title: Plumbagin treated Replicate 1

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

country: China

institute: Jilin university

description: Biological replicate 1 of 2.

hyb_protocol: The samples were hybridized with Agilent whole genome oligo microarray,performed by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)in Agilent’s SureHyb Hybridization Chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing:
Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization. The 8 microarray data sets were normalized in Agilent Feature Extraction Software (mainly LOWESS normalization), and then genes marked present (P) or marginal (M) in at least 4 out of 8 samples ("All Targets Value") were chosen for further analysis.
The resulting file (showing raw and normalized data) extracted from Agilent Feature Extraction Software is linked as a supplementary file on the Series record. The details of the 8 samples are described in a PDF file linked to the Series record (NOTE: The samples 'Plumbagin' and 'chelerythrine' represent the submissions to GEO).
The resulting files extracted from Agilent Feature Extraction Software (version10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis.  Filtering with the Agilent GeneSpring GX software (version 11.0) yielded 3442 genes (as shown in Data table below).

organism: Mycobacterium tuberculosis

label_protocol: The samples were labeled using the Agilent Quick Amp labeling kit.

growth_protocol: Mycobacterium tuberculosis H37Rv was incubated in a rotary shaker. Subsequently, Plumbagin stock solution, prepared in dimethyl sulfoxide (DMSO), and DMSO was added to the culture,respectively. Then, the the cells were further incubated for a certain time.

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

tag: agent

value: Plumbagin

value: control (DMSO)


title: HMLE, Gsc, rep1

status: Public on Sep 20 2010

type: RNA

city: Cambridge

first: Piyush

middle: B.

last: Gupta

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research/MIT

description: Global gene expression signature upon salinomycin treatment

hyb_protocol: Standard Affymetrix protocol; hybridization was performed with high-throughput HT_HG-U133A arrays in 96-well format

scan_protocol: Scanned using an Affymetrix HT Scanner

data_processing: The data were RMA-normalized using the open-source R-project statistical software with bioconductor packages.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HMLE breast epithelial cells transduced with Gsc

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were grown in a 1:1 mixture of DMEM+10%FBS, insulin, hydrocortisone and MEGM.

extract_protocol: Total RNA was extracted from culture plates for each cell type using an RNeasy Mini kit coupled with an RNase-free DNase set (Qiagen).

treatment_protocol: Following retroviral transduction, cells were treated for 5 days with blasticidin (5ng/ml); after drug selection, cells were grown for at least one week prior to RNA extraction.

tag: cell type

value: HMLE

tag: tissue

value: breast

tag: genotype

value: SV40ER, hTERT


title: Wild type 2

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Slides were scanned using a “Geniom Real Time Analyzer” (febit biomed gmbh, Heidelberg, Germany). Wizard software on standard Microsoft Windows Workstation PC was used.

data_processing: summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1

label: biotin

organism: Mus musculus

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood from Tff3 KO as well as WT mice was collected in RNAprotect® Animal Blood Tubes (Qiagen GmbH, Hilden). About 400-500µl of peripheral blood were obtained from each animal. Following centrifugation of the blood samples at 5000 g for 10 min at room temperature (RT), the supernatant was discarded while the pellet was resuspended in 5ml RNase free water. After a second centrifugation step at 5000 g for 10 min and RT, isolation of total RNA including miRNA was performed using the miRNeasy kit (Qiagen GmbH, Hilden).

treatment_protocol: stored at -20 degree

tag: genotype/variation

value: wild type

tag: gender

value: male


title: Plumbagin treated Replicate 2

description: Biological replicate 2 of 2.

tag: strain


title: HMLE, Twist, rep3

source_name: HMLE breast epithelial cells transduced with Twist


title: Wild type 1


title: Wild type 4

value: female


title: Umbillical Cord blood (CB)-G0 [US22502695_251485029250_1_1]

city: Indianapolis

first: Brahmananda

middle: Reddy

last: Chitteti

state: IN

address: 980 W Walnut Streeet R3-c356

institute: Indiana University School of Medicine

description: Gene expression of G0 phase cells of CB derived CD34+ cells

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4 x 44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES, v.9.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. The signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.
For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). This software offers – among other features – the possibility to compare two single intensity profiles in a ratio experimen. All samples were labeled with Cy3, here, the ratio experiments are shown as control versus (vs.) sample experiments.
The gIsPosAndSignif column indicates with a value = 1 that the signal intensity is positive and significant above the background and a value = 0 that the signal intensity is not positive and significant above the background.

source_name: Umbillical Cord blood (CB)- G0

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec’s undisclosed procedure. Briefly, the amplification is based on a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. Amplified cDNA samples were quantified using the ND-1000 Spectrophotometer (NanoDrop Technologies). The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: BM and UCB samples were ficolled and mononuclear cells were collected followed by CD34+ selection using Miltenyi Magnetically Activated Cell Sorting (MACS) columns according to the manufacturer’s directions (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Mobilization was achieved by daily granulocyte colony-stimulating factor administration at 5 mg/kg (maximum of 480 mg/day) for 4 consecutive days. Apheresis was performed on day 5 and CD34+ cells were isolated by immunomagnetic selection on an Isolex 300i system (Nexell, Irvine, CA). To generate distinct and unique sets of data, we did not pool multiple samples from any tissue studied so that each sample or its replicate was from a single donor.  Purity of selected CD34+ fractions was assessed by flow-cytometric analysis with an antibody recognizing a different CD34 epitope (BD Biosciences, San Jose, CA). The efficiency of the MACS columns was over 80% and the efficiency of the Isolex 300i system exceeded 95%. All samples of selected CD34+ cells were cryopreserved prior to their use.

value: Umbillical Cord blood

value: CD34+ cells

tag: cell cycle phase


title: Chelerythrine treated Replicate 2

description: Biological replicate 2 of 2.

growth_protocol: Mycobacterium tuberculosis H37Rv was incubated in a rotary shaker. Subsequently, Chelerythrine stock solution, prepared in dimethyl sulfoxide (DMSO), and DMSO was added to the culture,respectively. Then, the the cells were further incubated for a certain time.

value: chelerythrine


title: HMLE, Twist, rep2


title: Wild type 3


title: tff3 KO 6

value: tff3 KO


title: Mobilized peripheral blood (MPB)-G1 [US22502695_251485029166_1_2]

description: Gene expression of G1 phase cells of mobilized periphearal blood derived CD34+ cells

source_name: Mobilized peripheral blood (MPB)- G1

value: Mobilized peripheral blood


title: Mobilized peripheral blood (MPB)-G0 [US22502695_251485029166_1_3]

description: Gene expression of G0 phase cells of mobilized periphearal blood derived CD34+ cells

source_name: Mobilized peripheral blood (MPB)- G0


title: Chelerythrine treated Replicate 1

description: Biological replicate 1 of 2.


title: tff3 KO 5


title: tff3 KO 4


title: Mobilized peripheral blood (MPB)-G1 [US22502695_251485029166_1_4]


title: HMLE, Twist, rep1


title: Umbillical Cord blood (CB)-G1 [US22502695_251485029165_1_2]

description: Gene expression of G1 phase cells of CB derived CD34+ cells

source_name: Umbillical Cord blood (CB)- G1


title: HMLE, pWZL, rep3

description: Global gene expression signature upon paclitaxel treatment

source_name: HMLE breast epithelial cells transduced with pWZL


title: Bone marrow (hBM)-G1 [US22502695_251485029165_1_4]

description: Gene expression of G1 phase cells of bone marrow derived CD34+ cells

source_name: Bone marrow (hBM)- G1

value: Bone marrow


title: HMLE, pWZL, rep2


title: HMLE, TGFb, rep1

source_name: HMLE breast epithelial cells transduced with TGFb


title: tff3 KO 3


title: HMLE, TGFb, rep2


title: tff3 KO 2


title: Mobilized peripheral blood (MPB)-G0 [US22502695_251485029166_1_1]


title: HMLE, pWZL, rep1


title: HMLE, TGFb, rep3


title: tff3 KO 1


title: Umbillical Cord blood (CB)-G0 [US22502695_251485029165_1_1]


title: AP/N vs WT Replicate 2

city: Salt Lake City

first: Anne

last: Moon

state: UT

department: Eccles Institute of Human Genetics

institute: University of Utah

description: Comparison of WT lung to fgf8 hypomorph lung, replicate 2.

hyb_protocol: Agilent Two-color hyb/wash protocol

scan_protocol: Arrays were scanned on an Agilent G2505B scanner at 5 micron resolution using the extended dynamic range scanning protocol.

data_processing:
Images were processed using Agilent Feature Extraction software version 9.5.1.
Log2 ratios were calculated and LOWESS normalized by Agilent Feature Extraction software.

source_name: Total RNA from wild type E18.5 mouse lung

label_protocol: Agilent Two-Color LRILAK Labeling Protocol

extract_protocol: E18.5 lung lobes were dissected away from large airways and vessels and stored in RLT buffer (Qiagen) at –80°C. Three specimens of each genotype (Fgf8+/+, controls; Fgf8H/-, hypomorphic mutants) were pooled to generate each sample. Total RNA was extracted from four samples (RNeasy Micro Kit, Qiagen).

value: c57nl7/sv129 background

source_name: Total RNA from fgf8 hypomorphic E18.5 mouse lung

value: fgf8 hypomorph


title: AP/N vs WT Replicate 3

description: Comparison of WT lung to fgf8 hypomorph lung, replicate 3.


title: Adult human liver tissue expression replica 2

status: Public on Sep 18 2010

city: shanghai

first: yao

last: yu

address: yueyang road 320, room 123

institute: sibs

hyb_protocol: The pooled RNA sample from ten human-liver RNAs in same amount were hybridized to HG-U133plus 2.0 high-density oligonucleotide arrays (Affymetrix), which contains 54,675 probe sets representing 19164 human genes and 15136 ESTs on a single array.

scan_protocol: One ug of poly(A)+ RNA was annealed to oligo(dT) and transcribed using SurperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), Labeling, hybridization, washing and signal scan on the microarrays were performed according to the manufacturer's instructions.

data_processing: Primary image analysis of the arrays was performed by using GENECHIP 3.2 (Affymetrix, Santa Clara, CA), and normalization was performed using Mas 5.0 software (Affymetrix).

label_protocol: The pooled RNA sample from ten human-liver RNAs in same amount were labeled by biotin

extract_protocol: Adult human liver tissues from 10 adult human were surgically resected due to hemangioma in the liver. The samples were obtained from the portion unaffected by the hemangioma and were immediately frozen in liquid nitrogen. All procedures and risks were explained verbally, and patients provided written consent. The samples were sectioned and confirmed to be histologically normal. All laboratory data assessing hepatic function were within normal ranges, including serum alanine aminotransferase, aspartate aminotransferase, gamma-glutamyl transpeptidase, alkaline phosphatase, total bilirubin, albumin, prothrombin activity, glucose, cholesterol, and triglycerides (data not shown). Serological tests for hepatitis B surface antigen, hepatitis C virus antibodies, and human immunodeficiency virus antibodies also proved negative. Neither heavy alcohol consumption nor the intake of prescription or other drugs was observed before surgical resection. Total RNA was extracted according to the manufacturer’s instructions, and RNase-free DNase I was used to remove DNA contamination. Nucleic acid concentration and purity were assessed at 260 nm using a spectrophotometer (DU 530, Beckman-Coulter Inc., Fullerton, CA), and the quality was assessed using an Agilent 2100 Bioanalyzer. In order to address gene expression polymorphism, the total RNA from 10 livers was pooled.

value: normal liver tissues from patients with liver hemangioma


title: Adult human liver tissue expression replica 1

hyb_protocol: The pooled RNA sample from ten human-liver RNAs in same amount were  hybridized to HG-U133plus 2.0 high-density oligonucleotide arrays (Affymetrix), which contains 54,675 probe sets representing 19164 human genes and 15136 ESTs on a single array.


title: AP/N vs WT Replicate 1

description: Comparison of WT lung to fgf8 hypomorph lung, replicate 1.


title: 36_xylem_tech-rep3

city: Gainesville

first: Leandro

middle: Gomide

last: Neves

state: FL

address: 2033 Mowry Road

department: Plant Molecular and Cell Biology

institute: University of Florida

description: Technical repetition 3 of individual 36

hyb_protocol: Samples were hybridized at the Interdisciplinary Center for Biotechnology Research (ICBR) of the University of Florida following Agilent’s protocol, except for lowering the hybridization temperature to 55 oC to compensate for the shorter probes.

scan_protocol: As described elsewhere (http://www.chem.agilent.com/Library/usermanuals/Public/G2566-90017.pdf)

data_processing: The raw median signal intensity for each probe was log2 transformed and quantile-normalized using the Affy package on R.

organism: Eucalyptus grandis x Eucalyptus urophylla

source_name: Eucalyptus urophyla X Eucalyptus grandis segregationg population; xylem tissue

label_protocol: The Two-Color Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) was used to synthesize complementary RNA (cRNA) from 1ug of total RNA. Manufacturer’s protocol was followed except for dividing all reagents’ volume by two.

growth_protocol: Tissue was collected from field-grown, four-and-a-half-year-old trees maintained under operational silvicultural conditions in South of Brazil (Rio Grande do Sul State).

extract_protocol: Total RNA extracted (Chang et al. 1993) from xylem tissue samples was treated with RQ1 RNase-free DNase (Promega, Madison, WI, USA), purified in mini spin columns (RNeasy Plant Mini Kit, Qiagen) and had the quality visually checked on agarose gel.

treatment_protocol: None.

tag: sample type

value: 54-month-old, field grown trees

tag: age

value: 54 mo

value: xylem

tag: individual


title: 310_xylem_tech-rep2

description: Technical repetition 2 of individual 310


title: AP/N vs WT Replicate 4

description: Comparison of WT lung to fgf8 hypomorph lung, replicate 4.


title: Set8_deltaPIP2

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

description: U2OS cells were cultured in DMEM media with 10 % FBS and split daily at a 1:3 ratio.

hyb_protocol: For studying gene expression, RNA was extracted from U2OS 5 days posttransduction with Set8b_deltaPIP2, wt-Set8 or pMSCV-vector control retroviruses, by using Trizol Invitrogen) and hybridized to the Human HG-U133_Plus_2 array as described in the Affymetrix GeneChIP protocol (Affymetrix).

scan_protocol: Each microarray was scanned, visualized, and analyzed for the level of each individual transcript using a GeneChIP Scanner 3000 and GeneChIP Operating Software (GCOS; Affymetrix). Transcript signal was mapped against the chromosome coordinates (probe-by-probe basis) using the HG-U133_Plus_2 Annotations, CSV provided by the manufacturer (Affymetrix)

data_processing: Each microarray was scanned and analyzed for signal intensities by GeneChIP Scanner 3000 and GeneChIP operating software software (Affymetrix).

label_protocol: Labeling and hybridyzation was performed accoding to the affymetrix protocol.

extract_protocol: Total RNA extraction is according to the manufacturer's instructions (Invitrogen) using Trizole reagent.

treatment_protocol: U2OS cells were transduced with retroviruses encoding stable Set8b (Set8b_deltaPIP2), wt-Set8b or with empty vector (pMSCV-vector) and harvested 5 days post-trasduction according to standard procedures.

tag: cell line

tag: transfection


title: 293_xylem_tech-rep2

description: Technical repetition 2 of individual 293


title: 279_xylem_tech-rep2

description: Technical repetition 2 of individual 279


title: 270_xylem_tech-rep2

description: Technical repetition 2 of individual 270


title: 281_xylem_tech-rep2

description: Technical repetition 2 of individual 281


title: 288_xylem_tech-rep2

description: Technical repetition 2 of individual 288


title: Wt-Set8b


title: 277_xylem_tech-rep2

description: Technical repetition 2 of individual 277


title: 308_xylem_tech-rep2

description: Technical repetition 2 of individual 308


title: 297_xylem_tech-rep2

description: Technical repetition 2 of individual 297


title: 272_xylem_tech-rep2

description: Technical repetition 2 of individual 272


title: 256_xylem_tech-rep2

description: Technical repetition 2 of individual 256


title: pMSCV-vector

value: pMSCV-vector


title: 250_xylem_tech-rep2

description: Technical repetition 2 of individual 250


title: 248_xylem_tech-rep2

description: Technical repetition 2 of individual 248


title: 243_xylem_tech-rep2

description: Technical repetition 2 of individual 243


title: 264_xylem_tech-rep2

description: Technical repetition 2 of individual 264


title: 219_xylem_tech-rep2

description: Technical repetition 2 of individual 219


title: 216_xylem_tech-rep2

description: Technical repetition 2 of individual 216


title: 240_xylem_tech-rep2

description: Technical repetition 2 of individual 240


title: 241_xylem_tech-rep2

description: Technical repetition 2 of individual 241


title: 294_xylem_tech-rep2

description: Technical repetition 2 of individual 294


title: 234_xylem_tech-rep2

description: Technical repetition 2 of individual 234


title: 201_xylem_tech-rep2

description: Technical repetition 2 of individual 201


title: 172_xylem_tech-rep2

description: Technical repetition 2 of individual 172


title: 178_xylem_tech-rep2

description: Technical repetition 2 of individual 178


title: 169_xylem_tech-rep2

description: Technical repetition 2 of individual 169


title: 173_xylem_tech-rep2

description: Technical repetition 2 of individual 173


title: 187_xylem_tech-rep2

description: Technical repetition 2 of individual 187


title: 180_xylem_tech-rep2

description: Technical repetition 2 of individual 180


title: 179_xylem_tech-rep2

description: Technical repetition 2 of individual 179


title: 194_xylem_tech-rep2

description: Technical repetition 2 of individual 194


title: 138_xylem_tech-rep2

description: Technical repetition 2 of individual 138


title: 134_xylem_tech-rep2

description: Technical repetition 2 of individual 134


title: 153_xylem_tech-rep2

description: Technical repetition 2 of individual 153


title: 128_xylem_tech-rep2

description: Technical repetition 2 of individual 128


title: 136_xylem_tech-rep2

description: Technical repetition 2 of individual 136


title: 133_xylem_tech-rep2

description: Technical repetition 2 of individual 133


title: 126_xylem_tech-rep2

description: Technical repetition 2 of individual 126


title: 125_xylem_tech-rep2

description: Technical repetition 2 of individual 125


title: 239_xylem_tech-rep2

description: Technical repetition 2 of individual 239


title: 121_xylem_tech-rep2

description: Technical repetition 2 of individual 121


title: 120_xylem_tech-rep2

description: Technical repetition 2 of individual 120


title: 119_xylem_tech-rep2

description: Technical repetition 2 of individual 119


title: 113_xylem_tech-rep2

description: Technical repetition 2 of individual 113


title: 111_xylem_tech-rep2

description: Technical repetition 2 of individual 111


title: 123_xylem_tech-rep2

description: Technical repetition 2 of individual 123


title: 97_xylem_tech-rep2

description: Technical repetition 2 of individual 97


title: 71_xylem_tech-rep2

description: Technical repetition 2 of individual 71


title: 89_xylem_tech-rep2

description: Technical repetition 2 of individual 89


title: 47_xylem_tech-rep2

description: Technical repetition 2 of individual 47


title: 74_xylem_tech-rep2

description: Technical repetition 2 of individual 74


title: 64_xylem_tech-rep2

description: Technical repetition 2 of individual 64


title: 79_xylem_tech-rep2

description: Technical repetition 2 of individual 79


title: 59_xylem_tech-rep2

description: Technical repetition 2 of individual 59


title: 48_xylem_tech-rep2

description: Technical repetition 2 of individual 48


title: 67_xylem_tech-rep2

description: Technical repetition 2 of individual 67


title: 63_xylem_tech-rep2

description: Technical repetition 2 of individual 63


title: 42_xylem_tech-rep2

description: Technical repetition 2 of individual 42


title: MCF7 H3K4me3 ChIP-chip (replicate 1)

type: genomic

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: These custom arrays also contain 542 control Arabidopsis Thaliana probes, the data for which can be found in the supplementary files provided.  The microarray slides have three subarrays, and each Arabidopsis probe was spotted in triplicate, one on each subarray.

hyb_protocol: see NimbleGen website

scan_protocol: see NimbleGen website

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team). All data processing scripts are available upon request. The log2 ratio data from each of the arrays was subjected to lowess normalization.

molecule: genomic DNA

source_name: input

label_protocol: see NimbleGen website

extract_protocol: MCF7 breast carcinoma cells were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min. at 4°C.  The cells were collected by centrifugation and sonicated in Lysis Buffer [Tris•HCl pH 7.9, 10 mM EDTA, 50 mM NaCl, 1% SDS, and 1x protease inhibitor cocktail (Roche, cat no. 04 693 124 001)] to generate chromatin fragments of ~500 bp in length.  The material was clarified by centrifugation, diluted 10-fold in Dilution Buffer (20 mM Tris•HCl pH 7.9, 2 mM EDTA, 150 mM NaCl, 0.5% Triton X-100, 1x protease inhibitor cocktail), and pre-cleared by incubation with protein A-agarose beads.  The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against the factor of interest, or without antibodies as a control.  The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively.  The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.   The material was then amplified with LM-PCR.

tag: antibody

source_name: H3K4me3 ChIP


title: 58_xylem_tech-rep2

description: Technical repetition 2 of individual 58


title: 297_xylem_tech-rep1

description: Technical repetition 1 of individual 297


title: 189_xylem_tech-rep2

description: Technical repetition 2 of individual 189


title: 294_xylem_tech-rep1

description: Technical repetition 1 of individual 294


title: 293_xylem_tech-rep1

description: Technical repetition 1 of individual 293


title: 288_xylem_tech-rep1

description: Technical repetition 1 of individual 288


title: MCF7 PARP-1 ChIP-chip (replicate 1)

source_name: PARP-1 ChIP


title: 281_xylem_tech-rep1

description: Technical repetition 1 of individual 281


title: 21_xylem_tech-rep2

description: Technical repetition 2 of individual 21


title: 308_xylem_tech-rep1

description: Technical repetition 1 of individual 308


title: 55_xylem_tech-rep2

description: Technical repetition 2 of individual 55


title: MCF7 H3K4me3 ChIP-chip (replicate 2)


title: MCF7 H3 ChIP-chip (replicate 2)

source_name: H3 ChIP


title: 310_xylem_tech-rep1

description: Technical repetition 1 of individual 310


title: MCF7 PARP-1 ChIP-chip (replicate 2)


title: MCF7 H3 ChIP-chip (replicate 1)


title: 277_xylem_tech-rep1

description: Technical repetition 1 of individual 277


title: 239_xylem_tech-rep1

description: Technical repetition 1 of individual 239


title: 279_xylem_tech-rep1

description: Technical repetition 1 of individual 279


title: 264_xylem_tech-rep1

description: Technical repetition 1 of individual 264


title: 272_xylem_tech-rep1

description: Technical repetition 1 of individual 272


title: 169_xylem_tech-rep1

description: Technical repetition 1 of individual 169


title: 248_xylem_tech-rep1

description: Technical repetition 1 of individual 248


title: 36_xylem_tech-rep2

description: Technical repetition 2 of individual 36


title: 256_xylem_tech-rep1

description: Technical repetition 1 of individual 256


title: 250_xylem_tech-rep1

description: Technical repetition 1 of individual 250


title: 219_xylem_tech-rep1

description: Technical repetition 1 of individual 219


title: 241_xylem_tech-rep1

description: Technical repetition 1 of individual 241


title: 243_xylem_tech-rep1

description: Technical repetition 1 of individual 243


title: 178_xylem_tech-rep1

description: Technical repetition 1 of individual 178


title: 270_xylem_tech-rep1

description: Technical repetition 1 of individual 270


title: 173_xylem_tech-rep1

description: Technical repetition 1 of individual 173


title: 138_xylem_tech-rep1

description: Technical repetition 1 of individual 138


title: 180_xylem_tech-rep1

description: Technical repetition 1 of individual 180


title: 172_xylem_tech-rep1

description: Technical repetition 1 of individual 172


title: 240_xylem_tech-rep1

description: Technical repetition 1 of individual 240


title: 201_xylem_tech-rep1

description: Technical repetition 1 of individual 201


title: 189_xylem_tech-rep1

description: Technical repetition 1 of individual 189


title: POiPS#2

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

description: Gene expression of iPS

hyb_protocol: manufacturer's protocol

scan_protocol: manufacturer's protocol

data_processing: gProcessed signal value calculated by Agilent Scanner Feature Extract Software. All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity (see GSE24208 supplementary files).

source_name: Purmorphamine-treated NSC-like cells were then transduced with Oct4 to reprogram them into iPS cells (1F combination of purmorphamine and Oct4)

label_protocol: manufacturer's protocol

extract_protocol: RNA was prepared using Trizol reagents (Invitrogen) following the manufacturer's recommendations.

value: embryo fibroblasts


title: 30_xylem_tech-rep2

description: Technical repetition 2 of individual 30


title: 128_xylem_tech-rep1

description: Technical repetition 1 of individual 128


title: 216_xylem_tech-rep1

description: Technical repetition 1 of individual 216


title: OOiPS#1

description: Gene expression of iPS

source_name: Oxysterols-treated NSC-like cells were then transduced with Oct4 to reprogram them into iPS cells (1F combination of oxysteols and Oct4)


title: 194_xylem_tech-rep1

description: Technical repetition 1 of individual 194


title: 125_xylem_tech-rep1

description: Technical repetition 1 of individual 125


title: 153_xylem_tech-rep1

description: Technical repetition 1 of individual 153


title: 136_xylem_tech-rep1

description: Technical repetition 1 of individual 136


title: 187_xylem_tech-rep1

description: Technical repetition 1 of individual 187


title: POiPS#1

description: Gene expression of iPS


title: SOiPS

description: Gene expression of iPS

source_name: Shh-treated NSC-like cells were then transduced with Oct4 to reprogram them into iPS cells (1F combination of Shh and Oct4)


title: 121_xylem_tech-rep1

description: Technical repetition 1 of individual 121


title: MEF Bmi1 spheres

description: Gene expression of iPS

source_name: Bmi1-transduced NSC-like cells


title: OOiPS-TTF#1

description: Gene expression of iPS

source_name: combination of oxysterol and Oct4 on tail-tip fibroblasts (TTFs) (The cells were able to induce the formation of ES-like cells)

value: adult fibroblasts


title: MEF

description: Gene expression of MEF

source_name: mouse embryonic fibroblasts


title: 134_xylem_tech-rep1

description: Technical repetition 1 of individual 134


title: T conventional replicate 2

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description:
cjw196
CD4+/CD45RBhi/GFP- cells were purified by FACS and cultured without stimulation for 48 hours.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

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. An additive correction of 20 was then added to the signal before natural log transformation to stabilize the data. Batch correction was applied to some data using Partek Genomics Suite 6.4.

source_name: bone marrow, Tconv

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 1 ug of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: CD4+ T cells (subtype indicated above) were cultured in RPMI media, supplemented with 10% FBS.

extract_protocol: The Qiagen Rneasy Plus Mini kit was used to extract RNA according to the manufacturer's protocol.

treatment_protocol: CD4+ T cells were left untreated (samples cjw 173, 183, 193, 186, 196, 216) or were treated with control protein (lwc 001, 002, 003, 007, 008) or IL35 protein (lwc 004, 005, 006, 010, 011).

value: bone marrow

value: CD4+/CD45RBhi T conventional cells

tag: treatment

value: untreated

tag: batch

value: not applicable


title: T conventional replicate 3

description:
cjw216
CD4+/CD45RBhi/GFP- cells were purified by FACS and cultured without stimulation for 48 hours.


title: 179_xylem_tech-rep1

description: Technical repetition 1 of individual 179


title: T conventional replicate 1

description:
cjw186
CD4+/CD45RBhi/GFP- cells were purified by FACS and cultured without stimulation for 48 hours.


title: 119_xylem_tech-rep1

description: Technical repetition 1 of individual 119


title: 234_xylem_tech-rep1

description: Technical repetition 1 of individual 234


title: 71_xylem_tech-rep1

description: Technical repetition 1 of individual 71


title: 111_xylem_tech-rep1

description: Technical repetition 1 of individual 111


title: T reg resting replicate 1

description:
cjw173
CD4+/CD45RBlow/GFP+ cells were purified by FACS and cultured without stimulation for 48 hours.

source_name: bone marrow, Treg

value: CD4+/CD45RBlow regulatory T cells (Tregs)


title: 79_xylem_tech-rep1

description: Technical repetition 1 of individual 79


title: 89_xylem_tech-rep1

description: Technical repetition 1 of individual 89


title: ES

description: Gene expression of ES

source_name: mouse embryonic stem cells from 129/Ola mice

value: blastocysts


title: OOiPS#2

description: Gene expression of iPS


title: 133_xylem_tech-rep1

description: Technical repetition 1 of individual 133


title: 97_xylem_tech-rep1

description: Technical repetition 1 of individual 97


title: control_treated replicate 5

description:
lwc008
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of control protein.

source_name: bone marrow, control treated

value: wild-type

value: CD4+/CD45RBhi/CD25- T conventional cells

value: control protein


title: IL35_treated replicate 5

description:
lwc011
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of IL35 protein.

source_name: bone marrow, IL35 treated


title: OOiPS-TTF#2

description: Gene expression of iPS


title: control_treated replicate 4

description:
lwc007
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of control protein.


title: 64_xylem_tech-rep1

description: Technical repetition 1 of individual 64


title: AAA2

city: Shanghai

first: Liu

last: Guang

address: No. 639 Zhizaoju Rd

institute: Shanghai Jiao Tong University

description: miRNA expression after AAA formation

hyb_protocol: The hybridization used miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565A) using one color scan setting for 8x15k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The normalized log2 signal intensity data was generated by Quantile method using GeneSpring GX Software (Agilent).

organism: Rattus norvegicus

source_name: abdominal aortic aneurysm wall (infrarenal)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

growth_protocol: Sprague-Dawley male rats, 8 weeks old were housed three per cage in a room with controlled temperature and humidity and 12h light-dark cycles. The rats were fed with standard rat chow and tap water ad libitum. After one week of acclimatization, the animals were randomly divided into two groups (AAA and control(sham operation)).

extract_protocol: RNA was prepared using the mirVana RNA Isolation kit following the manufacturer's recommendations.

treatment_protocol: AAA model was established by calcium chloride and collagenase co-incubation method. After 28 days, three rats with confirmed AAAs and three normal (control) rats were euthanized and the aortas (specimens) were used for this experiment.Freshly drawn aortic wall form confirmed AAA and normal aortas.

value: Sprague-Dawley

value: aortic wall

value: male


title: IL35_treated replicate 1

description:
lwc004
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of IL35 protein.


title: 59_xylem_tech-rep1

description: Technical repetition 1 of individual 59

source_name: Eucalyptus urophyla X Eucalyptus grandis segregationg population; xylem tissue

value: 54-month-old, field grown trees

value: 54 mo


title: BOiPS#2

description: Gene expression of iPS

source_name: 2F combinations of Bmi1 and Oct4 (The cells were able to induce the formation of ES-like cells)


title: IL35_treated replicate 4

description:
lwc010
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of IL35 protein.


title: AAA3

description: miRNA expression after AAA formation


title: Normal1

description: miRNA expression (control)

source_name: normal aortic wall (infrarenal)


title: Normal3

description: miRNA expression (control)


title: Normal2

description: miRNA expression (control)


title: 55_xylem_tech-rep1

description: Technical repetition 1 of individual 55

value: xylem


title: IL35_treated replicate 3

description:
lwc006
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of IL35 protein.


title: 126_xylem_tech-rep1

description: Technical repetition 1 of individual 126


title: AAA1

description: miRNA expression after AAA formation


title: 51_xylem_tech-rep1

description: Technical repetition 1 of individual 51


title: T reg resting replicate 3

description:
cjw193
CD4+/CD45RBlow/GFP+ cells were purified by FACS and cultured without stimulation for 48 hours.


title: 58_xylem_tech-rep1

description: Technical repetition 1 of individual 58


title: 120_xylem_tech-rep1

description: Technical repetition 1 of individual 120


title: control_treated replicate 3

description:
lwc003
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of control protein.


title: 123_xylem_tech-rep1

description: Technical repetition 1 of individual 123


title: 113_xylem_tech-rep1

description: Technical repetition 1 of individual 113


title: 67_xylem_tech-rep1

description: Technical repetition 1 of individual 67


title: 74_xylem_tech-rep1

description: Technical repetition 1 of individual 74


title: BOiPS#1

description: Gene expression of iPS

value: embryo fibroblasts


title: 30_xylem_tech-rep1

description: Technical repetition 1 of individual 30


title: 63_xylem_tech-rep1

description: Technical repetition 1 of individual 63


title: PBW 2 vs PBB 2

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

description: For skin biopsies, a wool staple sample was removed by close clipping a region of approximately 5 cm2. Two skin trephines of 0.9 cm diameter were taken from the clipped region and immediately placed in RNA later (Ambion) for subsequent RNA extraction.

hyb_protocol: Fluorescently labelled cDNAs were mixed in 50 µL hybridisation mixture containing 50% deionised formamide, 4 × SSC, 0.5% SDS, 20 µg polydA and 10 µg bovine hyblock DNA (Applied Genetics Laboratories, Melbourne, Vic., Australia). The mixture was heated at 95°C for 5 min and incubated at 45°C for 45 min before application onto the microarray slides. Hybridisation was conducted in a humidified slide chamber (ArrayIt, Telechem International Inc.) at 45°C for 16 h. Slides were washed in 0.2 × SSC, 0.1% SDS for 15 min, 0.2 × SSC for 15 min, 0.06 × SSC for 5 min and spun at 500 rpm for 5 min at room temperature (Sigma 4K15)

scan_protocol: Scanned on an GenePix 4000A optical scanner

data_processing: An ANOVA mixed-effect model was employed to normalize the data as previously described (Reverter et al. 2005).

organism: Ovis aries

source_name: Skin biopsy

label_protocol: 5µg of total RNA were primed with 5ug of Random Primerat 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 1mmol/L each dATP, dCTP, dGTP, with 0.6mmol/L µM aa-dUTP, 0.4mmol/L dCTP, purified and incubat for 1hr RT with Cy3 or Cy5 (post-Labelling Reactive Dye Pack, Amersham Biosciences)

extract_protocol: Total RNA was prepared from the skin samples using TRI reagent in accordance with the manufacturer’s recommendations (Sigma, St Louis, MO, USA).

tag: pigmentation

value: PBW

value: skin

value: PBW - White sample from a piebald individual sheep

value: PBB

value: PBB - Black sample from a piebald individual sheep


title: PBW 2 vs RSW 2

value: RSW

value: RSW - White sample from a recissive black sheep taken from the inguinal, non-pigmented area


title: RSB 2 vs NOR 2

value: RSB

value: RSB - Black sample from a recessive black sheep

value: NOR

value: NOR - White sample from a normal, non-affected wild-type individual sheep


title: 6_xylem_tech-rep1

description: Technical repetition 1 of individual 6


title: control_treated replicate 2

description:
lwc002
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of control protein.

value: wild-type

value: bone marrow

value: CD4+/CD45RBhi/CD25- T conventional cells

value: control protein


title: PBW 1 vs NOR 1


title: 47_xylem_tech-rep1

description: Technical repetition 1 of individual 47

value: 54-month-old, field grown trees

value: 54 mo

value: xylem


title: 42_xylem_tech-rep1

description: Technical repetition 1 of individual 42


title: 36_xylem_tech-rep1

description: Technical repetition 1 of individual 36


title: 19_xylem_tech-rep2

description: Technical repetition 2 of individual 19


title: PBB 2 vs NOR 2

value: skin


title: NOR 2 vs PBW 2

value: PBW

value: PBW - White sample from a piebald individual sheep


title: 8_xylem_tech-rep2

description: Technical repetition 2 of individual 8


title: RSW 2 vs RSB 2


title: PBB 2 vs RSB 2

value: PBB

value: PBB - Black sample from a piebald individual sheep


title: RSB 1 vs RSW 1

value: RSW

value: RSW - White sample from a recissive black sheep taken from the inguinal, non-pigmented area


title: RSB 1 vs PBB 1

value: RSB

value: RSB - Black sample from a recessive black sheep


title: PBW 2 vs RSB 2


title: 21_xylem_tech-rep1

description: Technical repetition 1 of individual 21


title: NOR 1 vs RSB 1

value: NOR

value: NOR - White sample from a normal, non-affected wild-type individual sheep


title: A20-A1

city: Boston

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: A20 After resection

hyb_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: Affymetrix Scanner

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

Authors were unable to loacte the CEL files for this submission.

source_name: A20 after resection

label_protocol: For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.

extract_protocol: Total RNA was isolated using the RNAeasy kit (QIAGEN) following the manufacturer’s instructions.

treatment_protocol: beta-galactosidase (bgal) gene expression in the mouse liver was achieved by penile vein injection of 1x109 pfu of rAd. in 100uL of normal saline, which results in optimal transgene expression 5 days after injection in 30% to 40% of hepatocytes . Extended (78%) LR, consisting of resection of the lateral, medial, left, and right lobes, was performed 5 days following rAd. administration in 8-week old BALB/c mice weighing 25 to 30 grams (Taconic, Germantown, NY), as described (Longo et al, 2005).

value: BALB/c

value: rAd.A20 transduced liver


title: T reg resting replicate 2

description:
cjw183
CD4+/CD45RBlow/GFP+ cells were purified by FACS and cultured without stimulation for 48 hours.

value: bone marrow

value: CD4+/CD45RBlow regulatory T cells (Tregs)

value: untreated

value: not applicable


title: control_treated replicate 1

description:
lwc001
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of control protein.

value: wild-type

value: CD4+/CD45RBhi/CD25- T conventional cells

value: control protein


title: A20-B2

description: A20 Before resection

source_name: A20 before resection

treatment_protocol: A20 gene expression in the mouse liver was achieved by penile vein injection of 1x109 pfu of rAd. in 100ul of normal saline, which results in optimal transgene expression 5 days after injection in 30% to 40% of hepatocytes


title: 6_xylem_tech-rep2

description: Technical repetition 2 of individual 6

value: 54-month-old, field grown trees

value: 54 mo

value: xylem


title: 12_xylem_tech-rep2

description: Technical repetition 2 of individual 12


title: BG-A1

description: beta-galacatosidase expressing ramnant liver after resection

source_name: beta-galacatosidase expressing liver after resection

value: rAd.bgalactosidase transduced liver


title: IL35_treated replicate 2

description:
lwc005
CD4+CD45RBhi, CD25- Tconv cells were purified by FACS and activated with anti-CD3/CD28 coated latex beads for 72 hours, in the presence of IL35 protein.


title: BG-A2


title: NOR 2 vs RSW 2

value: skin

value: RSW

value: RSW - White sample from a recissive black sheep taken from the inguinal, non-pigmented area


title: RSB 1 vs PBW 1

value: RSB

value: RSB - Black sample from a recessive black sheep

value: PBW

value: PBW - White sample from a piebald individual sheep


title: A20-A2

description: A20 After resection

value: BALB/c

value: rAd.A20 transduced liver


title: RSW 2 vs PBB 2

value: PBB

value: PBB - Black sample from a piebald individual sheep


title: RSW 1 vs PBW 1


title: PBB 1 vs PBW 1


title: NOR 1 vs PBB 1

value: NOR

value: NOR - White sample from a normal, non-affected wild-type individual sheep


title: 48_xylem_tech-rep1

description: Technical repetition 1 of individual 48

value: 54-month-old, field grown trees


title: 12_xylem_tech-rep1

description: Technical repetition 1 of individual 12

value: 54 mo


title: PBB 1 vs RSW 1


title: RSW 1 vs NOR 1


title: 8_xylem_tech-rep1

description: Technical repetition 1 of individual 8

value: xylem


title: 19_xylem_tech-rep1

description: Technical repetition 1 of individual 19


title: A20-B1

description: A20 Before resection


title: BG-B1

description: beta-galacatosidase expressing liver before resection

treatment_protocol: beta-galactosidase (bgal) gene expression in the mouse liver was achieved by penile vein injection of 1x109 pfu of rAd. in 100uL of normal saline, which results in optimal transgene expression 5 days after injection in 30% to 40% of hepatocytes

value: rAd.bgalactosidase transduced liver


title: Control_brain_rep3

status: Public on Sep 17 2010

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: compare gene expression profiles in brains from normal mice to those infected with the Anka strain of Plasmodium berghei, a model of cerebral malaria

hyb_protocol: Each of the six Cy3-labeled brain extracts was co-hybridized overnight at 50°C against the Cy5-labeled reference with AECOM 32k Mouse oligonucleotide arrays, MO3 printing series (GPL5371). After hybridization, the slides were washed at room temperature, using solutions containing 0.1% sodium dodecyl sulfate (SDS) and 1% SSC (3M NaCl + 0.3M sodium citrate) to remove the non-hybridized cDNAs.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005

source_name: Universal mouse RNA reference

label_protocol: 60μg total RNA, extracted in Trizol® (Invitrogen, Carlsbad, CA) from the composite reference was reverse transcribed to incorporate Cy5-dUTP.

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

value: universal mouse RNA reference prepared from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females)

label_protocol: 60μg total RNA, extracted in Trizol® (Invitrogen, Carlsbad, CA) from brains of three infected (I) and three control (C) mice, purified with RNeasy® mini kit (Qiagen, Valencia, CA), were reverse transcribed into cDNA incorporating fluorescent Cy3-dUTP

growth_protocol: Mice were housed at controlled temperature (23ºC) with 12:12-hour light-dark cycle and received standard mouse chow and water ad libitum

treatment_protocol: Blood containing either 5X105 red blood cells (RBCs) parasitized with PbA or uninfected blood was diluted in PBS, and 200 microliters were injected via the intraperitoneal route. The mice were then separated into two groups of infected or uninfected mice.  Parasitemia, or the percentage of parasitized RBCs, was evaluated by examining Giemsa stained blood smears on day 6 post infection (PI). On day 6 PI, mice were euthanized using carbon dioxide and the brains were harvested, frozen in liquid nitrogen, and then stored at -80oC for future analysis.

value: 4-5 weeks

value: female

value: brain

tag: protocol

value: uninfected


title: Distal Lung Newborn biological rep 8

city: Iowa City

first: Shyam

last: Ramachandran

address: 240G EMRB

department: Pediatrics

institute: Univ of Iowa

hyb_protocol: biotinylated cRNA was hybridized to the Affymetrix Porcine GeneChip (23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes). Each tissue hybridization (trachea, bronchus, and distal lung) was performed on a separate day, with all genotypes represented in each run.

scan_protocol: The arrays were washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner

data_processing: data was collected using the GeneChip Operating Software (GCOS) v.1.4, using the manufacturer’s recommended protocols and default analysis settings

organism: Sus scrofa

source_name: NEWBORN CF PIGS

label_protocol: 5 μg of total RNA was used to generate biotinylated cRNA using the Affymetrix Gene Chip one-cycle target labeling kit (Affymetrix, Inc.; Santa Clara, CA) according to the manufacturer’s recommended protocols

extract_protocol: Total RNA was isolated with TRIzol Reagent (Invitrogen; Carlsbad, CA). Only RNA samples attaining a minimum of 7.0 RNA Integrity Number on the Agilent 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA) were processed.

treatment_protocol: Trachea, bronchus, and distal lung tissue samples were dissected from newborn piglets within 12 h of birth. Samples were cut into ~5 mm3 pieces and stored in RNAlater RNA Stabilization Reagent (Ambion; Austin, TX) using the manufacturer’s recommended protocols.

value: DISTAL LUNG

tag: developmental stage

value: newborn

tag: genome/variation

value: CF (CFTR genes targeted)


title: Distal Lung Newborn biological rep 9

tag: tissue


title: Distal Lung Newborn biological rep 14


title: BG-B2

source_name: beta-galacatosidase expressing liver before resection

value: BALB/c


title: Distal Lung Newborn biological rep 13


title: Distal Lung Newborn biological rep 3

source_name: NEWBORN WT PIGS

value: wild type


title: Distal Lung Newborn biological rep 1


title: Distal Lung Newborn biological rep 5


title: Distal Lung Newborn biological rep 7


title: Distal Lung Newborn biological rep 6


title: Control_brain_rep2


title: Distal Lung Newborn biological rep 11


title: Distal Lung Newborn biological rep 4


title: Distal Lung Newborn biological rep 10


title: Bronchus Newborn biological rep 14

value: BRONCHUS


title: Bronchus Newborn biological rep 12


title: Distal Lung Newborn biological rep 2


title: Control_brain_rep1


title: Bronchus Newborn biological rep 11


title: Distal Lung Newborn biological rep 12


title: Infected_brain_rep2

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Physiol Genomics 2005

value: infected with Plasmodium berghei ANKA (PbA)


title: Infected_brain_rep3


title: Bronchus Newborn biological rep 13


title: Infected_brain_rep1


title: Bronchus Newborn biological rep 9


title: Bronchus Newborn biological rep 10


title: Bronchus Newborn biological rep 6


title: Bronchus Newborn biological rep 8


title: Bronchus Newborn biological rep 3


title: Bronchus Newborn biological rep 7


title: UKH164_NM_ara_12_1

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

description: Effects of induced clp1 expression on rbf1-dependent gene regulation

hyb_protocol: EukGE2V4 protocol on a GeneChip Fluidics Station 400

scan_protocol: Affymetrix GSC3000

data_processing: MAS 5.1

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: U. maydis strain UKH164 grown for 12h in array medium/nitrate/arabinose

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray transcript labeling kit, except for a reaction temperature of 50°C for first-strand cDNA synthesis.

growth_protocol: Strain UKH164(a1 delta b::narP:rbf1 crg1P:clp1) was grown on a rotary shaker (200 rpm) to an OD600 of 0.4 to 0.6 at 28°C in liquid array medium: 6.25%(w/v) salt solution, 30 mM L-glutamine, 1% (w/v) glucose, pH 7.0 (filter sterilized). rbf1 and clp1 expression was induced in array medium containing 3 g/l nitrate instead of glutamine as nitrogen source and 1% (w/v) arabinose instead of glucose as carbon source for 12 hours.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) and further column purified (Qiagen RNeasy) and the quality check using a Bioanalyzer with an RNA 6000 Nano LabChip kit (Agilent).

tag: time

value: 12 h in array medium/nitrate/arabinose

value: UKH164 is a FB1 (a1 b1) derivative in which the b-mating type locus has been replaced by a nitrate-inducible rbf1 gene and an arabinose-inducible clp1 gene was integrated into the ip-locus..


title: Bronchus Newborn biological rep 1


title: Trachea Newborn biological rep 4

value: TRACHEA


title: UKH164_NM_ara_12_2

value: UKH164 is a FB1 (a1 b1) derivative in which the b-mating type locus has been replaced by a nitrate-inducible rbf1 gene and an arabinose-inducible clp1 has been integrated into the ip-locus.


title: Trachea Newborn biological rep 8


title: Bronchus Newborn biological rep 5


title: Trachea Newborn biological rep 12


title: Trachea Newborn biological rep 6


title: Trachea Newborn biological rep 9


title: UKH156_NM_ara_12_1

description: Control experiment (base line) for measuring the effects of induced clp1 expression on rbf1-dependent gene regulation

source_name: U. maydis strain UKH156 grown for 12h in array medium/nitrate/arabinose

growth_protocol: Strain UKH156(a1 delta b::narP:rbf1) was grown on a rotary shaker (200 rpm) to an OD600 of 0.4 to 0.6 at 28°C in liquid array medium: 6.25%(w/v) salt solution, 30 mM L-glutamine, 1% (w/v) glucose, pH 7.0 (filter sterilized). rbf1 expression was induced in array medium containing 3 g/l nitrate instead of glutamine as nitrogen source and 1% (w/v) arabinose instead of glucose as carbon source and grown for 12 hours.

value: UKH156 is a FB1 (a1 b1) derivative in which the b-mating type locus has been replaced by a nitrate-inducible rbf1 gene.


title: Trachea Newborn biological rep 11


title: Trachea Newborn biological rep 1


title: Trachea Newborn biological rep 3


title: UKH156_NM_ara_12_2


title: Trachea Newborn biological rep 10


title: Bronchus Newborn biological rep 4


title: Bronchus Newborn biological rep 2


title: Trachea Newborn biological rep 5


title: Trachea Newborn biological rep 2


title: Trachea Newborn biological rep 7


title: VS0016_GWP

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient VS0016

hyb_protocol: Following fragmentation, 90 micrograms of biotin-labeled DNA were hybridized for 16 hr at 49°C on GeneChip Human Mapping 250K NspI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Mapping 250K NspI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Images were acquired using Affymetrix GeneChip Operating System (GCOS 1.4). The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS), (Olshen et al., Biostatistics 2004) and the median of the estimated profiles was scaled back to a nominal multiplicity of two. After scaling, a k-means clustering algorithm was used on the cumulative profile of all the data to determine the thresholds for inferring discrete CN values. Inferred CN higher than 2.1 and 2.5 corresponded to gain and amplification whereas CN below 1.9 and 1.34 to loss and biallelic deletion, respectively.

The pre-processed data generated by GTYPE/CNAT are available in 'GSE16746_CNAT_signals.txt', which is linked to the Series GSE16746 record as a supplementary file.

source_name: Human B-cell chronic lymphocytic leukemia patient VS0016

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol starting from 250 nanograms of genomic DNA.

extract_protocol: Genomic DNA extraction was performed using the Wizard Genomic DNA Purification kit according to the manufacturer's instructions (Promega).

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: legend

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

tag: Sex

value: M

tag: vh status

value: mut

tag: disease

value: B-cell chronic lymphocytic leukemia (B-CLL)

tag: Stage

value: Binet A

tag: cell type

value: CD5/CD19/CD23 triple-positive B cells


title: RF0116_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RF0116

source_name: Human B-cell chronic lymphocytic leukemia patient RF0116

value: F


title: CS26_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS26

source_name: Human B-cell chronic lymphocytic leukemia patient CS26

value: unmut


title: VB0013_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient VB0013

source_name: Human B-cell chronic lymphocytic leukemia patient VB0013


title: RG0045_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RG0045

source_name: Human B-cell chronic lymphocytic leukemia patient RG0045


title: VP0089_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient VP0089

source_name: Human B-cell chronic lymphocytic leukemia patient VP0089


title: PS0044_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient PS0044

source_name: Human B-cell chronic lymphocytic leukemia patient PS0044


title: GE118_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE118

source_name: Human B-cell chronic lymphocytic leukemia patient GE118


title: SA0093_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient SA0093

source_name: Human B-cell chronic lymphocytic leukemia patient SA0093


title: NG0068_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient NG0068

source_name: Human B-cell chronic lymphocytic leukemia patient NG0068


title: MF0048_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient MF0048

source_name: Human B-cell chronic lymphocytic leukemia patient MF0048


title: MA0002_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient MA0002

source_name: Human B-cell chronic lymphocytic leukemia patient MA0002


title: LD0062_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient LD0062

source_name: Human B-cell chronic lymphocytic leukemia patient LD0062


title: CS95_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS95

source_name: Human B-cell chronic lymphocytic leukemia patient CS95


title: LG0038_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient LG0038

source_name: Human B-cell chronic lymphocytic leukemia patient LG0038


title: GC0015_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GC0015

source_name: Human B-cell chronic lymphocytic leukemia patient GC0015


title: PF0024_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient PF0024

source_name: Human B-cell chronic lymphocytic leukemia patient PF0024


title: CS0100_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS0100

source_name: Human B-cell chronic lymphocytic leukemia patient CS0100


title: MC0055_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient MC0055

source_name: Human B-cell chronic lymphocytic leukemia patient MC0055


title: CR0159_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CR0159

source_name: Human B-cell chronic lymphocytic leukemia patient CR0159


title: FT0019_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient FT0019

source_name: Human B-cell chronic lymphocytic leukemia patient FT0019


title: LL0130_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient LL0130

source_name: Human B-cell chronic lymphocytic leukemia patient LL0130


title: DC0017_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient DC0017

source_name: Human B-cell chronic lymphocytic leukemia patient DC0017


title: GG0027_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GG0027

source_name: Human B-cell chronic lymphocytic leukemia patient GG0027


title: IA0025_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient IA0025

source_name: Human B-cell chronic lymphocytic leukemia patient IA0025


title: NI0099_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient NI0099

source_name: Human B-cell chronic lymphocytic leukemia patient NI0099


title: EB0042_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient EB0042

source_name: Human B-cell chronic lymphocytic leukemia patient EB0042


title: RA0023_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RA0023

source_name: Human B-cell chronic lymphocytic leukemia patient RA0023


title: MA0088_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient MA0088

source_name: Human B-cell chronic lymphocytic leukemia patient MA0088


title: CM0057_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CM0057

source_name: Human B-cell chronic lymphocytic leukemia patient CM0057


title: CI0005_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CI0005

source_name: Human B-cell chronic lymphocytic leukemia patient CI0005


title: CD0018_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CD0018

source_name: Human B-cell chronic lymphocytic leukemia patient CD0018


title: TS7_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient TS7

source_name: Human B-cell chronic lymphocytic leukemia patient TS7


title: AS0012_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient AS0012

source_name: Human B-cell chronic lymphocytic leukemia patient AS0012


title: BR0014_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient BR0014

source_name: Human B-cell chronic lymphocytic leukemia patient BR0014


title: CS0030_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS0030

source_name: Human B-cell chronic lymphocytic leukemia patient CS0030


title: CG0037_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CG0037

source_name: Human B-cell chronic lymphocytic leukemia patient CG0037


title: TS12_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient TS12

source_name: Human B-cell chronic lymphocytic leukemia patient TS12


title: AR0131_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient AR0131

source_name: Human B-cell chronic lymphocytic leukemia patient AR0131


title: BC0047_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient BC0047

source_name: Human B-cell chronic lymphocytic leukemia patient BC0047


title: RC92_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC92

source_name: Human B-cell chronic lymphocytic leukemia patient RC92


title: TS3_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient TS3

source_name: Human B-cell chronic lymphocytic leukemia patient TS3


title: AM0034_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient AM0034

source_name: Human B-cell chronic lymphocytic leukemia patient AM0034


title: RC89_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC89

source_name: Human B-cell chronic lymphocytic leukemia patient RC89


title: TS18_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient TS18

source_name: Human B-cell chronic lymphocytic leukemia patient TS18


title: RC84_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC84

source_name: Human B-cell chronic lymphocytic leukemia patient RC84


title: RC7_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC7

source_name: Human B-cell chronic lymphocytic leukemia patient RC7


title: RC87_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC87

source_name: Human B-cell chronic lymphocytic leukemia patient RC87


title: RC93_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC93

source_name: Human B-cell chronic lymphocytic leukemia patient RC93


title: RC95_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC95

source_name: Human B-cell chronic lymphocytic leukemia patient RC95


title: RC75_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC75

source_name: Human B-cell chronic lymphocytic leukemia patient RC75


title: RC81_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC81

source_name: Human B-cell chronic lymphocytic leukemia patient RC81


title: TS45_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient TS45

source_name: Human B-cell chronic lymphocytic leukemia patient TS45


title: RC88_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC88

source_name: Human B-cell chronic lymphocytic leukemia patient RC88


title: TS21_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient TS21

source_name: Human B-cell chronic lymphocytic leukemia patient TS21


title: BC0035_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient BC0035

source_name: Human B-cell chronic lymphocytic leukemia patient BC0035


title: RC24_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC24

source_name: Human B-cell chronic lymphocytic leukemia patient RC24


title: RC22_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC22

source_name: Human B-cell chronic lymphocytic leukemia patient RC22


title: RC94_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC94

source_name: Human B-cell chronic lymphocytic leukemia patient RC94


title: RC18_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC18

source_name: Human B-cell chronic lymphocytic leukemia patient RC18


title: RC21_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC21

source_name: Human B-cell chronic lymphocytic leukemia patient RC21


title: RC12_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC12

source_name: Human B-cell chronic lymphocytic leukemia patient RC12


title: RC20_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC20

source_name: Human B-cell chronic lymphocytic leukemia patient RC20


title: RC14_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC14

source_name: Human B-cell chronic lymphocytic leukemia patient RC14


title: 180 min cax1-1 treatment #4

last: Visscher

address: Fifield Hall

department: Horticultural Science

description:
Gene expression in cax1-1 roots after 180 min of magnesium sulfate solution.
T3C_4

hyb_protocol: A total of 20 samples were hybridized to five 4x44k Arabidopsis microarray slides (Agilent). Microarray handling and data extraction was done according to the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (version 5.7).

data_processing: Median signal intensities were quantile normalized using R software.

organism: Arabidopsis thaliana

source_name: cax1-1 roots, magnesium sulfate treatment, 180 min

label_protocol: RNA from each sample was amplified and labeled with Cy3 dye by using the Agilent Quick Amp labeling kit, one color.

growth_protocol: Glass containers (2.6 L) were covered with opaque black plastic sheeting along the glass, and with opaque plastic lids across the top. In each opaque plastic lid, 18 holes (d = 1.43 cm) were made at regular intervals with a hole puncher. A 2-cm-long Rockwool (Grodan) plug (d = 1.59 cm) was placed in each hole. Containers were filled with a nutrient solution adjusted to pH 5.7 by KOH that was replaced once a week. It consisted of distilled water, 0.25 g/L MES buffer, and 1/32x MS salts during week 1 and 2, while the concentration of MS salts increased to 1/16x during week 3. Arabidopsis seeds were sterilized and stratified before planting about ten seeds per Rockwool plug. Col-0 seeds were planted on 18 containers, while cax1-1 seeds were planted on 6. Containers were covered with transparent plastic wrap during the first 3-5 days of germination. Holes were made in the plastic wrap after 1-3 days depending on the general atmospheric humidity. The containers were randomly placed over 3 benches (8 containers/bench). Air was supplied to the roots by one 3W air pump per 8 containers; each container had an airstone made from glass beads. After one week, seedlings were thinned to one seedling per Rockwool plug, so that every container supported 18 plants.

extract_protocol: RNA was extracted from root samples with the RNeasy Plant Mini Kit (Qiagen). Samples were weighed while still frozen and reagents were adjusted to the total measured weight for the grinding and lysing step. Two replicate extractions were completed per sample with lysate volumes corresponding to 100 mg frozen wet weight each. The remainder of a sample was stored at -80oC as cleared lysate according to the Qiagen protocol. The quality and quantity of the extracted RNA was checked with denaturing agarose gels stained with ethidium bromide and the NanoDrop 1000 Spectrophotometer (Thermo Scientific).

treatment_protocol: At day 21, col-0 and cax1-1 roots were exposed to the basic nutrient solution (0.25 g/L MES, 1/16x MS, pH 5.7) with an additional 2.08 mM magnesium sulfate (total Ca:Mg ratio = 1:15). Col-0 was exposed for 45 min., 90 min., or 180 min., while cax1-1 was exposed for 180 min. only. The col-0 control set received no extra magnesium sulfate and was harvested at 45 min. together with the first col-0 treatment set. Four replicate containers were harvested for the control and each of the treatment sets. Roots were cut below the Rockwool plug and pooled per container before being flash frozen in liquid nitrogen and stored at -80oC.

tag: cultivar

tag: genotype

value: cax1-1 mutant

value: roots

tag: age

value: 3 weeks

tag: growth method

value: hydroponics system

value: magnesium sulfate

tag: treatment time

value: 180 minutes

tag: # plants/sample


title: ScYap1R79K-1

city: La Jolla

first: Dwight

last: Kuo

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Images were quantified using GenePix Pro 6.0

data_processing: Background subtraction and LOWESS normalization, Rosetta Error Model

organism: Saccharomyces cerevisiae

source_name: Yeast cells

label_protocol: As recommended using Sigma WGA2 amplification and Invitrogen 18095011, Cy5 and Cy3

growth_protocol: Cells were innoculated to OD600=0.2, grown to 0.8 and treated for one hour with 0.03% MMS

extract_protocol: Cells were fixed with 1% formaldehyde for 20 minutes, inactivated with glycine and washed with TBS. Cells were lysed for 2 hours (Vibrax-VXR 2000) with glass beads and sonicated for 4 cycles of 20 seconds (+100 seconds rest) at power setting 2 (Misonex Sonicator 3000) on ice. Lysate was incubated with Dynabeads M-280 conjugated with anti-TAP antibody (Open Biosystems CAB1001) overnight. Cross-link reversal was performed overnight at 65C.

tag: fraction

value: IP enriched

tag: antibody

value: anti-TAP

tag: antibody manufacturer

value: Open Biosystems

tag: antibody cat#

value: whole cell extract input


title: ScYap4K252R-1


title: 180 min cax1-1 treatment #3

description:
Gene expression in cax1-1 roots after 180 min of magnesium sulfate solution.
T3C_3

scan_protocol: Microarray handling and data extraction was done according to the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (version 5.7).

tag: tissue

tag: treatment


title: ScYap4K252R-2


title: GE93_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE93

source_name: Human B-cell chronic lymphocytic leukemia patient GE93

tag: legend

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

tag: Sex

value: M


title: 180 min cax1-1 treatment #2

description:
Gene expression in cax1-1 roots after 180 min of magnesium sulfate solution.
T3C_2


title: ScYap1R79K-2


title: RC11_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC11

source_name: Human B-cell chronic lymphocytic leukemia patient RC11

tag: vh status

value: mut

tag: disease

value: B-cell chronic lymphocytic leukemia (B-CLL)


title: 180 min cax1-1 treatment #1

description:
Gene expression in cax1-1 roots after 180 min of magnesium sulfate solution.
T3C_1


title: RC1_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC1

source_name: Human B-cell chronic lymphocytic leukemia patient RC1

tag: Stage

value: Binet A

tag: cell type

value: CD5/CD19/CD23 triple-positive B cells


title: GE130_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE130

source_name: Human B-cell chronic lymphocytic leukemia patient GE130

value: unmut


title: GE98_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE98

source_name: Human B-cell chronic lymphocytic leukemia patient GE98


title: 180 min col-0 treatment #4

description:
Gene expression in col-0 roots after 180 min of magnesium sulfate solution.
T3_4

source_name: col-0 roots, magnesium sulfate treatment, 180 min

tag: cultivar

tag: genotype

value: wild-type


title: GE115_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE115

source_name: Human B-cell chronic lymphocytic leukemia patient GE115

value: F


title: GE163_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE163

source_name: Human B-cell chronic lymphocytic leukemia patient GE163


title: GE126_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE126

source_name: Human B-cell chronic lymphocytic leukemia patient GE126


title: GE99_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE99

source_name: Human B-cell chronic lymphocytic leukemia patient GE99


title: RC33_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC33

source_name: Human B-cell chronic lymphocytic leukemia patient RC33


title: GE225_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE225

source_name: Human B-cell chronic lymphocytic leukemia patient GE225


title: GE88_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE88

source_name: Human B-cell chronic lymphocytic leukemia patient GE88


title: 180 min col-0 treatment #2

description:
Gene expression in col-0 roots after 180 min of magnesium sulfate solution.
T3_2

value: roots

tag: age

value: 3 weeks

tag: growth method


title: GE117_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE117

source_name: Human B-cell chronic lymphocytic leukemia patient GE117


title: RC17_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC17

source_name: Human B-cell chronic lymphocytic leukemia patient RC17


title: 180 min col-0 treatment #1

description:
Gene expression in col-0 roots after 180 min of magnesium sulfate solution.
T3_1

value: hydroponics system

value: magnesium sulfate

tag: treatment time

tag: # plants/sample


title: GE173_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE173

source_name: Human B-cell chronic lymphocytic leukemia patient GE173


title: 90 min col-0 treatment #3

description:
Gene expression in col-0 roots after 90 min of magnesium sulfate solution.
T2_3

source_name: col-0 roots, magnesium sulfate treatment, 90 min

value: 90 minutes


title: 90 min col-0 treatment #4

description:
Gene expression in col-0 roots after 90 min of magnesium sulfate solution.
T2_4


title: RC19_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC19

source_name: Human B-cell chronic lymphocytic leukemia patient RC19


title: GE87_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE87

source_name: Human B-cell chronic lymphocytic leukemia patient GE87


title: GE101_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE101

source_name: Human B-cell chronic lymphocytic leukemia patient GE101


title: 90 min col-0 treatment #1

description:
Gene expression in col-0 roots after 90 min of magnesium sulfate solution.
T2_1


title: GE114_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE114

source_name: Human B-cell chronic lymphocytic leukemia patient GE114


title: 90 min col-0 treatment #2

description:
Gene expression in col-0 roots after 90 min of magnesium sulfate solution.
T2_2


title: 45 min col-0 treatment #3

description:
Gene expression in col-0 roots after 45 min of magnesium sulfate solution.
T1_3

source_name: col-0 roots, magnesium sulfate treatment, 45 min

value: 45 minutes


title: GE111_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE111

source_name: Human B-cell chronic lymphocytic leukemia patient GE111


title: GE110_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE110

source_name: Human B-cell chronic lymphocytic leukemia patient GE110


title: U20S H3 XY R1

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: U2O2 cells; H3.X & H3.Y knockdown; biological replicate 1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
R/bioconductor, 'oligo' package, default parameters
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: H3.X & H3.Y knockdown

label_protocol: standard Affymetrix protocol

growth_protocol: The cell lines were grown in DMEM + 10% FCS

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit. The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer.

treatment_protocol: U2OS cells were transfected transfected twice with siRNA against luciferase (control) or H3.X and/or H3.Yusing oligofectamine (invitrogen) according to the manufacturer's instructions. Cells were harvested 4 days after transfection.

tag: cell line

tag: rnai

value: H3.X H3.Y


title: U20S H3 XY R2

description: U2O2 cells; H3.X & H3.Y knockdown; biological replicate 2


title: 45 min col-0 treatment #2

description:
Gene expression in col-0 roots after 45 min of magnesium sulfate solution.
T1_2


title: GE107_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE107

source_name: Human B-cell chronic lymphocytic leukemia patient GE107


title: CZ7_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ7

source_name: Human B-cell chronic lymphocytic leukemia patient CZ7


title: U20S H3 Y R2

description: U2O2 cells; H3.Y knockdown; biological replicate 2

source_name: H3.Y knockdown


title: RC5_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient RC5

source_name: Human B-cell chronic lymphocytic leukemia patient RC5


title: CZ41_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ41

source_name: Human B-cell chronic lymphocytic leukemia patient CZ41


title: CZ78_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ78

source_name: Human B-cell chronic lymphocytic leukemia patient CZ78


title: CZ47_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ47

source_name: Human B-cell chronic lymphocytic leukemia patient CZ47


title: 45 min col-0 control #3

description:
Gene expression in col-0 roots after 45 min of control solution.
T1C_3

source_name: col-0 roots, control, 45 min

value: control


title: 45 min col-0 control #4

description:
Gene expression in col-0 roots after 45 min of control solution.
T1C_4


title: CZ42_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ42

source_name: Human B-cell chronic lymphocytic leukemia patient CZ42

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)


title: U20S H3 Y R1

description: U2O2 cells; H3.Y knockdown; biological replicate 1


title: Both Hormones Rep 4

status: Public on Sep 16 2010

city: Brisbane

first: Ashkan

last: Amirshahi

state: QLD

address: 60 Musk ave, Kelvin Grove

department: Infectious diseases

institute: Institute of Health and Biomedical Innovation (IHBI)

description: Human Endometrial cancer cells (ECC-1) were infected with the human pathogen Chlamydia trachomatis serovar D, in the presence or absence of human female reproductive hormones estradiol and progesterone. The bacterial gene expression levels were examined 48 hours post-infection

hyb_protocol: Hybridisation, blocking and washing protocols identical to the E.coli hybridization protocols were used to facilitate binding of the labelled chlamydial transcripts.

scan_protocol: Standard scan protocol as per the E.coli genome array was applied when scanning the custom Chlamydia array.

data_processing:
The matrix table was generated through Affymetrix’s GCOS software version 1.4, normalised and the resultant data was exported into a Microsoft Excel spreadsheet for further processing. Default parameters for the software was used.
- The fold change calculations were performed using normalised log2 ratio between the hormone-variant and non-hormone treated cell lines.

organism: Chlamydia trachomatis

source_name: Chlamydia trachomatis Serovar D supplemented with both hormones

label_protocol: Target labelling was facilitated using Affymetrix’s Prokaryotic Target Preparation, protocol as outlined in the Expression Analysis Technical Manual

growth_protocol: The hormone-responsive human endometrial cell line ECC-1 was cultured for 24 hours in physiological concentrations of estradiol and/or progesterone, and then infected with C. trachomatis serovar D at a Multipilicity of Infection (MOI) of 15. All cell lines were pre-treated in activated charcoal medium (name) for 26 weeks prior to the addition of the female reproductive hormones and Chlamydia trachomatis serovar D.

extract_protocol: For the extraction of prokaryotic messenger RNA, a Trizol (Invitrogen) protocol following the manufacturer’s instructions was used for total RNA, followed by Dynabead purification (poly A+ purification kit)  (Dynal Biotech ASA, Oslo, Norway) for isolation of prokaryotic RNA.

treatment_protocol: Average physiological concentrations of 17β-estradiol, progesterone, and a combination of 17β-estradiol and progesterone (1:1) were added to respective wells once cells have reached full confluence, and supplemented with hormones continuously for 24 hours prior to infection. Although the physiological concentration of progesterone is higher than estradiol, in this study a combination of 1:1, estradiol and progesterone, was chosen as starting point to merely determine the effect of both hormones together.

tag: serovar


title: 45 min col-0 control #2

first: Anne

description:
Gene expression in col-0 roots after 45 min of control solution.
T1C_2

tag: tissue


title: Both Hormones Rep 3

value: Human Endometrial cancer cells (ECC-1) were infected with the human pathogen Chlamydia trachomatis serovar D


title: CZ36_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ36

source_name: Human B-cell chronic lymphocytic leukemia patient CZ36

value: M


title: 45 min col-0 treatment #4

description:
Gene expression in col-0 roots after 45 min of magnesium sulfate solution.
T1_4

tag: treatment


title: U20S luci R1

description: U2O2 cells; Luciferase knockdown; biological replicate 1

source_name: Luciferase knockdown

value: luciferase


title: CZ26_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ26

source_name: Human B-cell chronic lymphocytic leukemia patient CZ26

tag: legend

value: mut

value: B-cell chronic lymphocytic leukemia (B-CLL)

value: Binet A


title: 45 min col-0 treatment #1

description:
Gene expression in col-0 roots after 45 min of magnesium sulfate solution.
T1_1

source_name: col-0 roots, magnesium sulfate treatment, 45 min

value: wild-type


title: 180 min col-0 treatment #3

description:
Gene expression in col-0 roots after 180 min of magnesium sulfate solution.
T3_3

source_name: col-0 roots, magnesium sulfate treatment, 180 min

value: 180 minutes


title: Both Hormones Rep 2


title: U20S luci R2

description: U2O2 cells; Luciferase knockdown; biological replicate 2


title: BMC transplanted chagasic heart rep1

description: Determine the transcriptomic recovery in mouse heart infected with the parasite T. cruzi following transplantation with bone marrow cells

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-labeled biological replica overnight at 50°C on a Duke MO30N mouse oligonucleotide array spotted with 30k Operon 70-mer oligonucleotides V3.0.1. Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Physiol Genomics 2005.

label: Alexa Fluor®_647

source_name: BMC transplanted chagasic heart

label_protocol: 20ug total RNA extracted from each heart were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: All animals were raised and maintained at the Gonçalo Moniz Research Center/FIOCRUZ and provided with rodent diet and water ad libitum. Animals were handled according to the NIH guidelines for animal experimentation. All procedures had prior approval from the local animal ethics committee.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: C57Bl/6 mice were infected by intraperitoneal injection with Colombian Trypanosoma cruzi trypomastigotes obtained from culture supernatants of infected LCC-MK2 cells. Parasitemia of infected mice was evaluated at various times after infection by counting the number of trypomastigotes in peripheral blood aliquots. Bone marrow cells obtained from femurs and tibiae of C57BL/6 mice were used in transplantation experiments (Soares et al, 2004: Goldenberg et al, 2008). Briefly, BMC were purified by centrifugation in Ficoll gradient at 1000 g for 15 minutes (Histopaque 1119 and 1077, 1:1; Sigma, St. Louis, MO). After two washings in RPMI medium (Sigma), the cells were resuspended in saline, filtered over nylon wool, and injected intravenously in chagasic mice (3x106 cells/mouse). Non-transplanted control mice received intravenous injections of the same volume (200 µl) of saline. Mice were sacrificed after 8 months of infection and hearts removed and quickly frozen in liquid nitrogen for five minutes.

tag: strain

value: heart

tag: infection

value: T. cruzi

tag: disease state

value: chronic chagasic cardiomyopathy

value: bone marrow cell transplantation


title: BMC transplanted chagasic heart rep2

label: Alexa Fluor®_555

label_protocol: 20ug total RNA extracted from each heart were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: 45 min col-0 control #1

description:
Gene expression in col-0 roots after 45 min of control solution.
T1C_1

value: roots

value: 3 weeks

value: hydroponics system


title: Both Hormones Rep 1


title: Control  Rep 4

source_name: Chlamydia trachomatis Serovar D supplemented in absence of human female reproductive hormones


title: BMC transplanted chagasic heart rep3


title: BMC transplanted chagasic heart rep4


title: Control  Rep 3


title: CS38_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS38

source_name: Human B-cell chronic lymphocytic leukemia patient CS38

tag: Sex

tag: vh status

tag: disease

tag: Stage

value: CD5/CD19/CD23 triple-positive B cells


title: Estradiol  only- Rep 3

source_name: Chlamydia trachomatis Serovar D supplemented with etradiol


title: CS3_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS3

source_name: Human B-cell chronic lymphocytic leukemia patient CS3

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

value: F

tag: cell type


title: Control  Rep 2

value: Human Endometrial cancer cells (ECC-1) were infected with the human pathogen Chlamydia trachomatis serovar D


title: Control  Rep 1


title: Progesterone only-Rep3

source_name: Chlamydia trachomatis Serovar D supplemented with progesterone


title: Estradiol  only- Rep 2


title: Progesterone only-Rep4


title: Estradiol  only- Rep 4


title: CS17_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS17

source_name: Human B-cell chronic lymphocytic leukemia patient CS17

value: unmut


title: CS12_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CS12

source_name: Human B-cell chronic lymphocytic leukemia patient CS12

value: M