vs control genomic DNA

value: AML/unclassified, bm blasts (%):30, sex/age at diagnosis (years):female/79, karyotype:46,XX,del(5)(q13q33)[3], % del5q (FISH):91, % del5q (karyogram)100


title: 600 nM alpha factor 30min

description: S.cerevisiae a-type cells were compared before and after (30 minutes) addition of alpha factor (600nM).

source_name: S.cerevisiae a-type cells 30 minutes after addition of alpha factor (600nM)


title: 0.6 nM alpha factor 5min

description: S.cerevisiae a-type cells were compared before and after (5 minutes) addition of alpha factor (0.6nM).

source_name: S.cerevisiae a-type cells 5 minutes after addition of alpha factor (0.6nM)


title: 1624-43

city: Atlanta

first: Samantha

middle: Ann

last: Roberts

state: GA

address: 1510 Clifton Road

department: Microbiology

institute: Emory University

description: JRS1616/pREG696 is our MGAS5005 covR rivRX double knockout carrying empty vector. JRS1616/pJRS1624 is our covR rivRX double knockout carrying a plasmid which overexpresses rivRX.

hyb_protocol: 60 pmol each of Cy-dye (reference cDNA (Cy5) and test cDNA (Cy3)) were combined in 60 ml hybridization buffer 1 (Ambion), denatured and hybridized to the array at 42°C for at least 16 h, followed by subsequent washes. Output data (F635 mean-B635, F532 mean-B532, flags) was filtered to set any spots that did not exceed 2SD above a background threshold to the threshold value to avoid spurious expression ratios. Remaining spots were averaged and normalized before statistical analysis.

scan_protocol: The washed arrays were scanned on a GenePix 4000A scanner (Axon instruments). The resulting images were inspected to remove values from bad spots (for example, those affected by scratches) and analyzed using GenePix Pro 3.0 software.

data_processing: Global normalization. Genes which had an average Cy3/Cy5 value below a threshold value (background + 1standard deviation) do not have a value. In addition, values are only given for genes which are present in the genome of MGAS5005 (ie, ID_REFs that begin with NT01).

organism: Streptococcus pyogenes

source_name: total RNA from M1 serotype GAS JRS1616/pJRS624

label_protocol: Labeled cDNA was generated using the Fairplay microarray labelling kit from Stratagene using random hexamers. Labeled cDNA was purified using QiaQuick PCR purification columns from Qiagen and concentrated using Microcon YM30 columns from Amicon. The amount of incorporated label was determined by measuring the absorbance at 550nm (Cy3) or 650nm (Cy5).

extract_protocol: Total RNA from mid-exponential phase cells was isolated using Epicentre Masterpure kit

value: JRS1616/pJRS1624  RNA prep:D

source_name: Pooled total RNA from M1 serotype GAS JRS1616/pREG696 and JRS1616/pJRS1624

tag: Strains

value: JRS1616/pREG696, JRS1616/pJRS1624   RNA preps:A, B, C, D for each strain


title: 0.06 nM alpha factor 30min

description: S.cerevisiae a-type cells were compared before and after (30 minutes) addition of alpha factor (0.06nM).

source_name: S.cerevisiae a-type cells 30 minutes after addition of alpha factor (0.06nM)


title: 0.06 nM alpha factor 60min

description: S.cerevisiae a-type cells were compared before and after (60 minutes) addition of alpha factor (0.06nM).

source_name: S.cerevisiae a-type cells 60 minutes after addition of alpha factor (0.06nM)


title: 0.2 nM alpha factor 90min

description: S.cerevisiae a-type cells were compared before and after (90 minutes) addition of alpha factor (0.2nM).

source_name: S.cerevisiae a-type cells 90 minutes after addition of alpha factor (0.2nM)


title: 0.2 nM alpha factor 120min

description: S.cerevisiae a-type cells were compared before and after (120 minutes) addition of alpha factor (0.2nM).

source_name: S.cerevisiae a-type cells 120 minutes after addition of alpha factor (0.2nM)


title: 1624-32

value: JRS1616/pJRS1624  RNA prep:B


title: 0.06 nM alpha factor 15min

description: S.cerevisiae a-type cells were compared before and after (15 minutes) addition of alpha factor (0.06nM).

source_name: S.cerevisiae a-type cells 15 minutes after addition of alpha factor (0.06nM)


title: 0.06 nM alpha factor 5min

description: S.cerevisiae a-type cells were compared before and after (5 minutes) addition of alpha factor (0.06nM).

source_name: S.cerevisiae a-type cells 5 minutes after addition of alpha factor (0.06nM)


title: 0.06 nM alpha factor 90min

description: S.cerevisiae a-type cells were compared before and after (90 minutes) addition of alpha factor (0.06nM).

source_name: S.cerevisiae a-type cells 90 minutes after addition of alpha factor (0.06nM)


title: 0.06 nM alpha factor 120min

description: S.cerevisiae a-type cells were compared before and after (120 minutes) addition of alpha factor (0.06nM).

source_name: S.cerevisiae a-type cells 120 minutes after addition of alpha factor (0.06nM)


title: bone_marrow_13

description: MDC vs control genomic DNA

hyb_protocol: Hybridization: 1. Add the following components in the order indicated to reaction tubes containing 150 l of purified Cy5- and Cy3-labeled sample mixture: 50µl Cot-1 DNA (1.0 mg/ml) (Invitrogen 15279-011), 50µl Agilent 10x Blocking Reagent, 250µl Agilent 2x Hybridization Buffer. 2. Transfer sample tubes to circulating water bath at 95°C.  Incubate at 95°C for 3.0 min, 3. then move to ice. 4. Transfer sample tubes to circulating water bath (bzw. Heizblock) 1at 37°C.  Incubate at 37°C for 30 min. 5. Remove samples from water bath. 6. Centrifuge 5 min at 17,900 x g (13,000 rpm in Eppendorf 5417R) in microfuge to pellet any precipitates. 7. Carefully remove supernatant materials. Detailed instructions on the use of Surehyb chambers can be found at www.agilent.com. Load a clean SureHyb gasket slide into the chamber base with the label facing up and aligned with the rectangular section of the chamber base.  Ensure that the gasket slide is flush with the chamber base and is not ajar.  Slowly dispense 490 l of hybridization mixture onto the gasket well in a “drag and dispense” manner. Place an array active side down onto the Surehyb gasket, so the numeric barcode side is facing up.  Assess that the sandwich-pair is properly aligned. Place the chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  Hand-tighten the clamp onto the chamber. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  Tap the assembly on a hard surface if necessary to move stationary bubbles. Set your hybridization rotator to rotate at 20 rpm.   Hybridize at 65oC for 40 hr. Wash: 1. Completely fill a first slide staining dish with Wash 1 (0.5x SSPE, 0.005% N-lauroylsarcosine) at room temperature. 2. Place slide rack into a second slide staining dish. Add magnetic stir bar. Fill the slide staining dish with enough Wash 1 (0.5x SSPE, 0.005% N-lauroylsarcosine) at room temperature to cover the slide rack. Place this dish on a magnetic stir plate. 3. Remove one hybridization chamber from incubator. 4. Disassemble the hybridization chamber and place the array-gasket sandwich in the first slide staining dish filled with Wash 1 (0.5x SSPE, 0.005% N-lauroylsarcosine) at room temperature. 5. With the sandwich completely submerged in Wash 1 (0.5x SSPE, 0.005% N-lauroylsarcosine), pry the sandwich open with one of the blunt ends of the tweezers. 6. Remove slide and place into slide rack in the second slide staining dish containing Wash 1 (0.5x SSPE, 0.005% N-lauroylsarcosine) at room temperature. Minimize exposure of the slide to air. 7. Repeat steps 7.9.6 and 7.9.7 for all remaining hybridization chambers in group.  A maximum of 4 disassembly procedures yielding 4 slides is advised if you are using a 10-slide rack. 8. When all slides in the group are placed into slide rack in staining dish, stir using setting 4 for 5.0 min. 9. During Wash 1 incubation put pre-warmed (37°C) 1.5 liter dish filled with water and containing a slide staining dish on the magnetic stirrer with heating element (setting 3.5). Fill the slide staining dish approximately ¾ full with Wash 2 (0.1x SSPE, 0.005% N-lauroylsarcosine) (pre-warmed to 37°C).  Add magnetic stir bar.  Maintain temperature of Wash 2 at 37°C. 10. Transfer slide rack to slide staining dish filled with Wash 2 at 37°C, and stir using setting 4 for 1.0 min. 11. Slowly remove slides from Wash2 trying to minimize droplets on the slide. It should take 5 to 10 s. to remove the slide rack. 12. Scan slides slides immediately to minimize impact of environmental oxidants on signal intensities.

label_protocol: Labelling: 1.) Digestion of genomic DNA: Mix the following components on ice in the order stated: 15µl Nuclease free water, 5µl 10x Buffer C (Promega), 2.5µl Alu I (10u/ul)( Promega P/N R6281), 2.5µl Rsa I (10U/ul) (Promega P/N R6371). Dilute 2-5 ug genomic DNA in 25 ul Water and add. Incubate the tubes in a circulating water bath or Thermocycler at 37oC for 2 hours, then transfer on ice. After the reaction is finished bring the volume of the reaction to 100 ul with water. 2.) Purification (Qiagen: QIAprep Miniprep Kit): 1. To prepare Buffer PE: Add ethanol (100%) to buffer PE (supplied with QIAprep Miniprep Kit) (see bottle label for volume). Mark appropriate checkbox to indicate that ethanol was added to bottle. 2. Add 500 µL of Buffer PB (supplied with QIAprep Miniprep Kit) to each 100 ul sample. 3. Apply sample to QIAprep Miniprep column. Centrifuge 60 s at 17,900 × g (13,000 rpm in Eppendorf 5417R) in a microcentrifuge. Discard flow-through. 4. Add 750-µL Buffer PE to each spin column. Centrifuge 60 s at 17,900 × g in a microcentrifuge. Discard flow-through. 5. Centrifuge 60 s at 17,900 × g in a microcentrifuge again. 6. Place the QIAprep spin column in a clean 1.5-mL microfuge tube. To elute DNA, add 25 µL of Buffer EB (10-mM Tris-Cl, pH 8.5) to the center of each spin column. Let stand at room temperature (RT) for 60 s. Centrifuge 60 s at 17,900 × g in a microcentrifuge to collect purified DNA. 7. Samples may be stored at –20 °C prior to labeling. 8. DNA concentration measurements using the NanoDrop ND-1000 UV-VIS spectrophotometer. 3.) Genomic DNA Labeling 1.Calculate volume (µL) of digested genomic DNA for a final 1.5 µg, 2. Transfer volume of digested genomic DNA calculated in step 1 to a nuclease-free 0.5-mL microfuge tube. 3. Add nuclease-free water to bring sample volume to a final volume of 21 µL. 4. Dispense 20-µL aliquots of 2.5× Random Primers Solution (supplied with BioPrime Kit) into each reaction tube. 5. Transfer sample tubes to thermocycler at 95 °C. Incubate at 95 °C for 5.0 min, then move to ice and incubate on ice 5.0 min. Mix the following components on ice: 5.0µl 10x dUTP Mix, 3µl Cy3-dUTP 1.0 mM or Cy3-dUTP 1.0 mM, 1µl ExoKlenow, dispense this 9µl mix into each reaction tube, transfer sample tubes to thermocycler at 37 °C. Incubate at 37 °C for 2 h, remove sample tubes from water bath, add 5.0 µL of Stop Buffer (supplied with BioPrime Kit) to each reaction tube. 4.) Cleanup of Labeled DNA: 1. Combine appropriate Cy5-labeled sample and Cy3-labeled sample for a mixture volume of approximately 100 µL, 2. Add 400 µL of 1× TE (pH 8.0) to each reaction tube, 3. Place Microcon YM-30 filters in a 1.5-mL microfuge tube, and load each sample into filter, 4. Centrifuge 10 min at 8,000 × g (8,700 rpm in Eppendorf 5417R) in a microcentrifuge at room temperature, 5. Discard flow-through, 6. Add 500-µL 1× TE (pH 8.0) to each filter. Centrifuge 10 min at 8,000 × g in a microcentrifuge at room temperature. 7. Discard flow-through. 8. Invert the filter into a fresh 1.5-mL microfuge tube. 9. Centrifuge 1.0 min at 8,000 × g in microcentrifuge at room temperature to collect purified sample. 10. Measure volume (µL) of each eluate until each sample volume is <150 µL. 11. Bring total sample volume to 150 µL with nuclease-free water.

value: 5q- syndrome, bm blasts (%):1, sex/age at diagnosis (years):female/72, karyotype:46,XX,del(5)(q22q33)[3]/46,XX[14], % del5q (FISH):45, % del5q (karyogram)18


title: 0.06 nM alpha factor 150min

description: S.cerevisiae a-type cells were compared before and after (150 minutes) addition of alpha factor (0.06nM).

source_name: S.cerevisiae a-type cells 150 minutes after addition of alpha factor (0.06nM)


title: 0.2 nM alpha factor 5min

description: S.cerevisiae a-type cells were compared before and after (5 minutes) addition of alpha factor (0.2nM).

source_name: S.cerevisiae a-type cells 5 minutes after addition of alpha factor (0.2nM)

source_name: S. cerevisiae grown in YPD at 30oC


title: 0.2 nM alpha factor 15min

description: S.cerevisiae a-type cells were compared before and after (15 minutes) addition of alpha factor (0.2nM).

source_name: S.cerevisiae a-type cells 15 minutes after addition of alpha factor (0.2nM)


title: 0.2 nM alpha factor 60min

description: S.cerevisiae a-type cells were compared before and after (60 minutes) addition of alpha factor (0.2nM).

source_name: S.cerevisiae a-type cells 60 minutes after addition of alpha factor (0.2nM)


title: 0.2 nM alpha factor 30min

description: S.cerevisiae a-type cells were compared before and after (30 minutes) addition of alpha factor (0.2nM).

source_name: S.cerevisiae a-type cells 30 minutes after addition of alpha factor (0.2nM)


title: 1624-42


title: 1624-40

value: JRS1616/pJRS1624  RNA prep:C


title: 1624-37

description: JRS1616/pREG696 is our MGAS5005 covR rivRX double knockout carrying empty vector. JRS1616/pJRS1624 is our covR rivRX double knockout carrying a plasmid which overexpresses rivRX. Four separate RNA preparations from each strain (RNA #A-D) were hybridized to duplicate arrays. Reference RNA consisted of pooled RNA from each preparation, labelled with Cy5.


title: 1624-36


title: CMix Self-Self 1

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

description: This experiment was conducted to study dye-byes effects. Channel 1 and Channel 2 have identical biological sample labeled with two different dyes.

hyb_protocol: Cy3 and Cy5 labeled probes were combined and competitively hybridized to microarrays for 18 hours at 37C.

scan_protocol: Slides were scanned using ScanArray 5000 fluorescent scanner (GSI Lumonics, Billerica, MA). The resulting images were quantified using QuantArray v3.0 image analysis software with the Fixed Circle spot finding algorithm software (GSI Lumonics, Billerica, MA) with a spot diameter of 150µm, an inner background diameter of 234µm, and an outer background diameter of 313µm. Minimum and maximum intensity limits for signal classification were the 55th and 90th percentile, and those for background classification were the 5th and 20th percentile.

data_processing: Raw quantitated array data was normalized using subaray-based quadratic correction algorithm.

source_name: CMix Ref1

label_protocol: indirect labeling protocol

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

tag: Total RNA was isolated from each of three rat livers and brains, and equal mass amounts of each of these six samples were combined to create a mixed RNA population. One 20 microgram aliquot of the total RNA mixture was used   to generate the labeled probe.

source_name: CMix Test1


title: CMix Self-Self 6

source_name: CMix Test2

tag: Total RNA was isolated from each of three rat livers and brains, and equal mass amounts of each of these six samples were combined to create a mixed RNA population. One 20 microgram aliquot of the total RNA mixture was used to generate the labeled probe.

source_name: CMix Ref2


title: CMix Self-Self 5


title: 1624-27

source_name: total RNA from M1 serotype GAS JRS1616/pJRS624

value: JRS1616/pJRS1624  RNA prep:A

source_name: Pooled total RNA from M1 serotype GAS JRS1616/pREG696 and JRS1616/pJRS1624


title: HeLa SNP

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description: genotype data

hyb_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual. Samples were hybridized at 48°C for 16 to 18 hours.

scan_protocol: Arrays were scanned with the GeneChip® Scanner 3000 using GeneChip Operating Software (GCOS).

data_processing: Genotyping was performed using GDAS (Affymetrix, Santa Clara, CA) and copy number values were calculated using dChip version 1.3. Stretches of homozygous SNPs equal or longer than 24 calls were defined as LOH.

label: Biotin Streptavidin Phycoerythin (SAPE)

source_name: HeLa

growth_protocol: cells were grown semiconfluent in RPMI 1640, supplemented with 10% FCS, streptomycin, and penicillin at 37ºC and 5% CO2

extract_protocol: DNA was isolated using the salting out procedure according to Miller and Polesky

tag: Cervical cancer cell line (HPV18)


title: CMix Self-Self 3

source_name: CMix Ref3

source_name: CMix Test3


title: CMix Self-Self 4

source_name: CMix Ref4

source_name: CMix Test4


title: CMix Self-Self 2


title: CMix Self-Self 7


title: 1624-28


title: bone_marrow_12

description: MDC vs control genomic DNA

source_name: bone marrow

value: 5q- syndrome, bm blasts (%):-, sex/age at diagnosis (years):female/73, karyotype:46,XX,del(5q)[4]/46,XX[17], % del5q (FISH):42, % del5q (karyogram)19

source_name: human genomic female DNA: Promega G1521


title: CMix Self-Self 8


title: CC10B

description: Copy number analysis of cervical cancer cell lines

hyb_protocol: Competitive hybridization

scan_protocol: GenePix Personal 4100A scanner (Axon Instruments, Westburg BV, Leusden, the Netherlands).

data_processing: limma

tag: DNA from cervical cancer cell line (HPV45)

source_name: Pooled reference DNA

extract_protocol: commercially available female DNA

tag: commercially available female DNAs (Promega, Leiden, the Netherlands) that represent DNA pools derived from at least seven individuals


title: 696-41

description: JRS1616/pREG696 is our MGAS5005 covR rivRX double knockout carrying empty vector. JRS1616/pJRS1624 is our covR rivRX double knockout carrying a plasmid which overexpresses rivRX.

source_name: total RNA from M1 serotype GAS JRS1616/pREG696

value: JRS1616/pREG696  RNA prep:D


title: SiHa SNP

description: genotype data

source_name: SiHa

label_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual.

tag: Cervical cancer cell line (HPV16)


title: SiHa

tag: DNA from cervical cancer cell line (HPV16)


title: bone_marrow_11

description: MDC vs control genomic DNA

value: MDS/unclassified, bm blasts (%):-, sex/age at diagnosis (years):female/80, karyotype:46,XX,del(5)(q22q33)[18]/46,XX[5], % del5q (FISH):63, % del5q (karyogram)78


title: 696-39


title: 696-38

value: JRS1616/pREG696  RNA prep:C


title: 696-35


title: CSCC7 SNP

description: genotype data


title: CC11+ SNP

description: genotype data

tag: Cervical cancer cell line (HPV67)


title: CSCC1 SNP

description: genotype data


title: HeLa

tag: DNA from cervical cancer cell line (HPV18)


title: bone_marrow_10

description: MDC vs control genomic DNA

value: 5q- syndrome, bm blasts (%):1, sex/age at diagnosis (years):female/42, karyotype:46,XX,del(5)(q13q33)[13]/46,XX[7], % del5q (FISH):72, % del5q (karyogram)65


title: 696-29

source_name: total RNA from JRS1616/pREG696

label_protocol: Labeled cDNA was generated using the Fairplay microarray labelling kit from Stratagene using random hexamers.  Labeled cDNA was purified using QiaQuick PCR purification columns from Qiagen and concentrated using Microcon YM30 columns from Amicon.  The amount of incorporated label was determined by measuring the absorbance at 550nm (Cy3) or 650nm (Cy5).

value: JRS1616/pREG696  RNA prep:A

tag: RNA preps

value: A, B, C, D for each strain


title: bone_marrow_04

description: MDC vs control genomic DNA

value: 5q- syndrome, bm blasts (%):<5, sex/age at diagnosis (years):female/69, karyotype:46,XX,del(5)(q22q33)[19]/46,XX[3], % del5q (FISH):78, % del5q (karyogram)86


title: CC8 SNP

description: genotype data

tag: Cervical cancer cell line (HPV45)


title: 696-26

source_name: JRS1616/pREG696 RNA prep A

source_name: Pooled total RNA from JRS1616/pREG696 and JRS1616/pJRS1624 RNA preps A,B,C, and D


title: CSCC1


title: bone_marrow_01

description: MDC vs control genomic DNA

value: 5q- syndrome, bm blasts (%):1, sex/age at diagnosis (years):male/84, karyotype:46,XY,del(5)(q14q33)[22], % del5q (FISH):75, % del5q (karyogram)100

value: pooled female DANN


title: bone_marrow_07

description: MDC vs control genomic DNA

value: 5q- syndrome, bm blasts (%):1, sex/age at diagnosis (years):female/68, karyotype:46,XX,del(5)(q13q33)[20], % del5q (FISH):82, % del5q (karyogram)100


title: CC10A


title: CasKi ArrayCGH

source_name: CasKi


title: 696-34

value: JRS1616/pREG696  RNA prep:B


title: 696-31


title: CC11-

tag: DNA from cervical cancer cell line (HPV67)


title: bone_marrow_06

description: MDC vs control genomic DNA

value: RAEB I, bm blasts (%):5, sex/age at diagnosis (years):male/72, karyotype:46,XY,del(5)(q22q33)[19]/46,XY[2], % del5q (FISH):85, % del5q (karyogram)86


title: CC11+


title: bone_marrow_08

description: MDC vs control genomic DNA

value: RAEB II, bm blasts (%):18, sex/age at diagnosis (years):female/71, karyotype:46,XX,del(5)(q22q33)[17]/46,XX[4], % del5q (FISH):83, % del5q (karyogram)77


title: CC11- SNP

description: genotype data


title: CC10B SNP

description: genotype data


title: CC10A SNP

description: genotype data


title: CS-B wt-rescued cell UVC-irradiated (2hour) replicate 3 U133A

status: Public on Sep 10 2007

city: Osaka-Sayama

first: Toshiro

last: Matsuda

state: Osaka

address: 377-2 Ohno-Higashi

department: Biochemistry

country: Japan

institute: Kinki University School of Medicine

description: Cockayne syndrome B wt-rescued cell

data_processing: Affymetrix Microarray suite version 5.0

source_name: cockayne syndrome B wt-rescued cell

label_protocol: Biotilated cRNA were prepared using RNA transcript labelling kit (Enzo).

extract_protocol: Cells were grown to 80-90% confluence, and total RNA collected in RNAeasy spin columns (Qiagen).

tag: cell line


title: bone_marrow_05

description: MDC vs control genomic DNA

value: 5q- syndrome, bm blasts (%):1, sex/age at diagnosis (years):female/49, karyotype:46,XX,del(5)(q13q33)[18]/46,XX[2], % del5q (FISH):43, % del5q (karyogram)90


title: CS-B wt-rescued cell UVC-irradiated (12hour) replicate 2 U133A

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell UVC-irradiated (12hour) replicate 3 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell UVC-irradiated (12hour) replicate 3 U133A

description: Cockayne syndrome B wt-rescued cell


title: CasKi

description: genotype data

source_name: CasKi SNP


title: CS-B wt-rescued cell UVC-irradiated (12hour) replicate 2 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell UVC-irradiated (12hour) replicate 1 U133A

description: Cockayne syndrome B wt-rescued cell


title: CC8


title: CS-B wt-rescued cell UVC-irradiated (2hour) replicate 3 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell UVC-irradiated (12hour) replicate 1 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell UVC-irradiated (2hour) replicate 2 U133A

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell unirradiated replicate 2 U133A

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell unirradiated replicate 3 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell unirradiated replicate 3 U133A

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell unirradiated replicate 1 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell UVC-irradiated (2hour) replicate 2 U133B

description: Cockayne syndrome B wt-rescued cell


title: CSCC7


title: CS-B wt-rescued cell UVC-irradiated (2hour) replicate 1 U133A

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell UVC-irradiated (2hour) replicate 1 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B wt-rescued cell unirradiated replicate 2 U133B

description: Cockayne syndrome B wt-rescued cell


title: CS-B cell UVC-irradiated (12hour) replicate 3 U133B

description: Cockayne syndrome B cell

source_name: cockayne syndrome B cell

extract_protocol: CS-B cells were grown to 80-90% confluence, and total RNA collected in RNAeasy spin columns (Qiagen).


title: CS-B cell UVC-irradiated (12hour) replicate 3 U133A

description: Cockayne syndrome B cell


title: CS-B cell UVC-irradiated (12hour) replicate 2 U133A

description: Cockayne syndrome B cell


title: CS-B cell UVC-irradiated (12hour) replicate 1 U133B

description: Cockayne syndrome B cell


title: CS-B wt-rescued cell unirradiated replicate 1 U133A

description: Cockayne syndrome B wt-rescued cell


title: CS-B cell UVC-irradiated (12hour) replicate 1 U133A

description: Cockayne syndrome B cell


title: CS-B cell UVC-irradiated (2hour) replicate 3 U133B

description: Cockayne syndrome B cell


title: CS-B cell UVC-irradiated (2hour) replicate 2 U133A

description: Cockayne syndrome B cell


title: CS-B cell UVC-irradiated (2hour) replicate 3 U133A

description: Cockayne syndrome B cell


title: CS-B cell UVC-irradiated (2hour) replicate 2 U133B

description: Cockayne syndrome B cell


title: WT 2 mon replicate 4

status: Public on Sep 08 2007

city: Ann Arbor

first: Swaroop

last: Anand

state: MI

address: 1000 Wall St.

department: Ophthalmology & Visual Sciences

institute: University of Michigan

description: Nrl ko samples were compared to wt at 2 months.

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix

data_processing: Signal quantification and normalization were performed using RMA

source_name: RNA

label_protocol: Enzo

extract_protocol: Trizol

tag: Tissue

value: whole retina


title: CS-B cell UVC-irradiated (2hour) replicate 1 U133B

description: Cockayne syndrome B cell

hyb_protocol: standard Affymetrix procedures


title: CS-B cell UVC-irradiated (12hour) replicate 2 U133B

description: Cockayne syndrome B cell


title: CS-B cell unirradiated replicate 1 U133B

description: Cockayne syndrome B cell


title: WT 2 mon replicate 3


title: CS-B cell UVC-irradiated (2hour) replicate 1 U133A

description: Cockayne syndrome B cell


title: CS-B cell unirradiated replicate 2 U133A

description: Cockayne syndrome B cell


title: CS-B cell unirradiated replicate 3 U133B

description: Cockayne syndrome B cell


title: WT 2 mon replicate 2


title: CS-B cell unirradiated replicate 1 U133A

description: Cockayne syndrome B cell

label_protocol: Biotilated cRNA were prepared using labelling kit (Enzo).


title: CS-B cell unirradiated replicate 3 U133A

description: Cockayne syndrome B cell


title: Nrl ko 2 mon replicate 3


title: WT 2 mon replicate 1


title: Nrl ko 2 mon replicate 4


title: CS-B cell unirradiated replicate 2 U133B

description: Cockayne syndrome B cell


title: Nrl ko 2 mon replicate 1


title: WT P10 replicate 4

description: Nrl ko samples were compared to wt at postnatal 10.


title: WT P10 replicate 1


title: Nrl ko P10 replicate 2


title: WT P10 replicate 2


title: WT P2 replicate 3

description: Nrl ko samples were compared to wt at postnatal 2.


title: WT P10 replicate 3


title: MA101: EC-test-rep 3

city: Hong Kong

first: Mary

last: Lee

address: 21 Sassoon Road

department: Dept of Pharmacology

country: China

institute: The University of Hong Kong

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Porcine Genome Array.

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

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

organism: Sus scrofa

source_name: coronary arterial endothelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA.

growth_protocol: porcine coronary arterial endothelial cells were brought to primary culture. Cultured endothelial cells for 1 weeks produced cells at passage one (control cells). Serial passaging was performed on a weekly basis until cells at passage four (senescent cells) were reached (test cells).

extract_protocol: Total RNA was extracted with Rneasy mini kit (Qiagen) performed according to the manufacturer's instructions.

treatment_protocol: Cultured endothelial cells for 1 weeks produced cells at passage one (control cells). Serial passaging was performed on a weekly basis until cells at passage four (senescent cells) were reached (test cells).  Both control and test cells at basal condition were collected for total RNA extraction for microarray analysis.

tag: farm pig/female/3 months


title: WT P2 replicate 4


title: Nrl ko 2 mon replicate 2


title: MA90: EC-test-rep 1


title: MA80: EC-control-rep 3


title: MA72: EC-control-rep 2


title: WT P2 replicate 2


title: Nrl ko P10 replicate 1


title: MA98: EC-test-rep 2


title: WT P2 replicate 1


title: Nrl ko P2 replicate 4


title: Nrl ko P2 replicate 3


title: MA69: EC-control-rep 1


title: Nrl ko P10 replicate 4


title: Nrl ko P2 replicate 1


title: Nrl ko P2 replicate 2


title: KIN28 0min

status: Public on Sep 07 2007

city: Tsukuba

first: Yoshinori

last: Murata

state: Ibaraki

address: 1-1 Ohwashi

department: Post-harvest Science and Technology Division

institute: Japan International Research Center for Agricultural Science

description: KIN28 overexpression 0min

hyb_protocol: The biotinyated cRNA (15 µg) prob was hybridized to DNA microarray at 45°C for 18 h

scan_protocol: The scanning of arrays was carried out using the GeneArray scanner (Agilent technologies)  Palto Alto, CA).

data_processing: The fluorescence intensities of array images were quantified using the Affymetrix  software package (Microarray Suite version 4.0.1). The statistical analysis after data  acquisition and normalization of expression data were carried out using the GeneSpring

source_name: S.cerevisiae before LiCl treatment

label_protocol: Accoding to the Affymetrix user's mannual

growth_protocol: The media used for S. cerevisiae were SC consisting of 2% glucose, 0.67% Bacto Yeast Nitrogen Base with ammonium sulfate (Difco Laboratories, Detroit, MI) and drop-out mix lacking leucine (SC-Leu), or lacking leucine and uracil (SC-Leu-Ura).

extract_protocol: Total RNA from S. cerevisiae was isolated by the method of Köhrer and Domdey. Poly A mRNA was enriched from total RNA by Oligotex dT30 mRNA purification kit (Takara Bio).

treatment_protocol: After incubation of the resultant transformants in SC-Ura or Sc-Leu-Ura medium at 25°C to the exponential growth phase, 200 mM LiCl was added. At the intervals (0-60 min), the cells were harvested and lysed.

tag: S.cerevisiae before LiCl treatment


title: KIN28 60min

description: KIN28 overexpression 60min

source_name: S.cerevisiae after 60min on LiCl treatment


title: POG1 60min

description: POG1 overexpression 60min

tag: S.cerevisiae after 60min on LiCl treatment


title: Nrl ko P10 replicate 3


title: POG1 0min

description: POG1 overexpression 0min


title: Control cells series 6, t=2 h after infection (ctrl_2h_rep3)

city: Haifa

first: Debbie

last: Lindell

address: Technion City

department: Department of Biology

institute: Technion - Israel Institute of Technology

description: no additional information

hyb_protocol: The cDNA was hybridized to the MD4-9313 custom Affymetrix array in aqueous hybridization solution (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, 7.8 % DMSO and 3 nM prelabeled Affymetrix hybridization B2 oligo control probe mix) during a 16 h incubation at 45 °C in a GeneChip Hybridization Oven 320 rotating at 60 rpm. Washes and stains were carried out on a GeneChip Fluidics Station 450 (Affymetrix) following the ProkGE_WS2v3 Affymetrix protocol. Briefly, following two stringency washes the array was sequentially incubated with 10 µg/mL streptavidin (Pierce Chemical), 5 µg/mL biotinylated anti-streptavidin goat antibody (Vector Laboratories) and 0.1 mg/mL goat IgG (Sigma) and 10 µg/mL streptavidin-phycoerythrin conjugate (Mol. Probes) each for 10 min at 25 °C and given a final wash.

scan_protocol: The arrays were scanned with the GeneChip Scanner (Affymetrix) at a 2.5 µm resolution with excitation set for 570 nm.

data_processing: The probe set summaries were calculated from perfect match probe intensities in Affymetrix CEL files using robust multi-array average (RMA) analysis with quantile normalization (as implemented in the Bioconductor package affy).

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

label_protocol: Synthesis of complementary DNA (cDNA), labeling, hybridization, staining and scanning was carried out according to Affymetrix protocols for E.coli with minor changes. Total RNA (2 µg) was denatured at 70 °C and annealed to random hexamer primers (25 ng/µl) at 25 °C for 10 min. The RNA was reverse transcribed to produce cDNA with Superscript II (25 U/µl – Invitrogen Life Technologies) and 0.5 mM dNTPs in the presence of 1 U/µl RNase Out RNase Inhibitor (Invitrogen). The mix was incubated at 25 °C for 10 min followed by 60 min incubations at 37 °C and 42 °C respectively. Superscript II was inactivated with a 10 min incubation at 70 °C. Sodium hydroxide (0.25 N) was used to remove RNA during a 30 min incubation at 65 °C, followed by neutralization with HCl. The cDNA was purified with MinElute PCR purification columns (Qiagen). Fragments of cDNA, 50-200 nt long, were produced from a 10 min incubation at 37 °C with DNase I (0.6 U per µg cDNA), followed by heat inactivation of the DNase I enzyme (10 min at 98 °C). The cDNA fragments were end-labeled with biotin using the BioArray Terminal Labeling Kit (Enzo) during a 60 min incubation at 37 °C. The reaction was stopped by freezing at –20 °C. The quality of biotin end-labeling was verified by gel-shift assays with NeutrAvidin (Pierce Chemicals) on 1% TBE agarose gels.

growth_protocol: Prochlorococcus MED4 was grown in the Pro99 seawater based medium amended with 10 mM HEPES (pH7.5) and 12 mM sodium bicarbonate at 21 °C under continuous white light at 25 µmol photon·m-1·s-1

extract_protocol: Total RNA was extracted using Ambion’s mirVana RNA isolation kit according to manufacturer’s instructions, after resuspending the pellet in 600 µl lysis/binding buffer from the kit. DNA was removed by DNase I digestion using the Turbo DNA-free kit (Ambion) according to manufacturer’s instructions. Eight µg of the nucleic acid extract was digested with 6 U of Turbo DNase during a 60 min incubation at 37 °C followed by DNase I inactivation with inactivation slurry. The RNA was purified and concentrated by sodium acetate/ethanol precipitation. DNA removal was verified by gel electrophoresis.

treatment_protocol: Prior to phage or spent medium addition, cells were concentrated to 108 cells·ml-1 by centrifugation (10,000 Xg for 10 min at 20 °C). The cultures were split into two subcultures. Just prior to t=0 h, phage or spent medium were added to the appropriate subcultures. Samples at different time points after treatment addition were collected by centrifugation (12,400 Xg for 15 min at 20 °C), resuspended in storage buffer (200 mM sucrose, 10 mM sodium acetate pH5.2, 5 mM EDTA), snap frozen in liquid nitrogen and stored at -80 °C. Prior to RNA extraction the samples were thawed on ice and the storage buffer was removed after spinning the cells for 2 min at 20,000 Xg at 20 °C.

tag: Uninfected control cells


title: Control cells series 6, t=1 h after infection (ctrl_1h_rep3)

description: no additional information


title: Control cells series 6, t=4 h after infection (ctrl_4h_rep3)

description: no additional information


title: Control cells series 6, t=3 h after infection (ctrl_3h_rep3)

description: no additional information


title: Foot Fibroblast UTX ChIP

city: Stanford

first: John

middle: Louis

last: Rinn

address: 2155 CCSR

department: Dermatology

institute: Stanford University

description: Foot IGG IP to normalize CHIP for spurious DNA

hyb_protocol: Nimblegen Hybridization protocol (http://www.nimblegen.com)

scan_protocol: Arrays were scanned using AXON 5 uM scanner

data_processing: Data was processed by the Nimblegen ChIP protocol in the Nimblescan software suite that uses TIFF images as input and generates PAIR (raw) and GFF (normalized) data files.

source_name: Human Foot Fibroblast

label_protocol: Nimblegen ChIP Labeling protocol (http://www.nimblegen.com)

growth_protocol: Cells were grown on 10 cM plates with DMEM media and 10% Fetal Bovine Serum

extract_protocol: Farnham lab ChIP protocol (http://www.genomecenter.ucdavis.edu/farnham/protocols/chips.html)

treatment_protocol: Cells were not treated other than trypsinization from the plates for cell pellet

tag: 73 year old male fibroblasts from ventral foot

source_name: FOOT IGG  Control

tag: Rabitt IGG control IP


title: Lung Fibroblast UTX ChIP

description: Lung IGG IP to normalize CHIP for spurious DNA

source_name: Human Lung Fibroblast

tag: Fetal Lung fibroblasts Cultured from Female embryo

source_name: Lung IGG  Control


title: Control cells series 6, t=8 h after infection (ctrl_8h_rep3)

description: no additional information


title: Control cells series 5, t=8 h after infection (ctrl_8h_rep2)

description: no additional information


title: KR_Isw2_ChIP_Input_Control

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N

institute: FHCRC

description: K215R Isw2 control "input" sample

hyb_protocol: according to manufacturers instructions

scan_protocol: according to manufacturers instructions

data_processing: Data was processed using Affymetrix Tiling Array Software. Data was quantile normalized, and log2 signals from each probe were reported.

label: 7ug of each sample was labeled with biotin

label_protocol: Samples were amplified and labeled according to manufacturers instructions

growth_protocol: Yeast cells grown in YPD 2% glucose to OD = 0.7

extract_protocol: Chip Assay: 500ml of yeast cells were grown to mid log phase (OD = 0.7), and cross-linked with the addition of formaldehyde to a final concentration of 1% for 20 minutes and then quenched with the addition of glycine to a final concentration of 125mM for 10 minutes.Cells were pelleted and washed in H20 then were digested with 3mg of Zymolase-100T (Seikagaku) in 30ml of buffer Z (50mM Tris:Cl pH 7.5, 1M sorbitol 10mM 2ME, 1mM PMSF, 2uM pepstatin, 0.6uM leupeptin, 2mM Benzamidine, 2ug/ml chymostatin-A) for 30 minutes at 30ºC with constant agitation. Nuclei were pelleted and resuspended with the addition of 5ml of buffer Q (10mM Tris:Cl pH7.5, 50mM NaCl, 10mM MgCl2, 1mM CaCl2, 0.075% NP40, 1mM PMSF, 2uM pepstatin, 0.6uM leupeptin, 2mM Benzamidine, 2ug/ml chymostatin-A) and nuclei were digested with the addition of ~200units of Micorococcal Nuclease (Worthington) for 20 minutes at 37ºC with constant agitation. Sample was flash frozen and thawed and 880ul of Buffer L was added (500mM Hepes KOH, 1.4M Nacl, 10mM EDTA, 10% Triton, 1% sodium Deoxycholate, 1mM PMSF, 2uM pepstatin, 0.6uM leupeptin, 2mM Benzamidine, 2ug/ml chymostatin-A). 1ml of the extract was saved and used as “input” whereas 4ml of this extract was then used in ChIP assay. As described in McConnell AD, Gelbart ME, Tsukiyama T. Mol Cell Biol. 2004 Apr;24(7):2605-13.

tag: Strain

value: S cerevisiae, BY 4741

tag: Isw2-K215R 3x Flag (MATa his3-1 leu2-0 met15-0 ura3-0 isw2::ISW2-K215R-3xFlag-KanMX)


title: Control cells series 5, t=3 h after infection (ctrl_3h_rep2)

description: no additional information


title: Control cells series 5, t=2 h after infection (ctrl_2h_rep2)

description: no additional information


title: Control cells series 5, t=0 h after infection (ctrl_0h_rep2)

description: no additional information


title: Control cells series 5, t=4 h after infection (ctrl_4h_rep2)

description: no additional information


title: WT_Isw2_ChIP_Input_Control

description: WT control "input" sample

tag: Isw2 3x Flag (MATa his3-1 leu2-0 met15-0 ura3-0 isw2::ISW2-3xFlag-KanMX)


title: WT Nucleosomes FL Biological Rep 2

description: Full length nucleosomal DNA ~150bp

hyb_protocol: Samples were hybridized according to the manufacturer's instructions.

scan_protocol: Samples were scanned according to the manufacturer's instructions.

source_name: WT Nucleosomes FL Biological Rep 2

label_protocol: Samples were labeled according to the manufacturer's instructions.

growth_protocol: Yeast were grown in a shaking flask log phase (OD = 0.7), in  YPD 2% Glucose at 30º C

extract_protocol: 500ml of yeast cells were grown to mid log phase (OD = 0.7), and cross-linked with the addition of formaldehyde to a final concentration of 2% for 20 minutes and then quenched with the addition of glycine to a final concentration of 125mM for 10 minutes. Cells were digested with 3mg of Zymolase-100T (Seikagaku) in 30ml of buffer Z (50mM Tris:Cl pH 7.5, 1M sorbitol 10mM 2ME) for 30 minutes at 30ºC with constant agitation. Nuclei were pelleted and resuspended with the addition of 5ml of buffer Q (10mM Tris:Cl pH7.5, 50mM NaCl, 10mM MgCl2, 1mM CaCl2, 0.075% NP40) and nuclei were digested with the addition of ~700units of Micorococcal Nuclease (Worthington) and 100units Exonuclease III for 20 minutes at 37ºC with constant agitation. Reaction was stopped with the addition of 1ml solution S (5% SDS, 100mM EDTA). RNA and proteins were removed with sequential additions of with RNaseA and Proteinase K. Crosslinks were reversed by incubation at 65ºC for 16 hours. SDS was precipitated from the solution with the addition of 2.5ml 3M potassium acetate pH5.5 followed by a centrifugation at 4000g for 5 minutes. DNA fragments were harvested from the supernatant with use of a G500 genomic column (Qiagen) according to instructions. DNA was then resolved on a 1.7% agarose gel and the band corresponding to mononucleosomal DNA (~150bp) was excised. The gel slice was placed in a dialysis bag and DNA extracted by electroelution and treated with CIP to remove terminal phosphates.

treatment_protocol: Log phase yeast cultures harvested by centrifugation

tag: S cerevisiae S288C  congenic to BY4741

tag: Genotype

value: WT (MATa his3-1 leu2-0 met15-0 ura3-0)


title: WT_Isw2_ChIP_biological_rep_2

description: Isw2 ChIP sample rep 1

tag: Strains


title: Control cells series 5, t=1 h after infection (ctrl_1h_rep2)

description: no additional information


title: Control cells series 4, t=8 h after infection (ctrl_8h_rep1)

description: no additional information


title: WT Nucleosomes FL Biological Rep 1

description: Full length nucleosomal DNA ~150bp

source_name: WT Nucleosomes FL Biological Rep 1


title: Control cells series 4, t=4 h after infection (ctrl_4h_rep1)

description: no additional information


title: Control cells series 4, t=3 h after infection (ctrl_3h_rep1)

description: no additional information


title: KR_Isw2_ChIP_biological_rep_1

description: KR Isw2 ChIP sample rep 1


title: Control cells series 4, t=1 h after infection (ctrl_1h_rep1)

description: no additional information


title: Control cells series 4, t=2 h after infection (ctrl_2h_rep1)

description: no additional information


title: isw2 Nucleosomes FL Biological Rep 1

description: Full length nucleosomal DNA ~150bp

source_name: isw2 Nucleosomes FL Biological Rep 1

value: delta isw2 (MATa his3-1 leu2-0 met15-0 ura3-0 isw2::HisG)