title: Pituitary_Nonylphenol-Control_rep5

status: Public on Jun 04 2012

city: Kearneysville

first: Laura

last: Robertson

state: WV

address: 11649 Leetown Rd.

department: Leetown Science Center

institute: USGS

description: biological replicate 5 of 8

hyb_protocol: Microarray slides from the same print batch were used for each tissue comparison.  Prior to hybridization, microarray slides were washed ten minutes in 0.1% SDS, and then rinsed five minutes in ultrapure water.  Slides were dried by centrifugation and pre-warmed at 50C for 30 minutes.  For each slide, 15 pmol of the Alexa 555 labeled aRNA or cDNA and 15 pmol of the Alexa 647 labeled aRNA or cDNA were combined and mixed with Ambion SlideHyb no. 2 to a volume of 60 µl for hybridization.  The combined samples and hybridization buffer were heated at 80C for ten minutes and pipetted under an Erie Scientific LifterSlip coverslip on top of the microarray slide.  The slides were incubated at 50C, shaking slowly, for 16-18 hours in a Boekel Scientific Shake ‘N’ Bake hybridization oven.  After hybridization, slides were washed on an orbital shaker for ten minutes in heated 2x SSC + 0.5% SDS; coverslips floated off the slides during this wash.  Slides were then washed for 5 minutes in heated 2x SSC + 0.5% SDS, five minutes in 0.5x SSC, and five minutes in 0.05x SSC.  Slides were dried by centrifugation and immediately scanned.

scan_protocol: Slides were scanned at 10 µm resolution in a Perkin Elmer ScanArray Gx scanner.  Laser power and PMT voltage were adjusted using the Line Scan Protocol such that the signal from the Alexa Fluor 555 dye was approximately equal to the signal from the Alexa Fluor 647 dye for each slide and the signal was saturated for approximately 0.3-0.5% of the features on the slide.

data_processing: Spot-finding was done with ScanArray Express Microarray Analysis System software version 4.0 using the adaptive circle method.  Median spot intensities and median background intensities were imported into the TM4 Microarray Software using the Express Converter version 2.1 utility; median background intensities were subtracted from median spot intensities.  Converted intensity files were imported into TM4 Midas version 2.20 with RMA and spots where the background-corrected intensity was less than zero for either channel (dye) were removed.  The log2 intensity ratios for each array were normalized using a local Lowess normalization (by subarray) and standard deviation regularization for the blocks.

organism: Salmo salar

source_name: female control pituitary

label_protocol: Pituitary RNA samples were amplified and then labeled using the Ambion Amino Allyl MessageAmpII aRNA amplification kit according to manufacturer’s instructions.  200ng or 500ngRNA was reverse transcribed into complementary DNA (cDNA) using an oligo(dT) primer containing a T7 promoter, then copied to create double-stranded DNA.  In a single round of amplification, this double-stranded DNA was used as a template to synthesize amino-allyl modified RNA (aRNA) with a T7 RNA polymerase in an 8 hour in vitro transcription reaction.  5µg of amino-allyl modified, amplified RNA was labeled with Alexa Fluor 555 or 647 dyes.  Liver, gill, hypothalamus, and olfactory rosette RNA samples were not amplified prior to labeling.  For these samples, 10ug total RNA was reverse transcribed and labeled using the Invitrogen Superscript Plus Indirect cDNA Labeling System and Invitrogen Alexa Fluor 555 or 647 dyes according to manufacturer’s instructions, with the following minor modifications:  Qiagen Qiaquick PCR Purification spin columns were used to clean the cDNA following first strand synthesis and following labeling with Alexa Fluor dyes.

growth_protocol: Atlantic salmon of Connecticut River stock obtained as parr from the White River National Fish Hatchery in fall 2005 were reared at the Conte Anadromous Fish Research Center in Turners Falls, MA.  Fish were held in 1.5 m diameter fiberglass tanks receiving flow-through (4 L min-1) Connecticut River water, maintained under natural photoperiod conditions.  Fish were reared under ambient river temperatures through the fall and then at 10 (+ 1) C from February through the remainder of the study.  Fish were fed to satiation twice daily with commercial feed.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to manufacturer instructions; all samples were treated with RNase-free DNase.

treatment_protocol: For the nonylphenol treatment group, smolts were injected with 150 µg/g body weight branched para-nonylphenol (CAS No. 84852-15-3) and for the control group, smolts were injected with a vehicle control on day 0 and on day 4 and then sampled on day 7.  Temperatures were 10 (+ 1) C and food was withheld throughout the treatment period. Fish were euthanized in 200 mg/L MS-222 neutralized to pH 7.0 and gill, liver, pituitary, hypothalamus and olfactory rosette tissues were collected in individual tubes and frozen at -80C for microarray analyses.

value: control

value: pituitary

value: female

source_name: male nonylphenol pituitary

value: nonylphenol

value: male


title: Pituitary_Nonylphenol-Control_rep8

type: RNA

country: USA

description: biological replicate 8 of 8

molecule: total RNA

tag: treatment

tag: tissue

tag: gender


title: Pituitary_Nonylphenol-Control_rep4

description: biological replicate 4 of 8

source_name: female nonylphenol pituitary


title: Pituitary_Nonylphenol-Control_rep6

description: biological replicate 6 of 8


title: Pituitary_Nonylphenol-Control_rep7

description: biological replicate 7 of 8


title: Rosettes_Nonylphenol-Control_rep5

description: biological replicate 5 of 8

source_name: female control rosettes

value: olfactory rosettes

source_name: male nonylphenol rosettes


title: LHS-ESE3KD_vs_LHS (merged dyeswaps)

status: Public on Jun 05 2012

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

description: 2 technical replicates: LHS-ESE3KD_vs_LHS and LHS-ESE3KD_vs_LHS_dyeswap

hyb_protocol: The same quantity of differentially labeled sample and reference was put together, fragmented and hybridized to oligonucleotide glass arrays with sequences representing more than 41K human unique genes and transcripts. All steps were performed using the Gene Expression Hybridization kit (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the Agilent wash procedure. A technical replicate, with dye swap scheme, was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing: Images were analyzed using Feature Extraction software (Agilent Technologies) version 9.5. Raw data were processed in R by using the LIMMA (Linear Models for Micro Array data) tool.

organism: Homo sapiens

source_name: LHS-ESE3KD, immortalized normal prostate epithelial cells (LHS) with stable expression of ESE3 specific shRNA [test]

label_protocol: For both sample and reference, equal amounts of mRNA were amplified and at the same time labeled according to the “Two-Color Microarray-Based Gene Expression Analysis” protocol (Agilent Technologies). Briefly: mRNA was reverse trascribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aRNA including Cyanine3/5-nucleotide (direct labeling method). Labeled RNAs underwent a purification step using RNeasy Mini Kit (Qiagen) columns with Agilent recommended procedure. mRNA quality, concentration and labeling were checked by means of Agilent 2100 Bioanalyzer and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA from LHSESE3KD and LHS cells was extracted using SV Total RNA Isolation System (Promega). After cleaning-up on RNAeasy minicolumns (Qiagen, Valencia, CA) and DNase treatment, RNA integrity, purity and quantity were checked by means of Agilent 2100 Bioanalyzer (Agilent Technologies) and NanoDrop (ThermoScientific)

tag: cell line

tag: protocol

value: shRNA-mediated ESE3 knockdown

source_name: LHS, immortalized normal prostate epithelial cells (LHS) with stable expression of a non targeting shRNA [reference]

value: control (non-targeting shRNA)


title: Rosettes_Nonylphenol-Control_rep6

description: biological replicate 6 of 8


title: Pituitary_Nonylphenol-Control_rep1

description: biological replicate 1 of 8

source_name: male control pituitary


title: Rosettes_Nonylphenol-Control_rep8

description: biological replicate 8 of 8


title: Rosettes_Nonylphenol-Control_rep7

description: biological replicate 7 of 8


title: Pituitary_Nonylphenol-Control_rep3

description: biological replicate 3 of 8


title: Pituitary_Nonylphenol-Control_rep2

description: biological replicate 2 of 8


title: Hypothalamus_Nonylphenol-Control_rep8

description: biological replicate 8 of 8

source_name: male nonylphenol hypothalamus

value: hypothalamus

source_name: female control hypothalamus


title: Rosettes_Nonylphenol-Control_rep4

description: biological replicate 4 of 8

source_name: female nonylphenol rosettes


title: Rosettes_Nonylphenol-Control_rep2

description: biological replicate 2 of 8

source_name: male control rosettes


title: Replication timing of Tc1-21 in Tc1 mouse CD4+ T lymphocytes, average of 2 biological replicates

type: genomic

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

description:
Hsa21 data
Two biological replicates: Both Early-replicating DNA samples were labeled with Cy3, both Late-replicating DNA samples with Cy5

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (6 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 70 bp across human chromosome 21.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing:
NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. For Tc1-21 datasets, early/late data was arranged according to the Tc1-21 sequence (Sequencing data for Tc1-21 is deposited in the ENA database, Study Accession number: ERP000439) prior to smoothing. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].
In this study we analyzed a mouse strain (Tc1) that contains a rearranged human chromosome 21 (Tc1-21). To make sense of Tc1-21 data from a human chromosome 21 array, we reordered the array probes to reflect Tc1-21's rearranged sequence and then processed the data. So some array probes are missing from the processed data file (correspond to deleted regions) while others are found twice (correspond to duplicated regions). The duplicated regions are present in the supplementary processed data (.txt) files on each Sample record.
HSA21_START = Start position of oligo in human chromosome 21 (Hg18, NCBI 36)
HSA21_END = End position of oligo in human chromosome 21 (Hg18, NCBI 36)
Tc1.21_START = Start position of oligo in Tc1 trans-chromosome 21 (Sequencing data for Tc1-21 is deposited in the ENA database, Study Accession number: ERP000439)

molecule: genomic DNA

organism: Mus musculus

source_name: Early-replicating DNA of Tc1 CD4+ T lymphocytes

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245]. For complete extraction protocol, please refer to PubMed ID: 21637205.

tag: strain

tag: cell type

value: mouse CD4+ T lymphocytes

tag: dna replication status

value: Early-replicating DNA

source_name: Late-replicating DNA of Tc1 CD4+ T lymphocytes

value: Late-replicating DNA


title: Hypothalamus_Nonylphenol-Control_rep6

description: biological replicate 6 of 8


title: Hypothalamus_Nonylphenol-Control_rep5

description: biological replicate 5 of 8


title: Rosettes_Nonylphenol-Control_rep3

description: biological replicate 3 of 8


title: Replication timing of Hsa21 in human CD4+ T lymphocytes, average of 2 biological replicates

source_name: Early-replicating DNA of human CD4+ T lymphocytes

value: human CD4+ T lymphocytes

source_name: Late-replicating DNA of human CD4+ T lymphocytes


title: Cotton drought induced 20 dpa sample, biological rep 3

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

country: India

institute: NRCPB

description: Gene expression data of 20 dpa sample of drought induced cotton plant

scan_protocol: The cotton GeneChip Genome arrays were scanned on a GeneChip scanner 3000.

data_processing: After scannig CEL files were analyzed using GeneSpring GX 11.0 software. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed.

label: biotin

organism: Gossypium hirsutum

source_name: Cotton drought induced plant

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5.0 µg total RNA Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

growth_protocol: G. hirsutum cv. Bikaneri Nerma was used in the present study. A rain out shelter (ROS) was specifically created at the University of Agricultural Sciences (UAS), Dharwad, Karnataka, India for creating and maintaining desired drought stress at various stages during the fibre development.   Plants were grown in twelve adjacent plots (six for control and six for drought induction) in the open filed. The ROS was used to cover six plots only when there was a rain to maintain the drought stress conditions. Watering was withheld during peak flowering stage for the induction of drought stress. Soil moisture content (SMC) was recorded every alternate day after stopping irrigation. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. This condition was observed 18-19 days after stopping the irrigation. About 20% of the soil moisture content was maintained throughout the sample collection period by spraying water if and when required. Samples at 20 dpa were collected from drought induced and control plots.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from fibre bearing ovules of 20 dpa collected from drought induced and control plants.

treatment_protocol: Cotton bolls at 20 dpa were collected from drought induced and control plants and immediately frozen in liquid nitrogen.

tag: cultivar

value: Bikaneri Nerma

tag: developmental stage

value: 20 dpa sample

value: drought induced


title: Replication timing of Tc1-21 in Tc1 MEFs, average of 3 biological replicates

description:
Hsa21 data
Three biological replicates: 348297_IMR901_635.pair, 348297_IMR902_532.pair and 348297_Tc1-21MEF3_635.pair raw data files represent the Early-replicating DNA, 348297_IMR901_532.pair, 348297_IMR902_635.pair and 348297_Tc1-21MEF3_532.pair represent the Late-replicating DNA

label: Cy5, Cy3, Cy5

source_name: Early-replicating DNA of Tc1 MEFs

value: Tc1 MEFs

label: Cy3, Cy5, Cy3

source_name: Late-replicating DNA of Tc1 MEFs


title: Hypothalamus_Nonylphenol-Control_rep7

description: biological replicate 7 of 8

value: control


title: Cotton drought induced 20 dpa sample, biological rep 2

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.


title: Rosettes_Nonylphenol-Control_rep1

description: biological replicate 1 of 8


title: Cotton control 20 dpa sample, biological rep 3

description: Gene expression data of 20 dpa sample of control cotton plant

source_name: Cotton control plant


title: Cotton drought induced 20 dpa sample, biological rep 1


title: Hypothalamus_Nonylphenol-Control_rep4

description: biological replicate 4 of 8

source_name: female nonylphenol hypothalamus


title: Cotton control 20 dpa sample, biological rep 2


title: Hypothalamus_Nonylphenol-Control_rep3

description: biological replicate 3 of 8


title: Replication timing of Hsa21 in IMR90 fibroblasts, average of 2 biological replicates

description:
Hsa21 data
Two biological replicates: 348297_IMR901_635.pair and 348297_IMR902_532.pair raw data files represent the Early-replicating DNA, 348297_IMR901_532.pair and 348297_IMR902_635.pair represent the Late-replicating DNA

label: Cy5, Cy3

source_name: Early-replicating DNA of IMR90 fibroblasts

value: IMR90 fibroblasts

label: Cy3, Cy5

source_name: Late-replicating DNA of IMR90 fibroblasts


title: Hypothalamus_Nonylphenol-Control_rep1

description: biological replicate 1 of 8

source_name: male control hypothalamus


title: Hypothalamus_Nonylphenol-Control_rep2

description: biological replicate 2 of 8


title: Cotton drought induced 5 dpa sample, biological rep 3

description: Gene expression data of 5 dpa sample of drought induced cotton plant

growth_protocol: G. hirsutum cv. Bikaneri Nerma was used in the present study. A rain out shelter (ROS) was specifically created at the University of Agricultural Sciences (UAS), Dharwad, Karnataka, India for creating and maintaining desired drought stress at various stages during the fibre development.   Plants were grown in twelve adjacent plots (six for control and six for drought induction) in the open filed. The ROS was used to cover six plots only when there was a rain to maintain the drought stress conditions. Watering was withheld during peak flowering stage for the induction of drought stress. Soil moisture content (SMC) was recorded every alternate day after stopping irrigation. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. This condition was observed 18-19 days after stopping the irrigation. About 20% of the soil moisture content was maintained throughout the sample collection period by spraying water if and when required. Samples at 5 dpa were collected from drought induced and control plots.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from 5 dpa bolls collected from drought induced and control plants.

treatment_protocol: Cotton  bolls at 5 dpa were collected from drought induced and control plants and immediately frozen in liquid nitrogen.

value: 5 dpa sample


title: BMA3-3, chip MOE430A

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project.  The biological material was submitted to the Ontario Genomics Innovation Centre by Amelie Faubert (amelie.faubert@umontreal.ca; ) for analysis.
Stembase Experiment ID:			E242
Stembase Experiment ID link:		see StemBase website
SCGP Sample ID:				S390
SCGP Sample ID link:			see StemBase website for SAMPLE_384
Short description:			Bone marrow cells were sorted and infected with Hoxa9+Meis retroviral particles, which provided fully leukemic complement to hematopoietic cells. These cells were injected into mice and leukemia onset was monitored in vivo. Leukemic stem cell (L-HSC) frequencies of these primary leukemias were evaluated using limiting dilution stem cell transfer in secondary recipients. , For this sample, number of Leukemic-HSC (L-HSC) per total Leukemic-Bone marrow cells (L-HSC frequency) was 1 in 129 (0.78%).,
Estimated purity:				95
RNA concentration:			0.05 ug/ul

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

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

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

label: Biotin

source_name: Total bone marrow cells, Bone Marrow

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

extract_protocol: RNA prep method:				RNeasy

tag: Strain:					C57bl/6 wild type

tag: Gender:					female


title: BMA5-2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project.  The biological material was submitted to the Ontario Genomics Innovation Centre by Amelie Faubert (amelie.faubert@umontreal.ca; ) for analysis.
Stembase Experiment ID:			E242
Stembase Experiment ID link:		see StemBase website
SCGP Sample ID:				S391
SCGP Sample ID link:			see StemBase website for SAMPLE_385
Short description:			Bone marrow cells were sorted and infected with Hoxa9+Meis retroviral particles, which provided fully leukemic complement to hematopoietic cells. These cells were injected into mice and leukemia onset was monitored in vivo. Leukemic stem cell (L-HSC) frequencies of these primary leukemias were evaluated using limiting dilution stem cell transfer in secondary recipients. , For this sample, number of Leukemic-HSC (L-HSC) per total Leukemic-Bone marrow cells (L-HSC frequency) was 1 in 183 (0.55%),
Estimated purity:				95
RNA concentration:			0.05 ug/ul


title: BMA5-3, chip MOE430A


title: Gill_Nonylphenol-Control_rep6

description: biological replicate 6 of 8

source_name: female control gill

value: gill

value: female

source_name: male nonylphenol gill

value: nonylphenol


title: Cotton drought induced 5 dpa sample, biological rep 1


title: Cotton control 5 dpa sample, biological rep 1

description: Gene expression data of 5 dpa sample of control cotton plant


title: Gill_Nonylphenol-Control_rep8

description: biological replicate 8 of 8

value: male


title: Cotton drought induced 5 dpa sample, biological rep 2


title: FLA2-1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project.  The biological material was submitted to the Ontario Genomics Innovation Centre by Amelie Faubert (amelie.faubert@umontreal.ca; ) for analysis.
Stembase Experiment ID:			E242
Stembase Experiment ID link:		see StemBase website
SCGP Sample ID:				S386
SCGP Sample ID link:			see StemBase website for SAMPLE_380
Short description:			Fetal liver cells were sorted and infected with Hoxa9+Meis retroviral particles, which provided fully leukemic complement to hematopoietic cells. These cells were injected into mice and leukemia onset was monitored in vivo. Leukemic stem cell (L-HSC) frequencies of these primary leukemias were evaluated using limiting dilution stem cell transfer in secondary recipients. , For this sample, number of Leukemic-HSC (L-HSC) per total Leukemic-Bone marrow cells (L-HSC frequency) was 1 in 1.4 (71.43%),
Estimated purity:				95
RNA concentration:			0.05 ug/ul

tag: Gender:					male


title: Gill_Nonylphenol-Control_rep7

description: biological replicate 7 of 8


title: FLB1-2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project.  The biological material was submitted to the Ontario Genomics Innovation Centre by Amelie Faubert (amelie.faubert@umontreal.ca; ) for analysis.
Stembase Experiment ID:			E242
Stembase Experiment ID link:		see StemBase website
SCGP Sample ID:				S387
SCGP Sample ID link:			see StemBase website for SAMPLE_381
Short description:			Fetal liver cells were sorted and infected with Hoxa9+Meis retroviral particles, which provided fully leukemic complement to hematopoietic cells. These cells were injected into mice and leukemia onset was monitored in vivo. Leukemic stem cell (L-HSC) frequencies of these primary leukemias were evaluated using limiting dilution stem cell transfer in secondary recipients. , For this sample, number of Leukemic-HSC (L-HSC) per total Leukemic-Bone marrow cells (L-HSC frequency) was 1 in 347 (0.29%),
Estimated purity:				95
RNA concentration:			0.05 ug/ul


title: BMA1-1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project.  The biological material was submitted to the Ontario Genomics Innovation Centre by Amelie Faubert (amelie.faubert@umontreal.ca; ) for analysis.
Stembase Experiment ID:			E242
Stembase Experiment ID link:		see StemBase website
SCGP Sample ID:				S389
SCGP Sample ID link:			see StemBase website for SAMPLE_383
Short description:			Bone marrow cells were sorted and infected with Hoxa9+Meis retroviral particles, which provided fully leukemic complement to hematopoietic cells. These cells were injected into mice and leukemia onset was monitored in vivo. Leukemic stem cell (L-HSC) frequencies of these primary leukemias were evaluated using limiting dilution stem cell transfer in secondary recipients. , For this sample, number of Leukemic-HSC (L-HSC) per total Leukemic-Bone marrow cells (L-HSC frequency) was unknown.,
Estimated purity:				95
RNA concentration:			0.05 ug/ul


title: ovary_15.5 dpc_1

city: Toyoake

first: Makiko

last: Tsutsumi

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

department: ICMS

country: Japan

institute: Fujita Health University

description: Gene expression data from 15.5 dpc ovaries.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in a fluidics system.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS, version 1) using Affymetrix default analysis settings.

source_name: Mouse fetal ovary

label_protocol: Biotinylated cRNA were prepared using MessageAmp aRNA Kit (Ambion) according to the manufacturer's instructions from 1 ug total RNA.

growth_protocol: The C57BL/6 mice were obtained from a commercial breeder.

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen) according to the
manufacturer's instructions.

treatment_protocol: Gonads were dissected from 15.5 dpc mice.

value: ovary

tag: age

value: 15.5 days postcoitum


title: Gill_Nonylphenol-Control_rep4

description: biological replicate 4 of 8

source_name: female nonylphenol gill


title: Gill_Nonylphenol-Control_rep5

description: biological replicate 5 of 8


title: BMA3-1, chip MOE430A


title: BMA3-2, chip MOE430A


title: Cotton control 5 dpa sample, biological rep 2


title: FLA2-3, chip MOE430A


title: Cotton drought induced 10 dpa sample, biological rep 3

description: Gene expression data of 10 dpa sample of drought induced cotton plant

growth_protocol: G. hirsutum cv. Bikaneri Nerma was used in the present study. A rain out shelter (ROS) was specifically created at the University of Agricultural Sciences (UAS), Dharwad, Karnataka, India for creating and maintaining desired drought stress at various stages during the fibre development.   Plants were grown in twelve adjacent plots (six for control and six for drought induction) in the open filed. The ROS was used to cover six plots only when there was a rain to maintain the drought stress conditions. Watering was withheld during peak flowering stage for the induction of drought stress. Soil moisture content (SMC) was recorded every alternate day after stopping irrigation. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. This condition was observed 18-19 days after stopping the irrigation. About 20% of the soil moisture content was maintained throughout the sample collection period by spraying water if and when required. Samples at 10 dpa were collected from drought induced and control plots.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from fibre bearing ovules of 10 dpa collected from drought induced and control plants.

treatment_protocol: Cotton bolls at 10 dpa were collected from drought induced and control plants and immediately frozen in liquid nitrogen.

value: 10 dpa sample


title: FLB2-2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project.  The biological material was submitted to the Ontario Genomics Innovation Centre by Amelie Faubert (amelie.faubert@umontreal.ca; ) for analysis.
Stembase Experiment ID:			E242
Stembase Experiment ID link:		see StemBase website
SCGP Sample ID:				S388
SCGP Sample ID link:			see StemBase website for SAMPLE_382
Short description:			Fetal liver cells were sorted and infected with Hoxa9+Meis retroviral particles, which provided fully leukemic complement to hematopoietic cells. These cells were injected into mice and leukemia onset was monitored in vivo. Leukemic stem cell (L-HSC) frequencies of these primary leukemias were evaluated using limiting dilution stem cell transfer in secondary recipients. , For this sample, number of Leukemic-HSC (L-HSC) per total Leukemic-Bone marrow cells (L-HSC frequency) was 1 in 72 (1.39%).,
Estimated purity:				95
RNA concentration:			0.05 ug/ul


title: Cotton drought induced 10 dpa sample, biological rep 1


title: Liver_Nonylphenol-Control_rep7

description: biological replicate 7 of 8

source_name: female control liver

value: liver

source_name: male nonylphenol liver


title: Cotton control 10 dpa sample, biological rep 3

description: Gene expression data of 10 dpa sample of control cotton plant


title: Liver_Nonylphenol-Control_rep6

description: biological replicate 6 of 8

source_name: female nonylphenol liver


title: ovary_adult_1

description: Gene expression data from 10-week-old ovaries.

source_name: Mouse adult ovary

treatment_protocol: Gonads were dissected from 10-week-old mice.


title: Cotton control 20 dpa sample, biological rep 1


title: BMA5-1, chip MOE430A


title: Liver_Nonylphenol-Control_rep5

description: biological replicate 5 of 8


title: Cotton drought induced 10 dpa sample, biological rep 2

source_name: Cotton drought induced plant


title: BMA1-2, chip MOE430A


title: Liver_Nonylphenol-Control_rep8

description: biological replicate 8 of 8


title: Cotton control 5 dpa sample, biological rep 3


title: Cotton drought induced 0 dpa sample, biological rep 2

description: Gene expression data of 0 dpa sample of drought induced cotton plant

growth_protocol: G. hirsutum cv. Bikaneri Nerma was used in the present study. A rain out shelter (ROS) was specifically created at the University of Agricultural Sciences (UAS), Dharwad, Karnataka, India for creating and maintaining desired drought stress at various stages during the fibre development.   Plants were grown in twelve adjacent plots (six for control and six for drought induction) in the open filed. The ROS was used to cover six plots only when there was a rain to maintain the drought stress conditions. Watering was withheld during peak flowering stage for the induction of drought stress. Soil moisture content (SMC) was recorded every alternate day after stopping irrigation. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. This condition was observed 18-19 days after stopping the irrigation. About 20% of the soil moisture content was maintained throughout the sample collection period by spraying water if and when required. Samples at 0 dpa were collected from drought induced and control plots.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from 0 dpa bolls collected from drought induced and control plants.

treatment_protocol: Cotton leaf sample and bolls at 0 dpa were collected from drought induced and control plants and immediately frozen in liquid nitrogen.

value: 0 dpa sample


title: Cotton control 10 dpa sample, biological rep 1


title: Gill_Nonylphenol-Control_rep2

description: biological replicate 2 of 8

source_name: male control gill


title: FLB2-1, chip MOE430A


title: testis_15.5 dpc_1

description: Gene expression data from 15.5 dpc testes.

source_name: Mouse fetal testis

value: testis


title: Gill_Nonylphenol-Control_rep1

description: biological replicate 1 of 8


title: Cotton drought induced 0 dpa sample, biological rep 3

value: Bikaneri Nerma


title: FLA2-2, chip MOE430A


title: BMA1-3, chip MOE430A


title: Liver_Nonylphenol-Control_rep4

description: biological replicate 4 of 8

source_name: male control liver


title: ovary_neonatal day 1_1

description: Gene expression data from 1-day-old ovaries.

source_name: Mouse neonatal day 1 ovary

treatment_protocol: Gonads were dissected from 1-day-old mice.

value: 1-day old


title: testis_adult_1

description: Gene expression data from 10-week-old testes.

source_name: Mouse adult testis


title: Gill_Nonylphenol-Control_rep3

description: biological replicate 3 of 8


title: Liver_Nonylphenol-Control_rep3

description: biological replicate 3 of 8


title: Cotton drought induced 0 dpa sample, biological rep 1

value: drought induced


title: Cotton control 10 dpa sample, biological rep 2

source_name: Cotton control plant


title: Cotton control 0 dpa sample, biological rep 2

description: Gene expression data of 0 dpa sample of control cotton plant


title: Liver_Nonylphenol-Control_rep2

description: biological replicate 2 of 8


title: testis_neonatal day 1_1

description: Gene expression data from 1-day-old testes.

source_name: Mouse neonatal day 1 testis


title: Cotton control 0 dpa sample, biological rep 1


title: Cotton control 0 dpa sample, biological rep 3


title: FLB1-3, chip MOE430A

source_name: Total bone marrow cells, Bone Marrow


title: Cotton drought induced leaf sample, biological rep 3

description: Gene expression data of leaf sample of drought induced cotton plant

growth_protocol: G. hirsutum cv. Bikaneri Nerma was used in the present study. A rain out shelter (ROS) was specifically created at the University of Agricultural Sciences (UAS), Dharwad, Karnataka, India for creating and maintaining desired drought stress.   Plants were grown in twelve adjacent plots (six for control and six for drought induction) in the open filed. The ROS was used to cover six plots only when there was a rain to maintain the drought stress conditions. Watering was withheld during peak flowering stage for the induction of drought stress. Soil moisture content (SMC) was recorded every alternate day after stopping irrigation. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. This condition was observed 18-19 days after stopping the irrigation. Leaf samples were collected from drought induced and control plots.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from cotton leaves.

treatment_protocol: Cotton leaf sample were collected from drought induced and control plants and immediately frozen in liquid nitrogen.

value: Leaf


title: Cotton control leaf sample, biological rep 2

description: Gene expression data of leaf sample of control cotton plant

value: control


title: Cotton drought induced leaf sample, biological rep 1


title: Cotton drought induced leaf sample, biological rep 2


title: EndometrialStromalCell_Choco_Ectopic_2-H2O2

city: Nagoya

first: Shinya

last: Toyokuni

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Scanner Settings).

data_processing:
Microarray data were analyzed following import into GeneSpring 11.5 software (Agilent Technologies)
Threshold: 1.0
Logbase: 2
Technology: Agilent.SingleColor.14850
Normalization: Shift to 75 percentile
Baseline Transformation: None

source_name: ectopic endometrial stromal cell from patients with ovarian endometrioma, treated with H2O2

growth_protocol: Endometrial stromal cells were incubated in DMEM (Sigma D5921) + 10% FBS (BioWest) + 200IU/ml potassium benzylpenicillin (Meiji) + 200ug/ml streptomycin sulfate (Meiji) + 2.5mg/ml amphotericin B (Sigma A2942) for 24 hours.

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: After 24 hours of incubation, medium was exchanged with Phenol Red-free DMEM(Sigma D5921) + 1uM hydrogen peroxide + 200IU/ml potassium benzylpenicillin(Meiji) + 200ug/ml streptomycin sulfate(Meiji) + 2.5mg/ml amphotericin B(Sigma A2942). After 60 hours of incubation, RNA was collected. Supplementary hydrogen peroxide was added to medium every 48 hours. Control cells were incubated in Phenol Red-free DMEM(Sigma D5921) + 200IU/ml potassium benzylpenicillin(Meiji) + 200ug/ml streptomycin sulfate(Meiji) + 2.5mg/ml amphotericin B(Sigma A2942) for 60 hours and its RNA was collected.

value: ectopic endometrial stromal

tag: cycle phase

value: treated with GnRH

tag: diagnosis

value: endometriosis

tag: r-afs stage(score)


title: Cotton control leaf sample, biological rep 3

tag: treatment


title: Liver_Nonylphenol-Control_rep1

description: biological replicate 1 of 8

tag: tissue

value: female


title: EndometrialStromalCell_Choco_Ectopic_2-Ctrl

source_name: ectopic endometrial stromal cell from patients with ovarian endometrioma, untreated with H2O2

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008).


title: EndometrialStromalCell_Choco_Eutopic_2-H2O2

source_name: eutopic endometrial stromal cell from patients with ovarian endometrioma, treated with H2O2

value: eutopic endometrial stromal

value: early proliferative


title: EndometrialStromalCell_Choco_Ectopic_3-H2O2

value: late secretary


title: Cotton control leaf sample, biological rep 1


title: Bark_sucrose_replicate 1_72h

city: college park

first: rongshuang

last: lin

state: MD

address: Plant Sci building

department: Plant sci

institute: Univ Maryland

description: Expression data for bark tissues from excised stems treated with sucrose

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed using RMA function  in the affy package in R.

organism: Populus trichocarpa

source_name: Barks from sucrose treatment for 72h for replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT expression kit manual).

growth_protocol: Poplar plants were grown in greenhouse under long-day photoperiod.

extract_protocol: Extraction of total RNA was performed using Qiangen RNeasy plant mini kit with Qiancube with modifications.

treatment_protocol: Excised stems from the LD-grown plants were trimmed off the basal leaves and kept 5 apical leaves; the basal end was immediately placed in water for pre-incubation for 24 h in growth chamber under 16-h light/8-h dark photoperiod. After 24 h, the stems were then transferred to aqueous solutions of 25 mM glutamine, glucose, sucrose, glycine, glutamine+glucose, glutamine+sucrose, for 48 or 72 h at the same condition.

value: Bark

tag: genotype

value: Nisqually

value: sucrose

tag: time

tag: replicate


title: Bark_sucrose_replicate 3_72h

source_name: Barks from sucrose treatment for 72h for replicate 3


title: Bark_sucrose_replicate 2_72h

source_name: Barks from sucrose treatment for 72h for replicate 2


title: EndometrialStromalCell_Choco_Ectopic_1-Ctrl

value: endometriosis and leiomyoma


title: EndometrialStromalCell_Choco_Ectopic_3-Ctrl


title: EndometrialStromalCell_Choco_Eutopic_2-Ctrl

source_name: eutopic endometrial stromal cell from patients with ovarian endometrioma, untreated with H2O2


title: EndometrialStromalCell_Choco_Ectopic_1-H2O2


title: EndometrialStromalCell_Choco_Eutopic_3-H2O2


title: Bark_glutamine+sucrose_replicate 3_48h

description: Expression data for bark tissues from excised stems treated with glutamine+sucrose

source_name: Barks from glutamine+sucrose treatment for 48h for replicate 3

value: glutamine+sucrose


title: EndometrialStromalCell_Choco_Eutopic_1-Ctrl


title: P19_RA-treated_48h_rep1

city: Rennes

first: Aurelien

last: Serandour

address: Bâtiment 13, Campus de Beaulieu

department: UMR CNRS 6290

country: France

institute: Université de Rennes 1

description:
This sample is of RA-treated P19.6 cells. First of three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).

hyb_protocol: Hybridization was performed by NimbleGen Systems (Services, Reykjavic) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Standard NimbleGen protocols (scanned at NimbleGen services, Reykjavic). See www.nimblegen.com.

data_processing: Raw data (.pair) were subjected to the RMA algorithm (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) with quantile settings (Bolstad et al. Bioinformatics 19(2):185) for background correction and normalization, as implemented within the ArrayStar software package (DNAstar, Inc.).

source_name: P19.6 cells treated for 48 hours with 1µM RA

label_protocol: Labeling was performed by NimbleGen Systems (Services, Reykjavic) following their standard operating protocol. See www.nimblegen.com.

growth_protocol: P19.6 mouse embryonal carcinoma cells were grown in high glucose Dulbeccos’ Modified Eagle’s Medium (DMEM) containing 10% fetal calf serum (GIBCO).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen). Integrity and purity of the RNAs were controlled on an Agilent Bioanalyzer using the RNA 6000 Nano Assay (Agilent). Ten ug of selected samples exhibiting a RIN >9.8 were then subjected to cDNA synthesis using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and a mix of 50 pmol random hexamers and 50 pmol of Oligo-dT. cDNAs were then treated for 10 min at 37°C with 5 µg RNaseA (Invitrogen), purified through a phenol:chloroform:isoamyl alcohol extraction on Phase Lock light gels (Fisher Scientific) and then precipitated following a quality control on 250 ng cDNA on agarose/BET gels.

treatment_protocol: P19.6 cells were differentiated with 1 µM all-trans retinoic acid (RA) for 48 hours.

tag: cell line

value: embryonal carcinoma cells

tag: background strain

value: all-trans retinoic acid (RA)

tag: treatment dosage

tag: treatment duration

value: 48 hours


title: EndometrialStromalCell_Choco_Eutopic_3-Ctrl

tag: cell type


title: P19_RA-treated_48h_rep3

description:
This sample is of RA-treated P19.6 cells. Third of three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).


title: Bark_glutamine+sucrose_replicate 1_48h

source_name: Barks from glutamine+sucrose treatment for 48h for replicate 1


title: Bark_glutamine+sucrose_replicate 2_48h

source_name: Barks from glutamine+sucrose treatment for 48h for replicate 2


title: Bark_sucrose_replicate 3_48h

source_name: Barks from sucrose treatment for 48h for replicate 3


title: P19_RA-treated_48h_rep2

description:
This sample is of RA-treated P19.6 cells. Second of three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).


title: EndometrialStromalCell_Normal_Eutopic_3-H2O2

source_name: eutopic endometrial stromal cell from patients without endometriosis, treated with H2O2

value: cervical cancer


title: Bark_sucrose_replicate 2_48h

source_name: Barks from sucrose treatment for 48h for replicate 2


title: P19_non-RA-treated_rep3

description:
This sample is of non-treated P19.6 cells. Third of three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).

source_name: non-treated P19.6 cells


title: P19_non-RA-treated_rep2

description:
This sample is of non-treated P19.6 cells. Second of three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).


title: Bark_glutamine+sucrose_replicate 3_72h

source_name: Barks from glutamine+sucrose treatment for 72h for replicate 3


title: EndometrialStromalCell_Choco_Eutopic_1-H2O2


title: EndometrialStromalCell_Normal_Eutopic_3-Ctrl

source_name: eutopic endometrial stromal cell from patients without endometriosis, untreated with H2O2


title: EndometrialStromalCell_Normal_Eutopic_1-H2O2

value: mature cystic teratoma and leiomyoma


title: EndometrialStromalCell_Normal_Eutopic_2-H2O2

value: mid secretary

value: leiomyoma


title: P19_non-RA-treated_rep1

description:
This sample is of non-treated P19.6 cells. First of three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).


title: SKBR3wH

status: Public on Jun 03 2012

type: other

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

description: SKBR3, with Herceptin

hyb_protocol: The labeled samples were individually hybridized onto DNA chip surface, and incubated at 42 ℃ for 16 hours.

scan_protocol: Washed and dried DNA chip in an ozone-removed environment was scanned using a ProScanArray™ microarray scanner. The obtained microarray images were analyzed using the Genepix Pro™ 4.0 software.

data_processing: The median values of the foreground signal minus the local background were represented as feature intensities. All data obtained from microarray experiments were normalized by a quantile normalization method.

molecule: other

source_name: SKBR3, with Herceptin

label_protocol: For each patient, 500 ng of total RNA derived from tumor and non-tumor samples were labeled using miRCURY LNA™ microRNA Power Labeling Kits Hy5

extract_protocol:
Total RNA samples from breast cancer cell lines were extracted by a phenol-chloroform RNA extraction method.
Tumor and non-tumor tissues were obtained and frozen in liquid nitrogen immediately after hepatic resection, and stored in liquid nitrogen until RNA extraction. Total RNA samples were extracted by a phenol-chloroform RNA extraction method.

value: with Herceptin


title: BT474wH

description: BT474, with Herceptin

source_name: BT474, with Herceptin


title: MB231wH

description: MDA-MB-231, with Herceptin

source_name: MDA-MB-231, with Herceptin


title: SKBR3woH

description: SKBR3, without Herceptin

source_name: SKBR3, without Herceptin

value: without Herceptin


title: MB231woH

description: MDA-MB-231, without Herceptin

source_name: MDA-MB-231, without Herceptin


title: EndometrialStromalCell_Normal_Eutopic_1-Ctrl

value: eutopic endometrial stromal


title: MCF7wH

description: MCF7, with Herceptin

data_processing: The median values of the foreground signal minus the local background were represented as feature intensities. All data obtained from microarray experiments were normalized by a quantile normalization method, and filtered.

source_name: MCF7, with Herceptin


title: Bark_glutamine+sucrose_replicate 1_72h

source_name: Barks from glutamine+sucrose treatment for 72h for replicate 1


title: MCF7woH

description: MCF7, without Herceptin

source_name: MCF7, without Herceptin


title: Bark_glutamine+sucrose_replicate 2_72h

source_name: Barks from glutamine+sucrose treatment for 72h for replicate 2


title: BT474woH

description: BT474, without Herceptin

source_name: BT474, without Herceptin


title: EndometrialStromalCell_Normal_Eutopic_2-Ctrl


title: Bark_glycine_replicate 3_48h

description: Expression data for bark tissues from excised stems treated with glycine

source_name: Barks from glycine treatment for 48h for replicate 3

value: glycine


title: Bark_glycine_replicate 1_48h

source_name: Barks from glycine treatment for 48h for replicate 1


title: Bark_glycine_replicate 2_48h

source_name: Barks from glycine treatment for 48h for replicate 2


title: Bark_glycine_replicate 3_72h

source_name: Barks from glycine treatment for 72h for replicate 3


title: Bark_glycine_replicate 2_72h

source_name: Barks from glycine treatment for 72h for replicate 2


title: Bark_sucrose_replicate 1_48h

source_name: Barks from sucrose treatment for 48h for replicate 1


title: Water blank

city: Beltsville

first: Anthony

middle: V.

last: Capuco

address: 10300 Baltimore Ave., Bldg 200, Rm 14

department: Beltsville Agricultural Research Center

institute: USDA-ARS

description: water blank used for reverse transcription and amplification reaction

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

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

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

organism: Bos taurus

source_name: amplification water blank

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

growth_protocol: Mammary tissue was collected from the outer parenchymal region (region in close proximity to the border with mammary fat pad) of a rear mammary gland. Individual samples were immediately embedded in OCT compound (Sakura, Torrance, CA, USA), frozen in liquid nitrogen vapor and stored at -80°C until use.

extract_protocol: Cells within the cap were dissolved in 2 µl of lysis buffer (WT-Ovation™ One-Direct RNA Amplification System; NuGEN Technologies, Inc. San Carlos, CA). The tube was capped and centrifuged for one minute at 13000 rpm, after which the tube and contents were vortexed gently for 30 seconds and centrifuged briefly before placing on ice. First stand cDNA synthesis and amplification reaction was carried out using Ribo-SPIA-based RNA amplification according to the manufacturer’s recommendations. Concentrations of amplified cDNA were determined spectrophotometrically (ND-1000, NanoDrop Technologies, Rockland, DE). A known amount of RNA (250 pg, RIN 7.5) was used as positive control for cDNA amplification. Nuclease-free water was used as a no-template control of cDNA amplification.

treatment_protocol: An optimized method for BrdU immunostaining that retains RNA quality in tissue cryosections was used (Choudhary et al., J Dairy Sci 93 (6):2574-2579) to identify the label retaining epithelial cells (LREC). Immediately after staining slides were examined and cells excised with a laser microdissection system equipped for epifluorescence microscopy (Leica AS-LMD, Mannheim, Germany). Four categories of LREC and contol (non-LREC) epithelial cells were excised. The four categories were LREC from basal (LRECb) and embedded epithelial layers (LRECe), and epithelial control cells from basal (ECb) and embedded layers (ECe).

tag: breed

value: Blank

tag: cell

tag: location


title: NNI-5 (AFG1133-5)

city: Cambridge

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: Cambridge Institute for Medical Research

description:
replicate 1
Raw data file: AFG1133-5.CEL

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing:
The data were processed using mas5.0 and quantile normalized.  Probes with 'Absent' call in all samples were removed.
All processing done in R statistical software v2.12.1 using the 'affy' and 'Biobase' Bioconductor packages.

source_name: Primary neurosphere culture

label_protocol: Standard Affymetrix label protocol

growth_protocol: Graded brain tumor specimens were obtained with informed consent, as part of a study protocol approved by the institutional review board. Cells were seeded at a density of 2,500 per cm2 in chemically defined serum-free selection growth medium consisting of basic fibroblast growth factor, bFGF (20 ng/ml, Chemicon), epidermal growth factor, EGF (20 ng/ml, Chemicon), heparin (5 µg/ml, Sigma-Aldrich) and serm-free supplement, B27 (1x, Gibco) in a 3:1 mix of Dulbecco’s Modified Eagle Medium (Sigma-Aldrich) and F-12 Nutrient Mixture (Gibco).  The cultures were incubated at 37 deg C in a water-saturated atmosphere containing 5% CO2 and 95% air.  To maintain the undifferentiated state of neurosphere cultures, growth factors were replenished every 2 days.

extract_protocol: Total RNA was isolated from neurosphere cells using TRI Reagent (Molecular Research Center) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). Reverse transcription and cRNA amplification were performed using an RNA Amplification kit (Ambion, Austin, TX).

tag: histology

value: Glioblastoma multiforme

tag: grade

value: IV

tag: growth pattern

value: Free floating

tag: patient

tag: gender

value: Male

tag: age


title: NNI-3 (AFG1133-24)

description:
replicate 2
Raw data file: AFG1133-24.CEL


title: NNI-8 (AFG1133-27)

description:
replicate 2
Raw data file: AFG1133-27.CEL

value: Anaplastic Oligoastrocytoma

value: III


title: 5188-LRECb

description: BrdU label retaining cells (6-13 objects) laser-microdissected dissected from the basal epithelial layer

source_name: calf 5188-mammary LRECb

value: Holstein

value: Label retaining epithelial

value: basal layer epithelium


title: Bark_glycine_replicate 1_72h

source_name: Barks from glycine treatment for 72h for replicate 1

tag: tissue

value: Bark

tag: genotype

value: Nisqually

tag: treatment


title: NNI-8 (AFG1133-6)

description:
replicate 1
Raw data file: AFG1133-6.CEL


title: NNI-8 (AFG1133-37)

description:
replicate 2
Raw data file: AFG1133-37.CEL

source_name: Primary tumor


title: NNI-2 (AFG1133-2)

description:
replicate 1
Raw data file: AFG1133-2.CEL

value: Female


title: NNI-4 (AFG1133-25)

description:
replicate 2
Raw data file: AFG1133-25.CEL

value: Semi-adherent


title: HEK293T cell culture, untreated, biological rep 1

city: Lincoln

first: Timothy

last: Martin

state: NE

address: 32 Chase Hall

department: Biological Systems Engineering

institute: University of Nebraska-Lincoln

description: 24 h gene profile of untreated HEK293T cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm.

data_processing: The data was analysed using R 2.9.0 with Bioconductor 2.4. Arrays were normalised via RMA, and all treatments were compared to the control LA via the limma package. Benjamini-Hochberg adjusted p-values were used as significance measurement.

source_name: HEK293T human embryonic epithelial kidney cell culture, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HEK293T cells were grown in T75 in DMEM supplemented with 10% FBS, 1% Pen/Strep, 1% Sodium Pyruvate.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's (Invitrogen) instructions.

treatment_protocol: Cationic PEI polymer mixed with pEGFP-LUC to form polyplexes. Cells were treated with polyplexes 18 h after seeding and flow separated after another 24 h.

tag: cell line

tag: cell population

value: untreated


title: 5182-LRECe

description: BrdU label retaining cells (6-13 objects) laser-microdissected dissected from embedded basal epithelial layer

source_name: calf 5182-mammary LRECe

value: embedded layer epithelium


title: NNI-8 (AFG1133-16)

description:
replicate 1
Raw data file: AFG1133-16.CEL


title: NNI-3 (AFG1133-3)

description:
replicate 1
Raw data file: AFG1133-3.CEL


title: 5182-ECe

description: Control cells (6-13 objects) laser-microdissected dissected from an embedded epithelial layer

source_name: calf 5182-mammary ECe

value: Control epithelial


title: 5188-LRECe

source_name: calf 5188-mammary LRECe


title: HEK293T cell culture, untreated, biological rep 2


title: 5182-LRECb

source_name: calf 5182-mammary LRECb


title: NNI-5 (AFG1133-26)

description:
replicate 2
Raw data file: AFG1133-26.CEL


title: 5181-LRECe

source_name: calf 5181-mammary LRECe


title: NNI-2 (AFG1133-23)

description:
replicate 2
Raw data file: AFG1133-23.CEL


title: NNI-4 (AFG1133-4)

description:
replicate 1
Raw data file: AFG1133-4.CEL


title: NNI-1 (AFG1133-1)

description:
replicate 1
Raw data file: AFG1133-1.CEL


title: NNI-1 (AFG1133-22)

description:
replicate 2
Raw data file: AFG1133-22.CEL


title: 5188-ECe

source_name: calf 5188-mammary ECe


title: 5181-LRECb

source_name: calf 5181-mammary LRECb


title: 5188-ECb

description: Control cells (6-13 objects) laser-microdissected dissected from the basal epithelial layer

source_name: calf 5188-mammary ECb


title: 5182-ECb

source_name: calf 5182-mammary ECb


title: 5181-ECe

source_name: calf 5181-mammary ECe


title: 5170-LRECb

source_name: calf 5170-mammary LRECb


title: 5161-LRECe

source_name: calf 5161-mammary LRECe


title: 5161-LRECb

source_name: calf 5161-mammary LRECb


title: 5161-ECe

source_name: calf 5161-mammary ECe


title: 5170-LRECe

source_name: calf 5170-mammary LRECe


title: WT2

description: this data was normalized by quantile normalization method

source_name: Hepatic Stellate Cells

label_protocol: For each mouse 500 ng of total RNA derived from tumor and non-tumor samples were labeled using miRCURY LNA™ microRNA Power Labeling Kits Hy5

extract_protocol: Total RNA samples were extracted by a phenol-chloroform RNA extraction method.

tag: disease state

value: CCl4-induced Liver Cirrhosis

value: wild type

value: Hepatic Stellate Cells


title: 5181-ECb

source_name: calf 5181-mammary ECb


title: 5161-ECb

source_name: calf 5161-mammary ECb


title: WT1


title: 5170-ECb

source_name: calf 5170-mammary ECb


title: WT3


title: Sporadic MMR proficient_AS53

status: Public on Jun 02 2012

city: Hvidovre

first: Christina

last: Therkildsen

state: Hvidovre

address: Kettegaard Alle 30

department: Clinical Research Centre

country: Denmark

institute: Copenhagen University Hospital

description:
Analysis used male reference DNA to investigate the genomic alterations appearing in sporadic MMR procifient tumors
The dye information in the .gpr files represent the compound used to label the tumor sample.

hyb_protocol: Prior to hybridization, sample DNA and reference DNA were pooled with 100 ug human Cot-1 DNA (Invitrogen). Following the Pronto Universal Hybridization System (Corning Inc., Corning, NY, USA) BAC arrays were hybridized for 48 hrs at 37 degrees using the MAUI® Hybridization System (BioMicro system Inc., Salt Lake City, UT, USA).

scan_protocol: The arrays were scanned with an Agilent Microarray Scanner (Agilent Technologies).

data_processing: Images were processed using the GenePix Pro.4.1 software (Axon Instruments INC., Foster City, CA, USA). The output of GenePix were uploaded in the in-house develeoped web-based BioArray Software Environment (BASE, http://base.onk.lu.se). Median spot pixel values were used to calculate background corrected intensities and spots were considered missing if they were flagged or had a signal-to-noise ratio <3. Spots from dye-swap hybridization were merged using geometric mean of ratios and the log2 transformed and normalized (LOWESS) values were plotted against their genomic location.

source_name: Colorectal cancer

label_protocol: 2-8 ug genomic tumor DNA and 2 ug male reference DNA (Promega Corporations, Madison, WI, USA) was fluorescently labeled with Cy3-dCTP and Cy5-dCTP (GE Healthcare U Limited) using a BioPrime® Array CGH Genomic Labeling System (Invitrogen Corporations, Carlsbad, CA, USA) according to manufacture's instructions. Labeled DNA was purified using PureLink PCR Purification Kit (Invitrogen).

extract_protocol: Genomic tumor DNA was located and extracted from formalin-fixed paraffin-embedded tissue using a Phenol-Cloroform-Isoamyl purification step twice and DNA was precipitated and spun down according to the protocol (UCSF Waldman Laboratory, San Fransisco, CA, USA, http://waldman.ucsf.edu/Protocols/paraffin.html)

tag: mmr status

value: No family history

tag: tumor location

value: proximal

tag: tumor stage

tag: age at onset

tag: Sex

source_name: Promega Male reference

tag: reference

value: Promega Male reference


title: SigR_diamide_20min

type: mixed

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

hyb_protocol: 4 ug of labelled DNA were hybridized on 385K NimbleGen custom arrays according to NimbleGen's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The signal from the sigRrsrA mutant ChIP was subtracted from the signals from the wild-type ChIP after normalization to remove non-specific signal.

organism: Streptomyces coelicolor A3(2)

source_name: genomic DNA control

label_protocol: Before labelling, the ChIP DNA was amplified using ligation mediated PCR. 1 ug of DNA was labelled using the NimbleGen Dual-color DNA labelling Kit (05223547001) according to the manufacturer's protocol.

growth_protocol: S. coelicolor cells were grown to exponential phase (OD~0.3) and were treated with 0.5 mM diamide for 20 min.

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 4 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA. The lysate was was incubated without any antibodies at 4°C over night as a mock immuno-precipitation step to obtain the control DNA. Then, ProteinA coated sepharose beads were added to the lysate, which was incubated for another 3 hours. Beads were centrifuged from the sample and discarded. The remaining DNA in solution was cleaned using QIAGen DNA purification kit.

tag: strain

value: wild-type M145

tag: antibody

value: 0.5 mM diamide for 20 min

source_name: SigR chromatin immunoprecipitation

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was was incubated with polyclonal antibodies against SigR at 4°C over night. Then, ProteinA coated sepharose beads were added to the lysate, which was incubated for another 3 hours to capture antibodies. Beads were washed once with LiCl buffer (125 mM LiCL, 50 mM Tris pH 8, 1 % TritonX-100), twice with 600 mM NaCl Tris buffer, twice with 300mM NaCl Tris buffer and twive with TE buffer (10 mM Tris ph 8, 1 mM EDTA). Beads were ressupended in 200 uL Elution buffer (50 mM Tris pH 8, 10 nM EDTA, 1% SDS) and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.

value: SigR (non-commercial)


title: Sporadic MMR proficient_AS63

value: distal


title: 5170-ECe

source_name: calf 5170-mammary ECe

tag: breed

value: Holstein

tag: cell

tag: location


title: Sporadic MMR proficient_AS56

value: Male


title: Sporadic MMR proficient_AS50

value: Female


title: Sporadic MMR proficient_AS44


title: Sporadic MMR proficient_AS33


title: KO1

tag: cell type


title: Sporadic MMR proficient_AS16


title: Sporadic MMR proficient_AS39


title: Sporadic MMR proficient_AS35


title: KO2

tag: genotype


title: Sporadic MMR proficient_AS36


title: Sporadic MMR proficient_AS23


title: Sporadic MMR proficient_AS25


title: KO3


title: Sporadic MMR proficient_AS37


title: Sporadic MMR proficient_AS38


title: Sporadic MMR proficient_AS22


title: Sporadic MMR proficient_AS3


title: Sporadic MMR proficient_AS2


title: Sporadic MMR deficient_AM59

description:
Analysis used male reference DNA to investigate the genomic alterations appearing in sporadic MMR decifient tumors
The dye information in the .gpr files represent the compound used to label the tumor sample.

value: MLH1/PMS2 deficient, no family history


title: Sporadic MMR proficient_AS29


title: Sporadic MMR proficient_AS12


title: Sporadic MMR proficient_AS11


title: Sporadic MMR proficient_AS1


title: Sporadic MMR deficient_AM54


title: Sporadic MMR deficient_AM57


title: Sporadic MMR deficient_AM52


title: Sporadic MMR deficient_AM51


title: Sporadic MMR deficient_AM49


title: Sporadic MMR proficient_AS15


title: Sporadic MMR deficient_AM56


title: Sporadic MMR deficient_AM53


title: Sporadic MMR deficient_AM50


title: Sporadic MMR deficient_AM47


title: Sporadic MMR deficient_AM35


title: Sporadic MMR deficient_AM41


title: Sporadic MMR deficient_AM46


title: Sporadic MMR deficient_AM38


title: FCCTX_AA78

description:
Analysis used male reference DNA to investigate the genomic alterations appearing in FCCTX tumors
The dye information in the .gpr files represent the compound used to label the tumor sample.

value: No MMR gene mutated

value: Rectum


title: Sporadic MMR deficient_AM16


title: Sporadic MMR deficient_AM32


title: FCCTX_AA56

value: Splenic flexure

value: Dead female


title: Sporadic MMR deficient_AM3


title: Sporadic MMR deficient_AM4


title: FCCTX_AA26

value: Sigmoid colon


title: Sporadic MMR deficient_AM2


title: FCCTX_AA38


title: Sporadic MMR deficient_AM43


title: FCCTX_AA66

value: Cecum


title: Sporadic MMR deficient_AM29


title: FCCTX_AA52


title: FCCTX_AA77


title: FCCTX_AA42


title: Sporadic MMR deficient_AM1


title: FCCTX_AA49


title: FCCTX_AA39

value: Ascending colon

value: Dead male


title: FCCTX_AA25

value: Promega Male reference


title: Sporadic MMR deficient_AM19

value: proximal


title: FCCTX_AA55


title: FCCTX_AA46


title: FCCTX_AA15


title: FCCTX_AA41


title: FCCTX_AA24


title: FCCTX_AA75


title: LIX11 Log rep1 VM24_Cy5 vs. VM22 Rv Log rep1_Cy3: logarithmic phase

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Biological replicate 1 LIX11 Log  vs H37Rv Log

hyb_protocol: 300ng of Cy3 labeled sample and 300ng of Cy5 labeled sample were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1

data_processing: Data Analysis was performed using Genespring GX Software using LOWESS normalization.(Gene based analysis was performed)

organism: Mycobacterium tuberculosis H37Rv

source_name: H37Rv wild type in logarithmic phase (day 3)

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies).Then  the samples  were labeled using Agilent Quick-Amp labeling Kit (p/n:5190-0444).  Five hundred nanograms each of the samples were incubated with reverse transcription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP(Agilent) and Cy5-CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: M. tuberculosis H37Rv and LIX11 cultures were grown with aeration in Middlebrook 7H9 medium supplemented with 0.05% Tween 80 and 10% ADS supplement till logarithmic phase (day 3) and stationary phase (day 30) as described in Malhotra et al., 2010.

extract_protocol: Total RNA was extracted using TRI reagent (Ambion) following the manufacturers instructions.

treatment_protocol: The pknK gene was replaced with hygromycin resistance gene in M. tuberculosis by allelic exchange and is termed the LIX11 mutant strain

tag: genotype/variation

value: H37Rv wild type

tag: growth stage

value: logarithmic phase (day 3)

source_name: ΔpknK mutant in logarithmic phase (day 3)

value: ΔpknK mutant


title: LIX11 Log rep2 VM25_Cy3 vs. Rv Log rep2 VM23_Cy5 (DS): logarithmic phase

description: Biological replicate 2 LIX11 Log  vs H37Rv Log Dye Swap


title: FCCTX_AA2

value: Transverse colon


title: Lynch Syndrome_AH142

description:
Analysis used male reference DNA to investigate the genomic alterations appearing in Lynch syndrome tumors
The dye information in the .gpr files represent the compound used to label the tumor sample.

value: MSH2 mutation


title: Lynch Syndrome_AH180

value: MSH6 mutation

value: Female


title: Mock, biological replicate 2

city: Cold Spring Harbor

last: Mazurek

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

hyb_protocol: Fragmented and labelled cDNA were hybridized according to Affymetrix HWS kit P/N 900720, and Affymetrix Fluidics script FS450_0007

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner, using GCOS v 1.4

data_processing: Raw data from the arrays were processed using the RMA method with an up-to-date probe set definition (Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U. and Speed, T.P. Biostatistics 4:249-264 and Dai, M., Wanf, P., Boyd, A.D., Kostov, G., Athey, B., Jones, E.G., Bunney, W.E., Myers, R.M., Speed, T.P., Akil, H., Watson, S.J. and Meng, F. Nucleic Acids Research 33:e175). Gene set analysis was performed using generally applicable gene set enrichment (Luo, W., Friedman, M.S., Shedden, K., Hankenson, K.D., and Wolf, P.J. BMC Bioinformatics 10:161).

source_name: HCT116 cell line transfected with no siRNA

label_protocol: Samples were amplified using WT-Ovation Pico Module, the cDNA strand was changed using the Exon Module, then frgamented and labelled with FL-Ovation, according to manufacturer's instructions Nugen (User Guide cat #D01012 Version 05.13.08)

growth_protocol: Eleven HCT116 cultures were seeded 24hrs prior to siRNA transfection each with 200,000 cells per well in 6-well plates in 2mL DMEM media + 10% fetal bovine serum per well.

extract_protocol: 24hrs after siRNA transfection cells in each well were trypsinized then suspended in DMEM + 10% fetal bovine serum. RNA was extracted from 1,000,000 cells per suspension using the Qiagen Rneasy Kit (#74104) including on-cloumn Dnase digestion as per the manufacturer's protocol.

treatment_protocol: Groups of 3 cultures were transfected with either the DDX5si2008, DDX5si2053, or EBNA1si1666 siRNA's or a group of two cultures were transfected with no siRNA (mock) using lipfectamine RNAiMAX (Invitrogen 13778-075) and the manufacturer's protocol.

tag: cell line

tag: transfection

value: Mock

tag: timepoint after sirna transfection


title: FCCTX_AA1

tag: mmr status

value: No MMR gene mutated

tag: tumor location


title: Mock, biological replicate 1


title: FCCTX_AA14

tag: tumor stage

tag: age at onset

value: Male


title: Lynch Syndrome_AH139

tag: Sex

tag: reference


title: EBNA1si1666, biological replicate 3

source_name: HCT116 cell line transfected with EBNA1si1666 siRNA


title: FCCTX_AA3

value: Descending colon

value: Dead female


title: Lynch Syndrome_AH7


title: Lynch Syndrome_AH192

value: Cecum


title: FCCTX_AA5

value: Hepatic flexure


title: EBNA1si1666, biological replicate 2


title: Lynch Syndrome_AH188


title: Lynch Syndrome_AH136

value: Rectum


title: Lynch Syndrome_AH143

value: Splenic flexure

value: Promega Male reference


title: Lynch Syndrome_AH177

value: Sigmoid colon


title: FCCTX_AA6


title: Lynch Syndrome_AH191


title: EBNA1si1666, biological replicate 1


title: DDX5si2053, biological replicate 2

source_name: HCT116 cell line transfected with DDX5si2053 siRNA


title: Lynch Syndrome_AH4

value: Ascending colon


title: Lynch Syndrome_AH130


title: Lynch Syndrome_AH190


title: Lynch Syndrome_AH80

value: MLH1 mutation


title: DDX5si2053, biological replicate 3


title: Lynch Syndrome_AH79


title: Lynch Syndrome_AH77


title: Lynch Syndrome_AH75

value: Transverse colon


title: DDX5si2053, biological replicate 1


title: DDX5si2008, biological replicate 2

source_name: HCT116 cell line transfected with DDX5si2008 siRNA


title: Lynch Syndrome_AH70


title: DDX5si2008, biological replicate 3


title: Lynch Syndrome_AH6


title: DDX5si2008, biological replicate 1


title: Lung_EM_biological rep3

city: New York

first: Rui

last: Xiao

state: NY

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

description: Left lung from 23 weeks male Balb/c mouse in-utero exposure to SHS, adult exposure to OVA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array.in a GeneChip Hybridization Oven 640, followed by washing and staining in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with R/bioconductor platform. Packages used: AffyExpress, Limma

source_name: Left lung, in-utero exposure to SHS, adult exposure to OVA, male offspring

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol.

growth_protocol: We housed and handled Balb/c mice on a 12-hr light dark cycle. Mice had food and water ad libitum except when in the exposure chambers.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (QIAGEN).

treatment_protocol: Animals were exposed to sidestream smoke (as a surrogate for SHS) with a suspended particle load of 10 mg/m3 during the smoke exposure or to filtered-air as control (5 hr/day, 7 days a week), then sensitized by OVA injections at 19 & 21 weeks of age, followed by OVA aerosol challenge every other day in weeks 22 & 23.

tag: tissue

value: Left Lung

tag: gender

value: male

tag: strain

value: Balb/c

tag: age

value: lungs from 23 weeks old mice


title: Lung_EF_biological rep3

description: Left lung from 23 weeks female Balb/c mouse in-utero exposure to SHS, adult exposure to OVA

source_name: Left lung, in-utero exposure to SHS, adult exposure to OVA, female offspring

value: female


title: Kum (SERCA) Rescue1 vs Mutant1

first: Gaiti

last: Hasan

address: GKVK Campus,

institute: NCBS, TIFR

description: Kum (SERCA) Rescue1 vs Mutant1

hyb_protocol: Hybridization Kit: Agilent’s In situ Hybridization kit 5188-52441. 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint. Small bubbles will not to lose hybridization.  3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

scan_protocol: The array slides were scanned immediately by PerkinElmer Scan array Gx Microarray scanner. The Scan array software (PerkinElmer) was used for grid wise normalization of array images. Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using GeneSpring GX v7.3. Per spot per chip lowess normalization was done. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

organism: Drosophila melanogaster

source_name: Drosophila itpr mutant heteroallelic combination sv35/ug3 rescued by SERCA mutant

label_protocol: Labeling kit: Agilent’s Quick-Amp labeling Kit (p/n5190-0444). T7 promoter based-linear amplification to generate labeled complementary RNA (Two Color Microarray-Based Gene Expression Analysis).

extract_protocol: RNA quality was checked using Bioanalyzer. Total RNA and cRNA Purification Kit: Qiagen’s RNeasy minikit Cat#74104. The total RNA was isolated from control, mutant and rescued 60hrs larvae using TRIZOL (Sigma) method.

tag: developmental stage

value: 60hr larvae


title: Lung_EM_biological rep2


title: Kum (SERCA) Rescue2 vs Mutant2

description: Kum (SERCA) Rescue2 vs Mutant2

tag: genotype

source_name: Drosophila itpr mutant heteroallelic combination sv35/ug3


title: dermal_exvivoLECs_ nondiabetic_rep3

city: Vienna

first: Brigitte

last: Hantusch

address: Waehringer Guertel 18-20

department: Clinical Institute of Pathology

country: Austria

institute: Medical University of Vienna

hyb_protocol: Gene chips were hybridized with cRNA according to the manufacturer's protocol (Affymetrix). Chips were washed (Gene expression hybridization and wash buffer kits, Agilent) and stained with recombinant streptavidin and fluorescent secondary antibody.

scan_protocol: Fluorescent images were captured using Gene Chip® 3000 7G Scanner (Affymetrix) and GCOS1.2 software (Affymetrix) to summarize probe cell intensity data into Cell Intensity files (CEL) .

data_processing: After background correction and normalization with the robust multi-array average (RMA) method, datasets were analyzed using two-sample t-test and relative variance method (RVM) (Stokic et al, Applied Bioinformatics 2006). Only genes with postnormalization values above the BioB control were included and a P-value < 0.05 was considered to identify genes significantly different between dLECs and ndLECs.

source_name: Dermal microvascular cells; skin samples obtained from healthy human donors during elective surgery at the General Hospital_Vienna (with full ethical approval)

label_protocol: 1 microgram of cRNA was used in Ambion MessageAmpTMII-Biotin labeling Kit Cat. no. AM1791.

growth_protocol: Ex vivo isolated and freshly sorted HDLECs were immediately lysed without intermediate culturing.

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit (Cat.No. 74104), QIAshredder (Qiagen, Cat.No. 79654) and RNase-free DNase Set (Qiagen, Cat.No. 79254). Two RNA amplication steps were added using the MessageAmp® II aRNA Amplification Kit (Ambion Cat.No. AM1751).

treatment_protocol: No treatment. Human skin samples were dermatomized and epidermis and dermis dislocated by incubation in dispase solution (Roche, no. 04942086001). Cells were isolated mechanically using a scalpel and FACS-sorted using antibodies against podoplanin, CD45 and CD31 in a three-step procedure with intermediate washing steps.

tag: cell type

value: Human dermal microvascular lymphatic endothelial cells (HDLEC)

tag: disease status

value: healthy adults undergoing elective surgery (abdominoplasty)


title: Lung_EF_biological rep2


title: Lung_EM_biological rep1


title: Lynch Syndrome_AH36

value: Male


title: Lynch Syndrome_AH68

value: Cecum

value: Female


title: Lung_EF_biological rep1


title: Lynch Syndrome_AH5


title: dermal_exvivoLECs_ nondiabetic_rep2


title: dermal_exvivoLECs_ nondiabetic_rep4


title: dermal_exvivoLECs_ type2diabetic_rep4

source_name: Dermal microvascular cells; skin samples obtained from human donors during elective surgery at the General Hospital_Vienna (with full ethical approval)

value: type 2 diabetic adult undergoing leg amputation


title: Lung_AM_biological rep4

description: Left lung from 23 weeks male Balb/c mouse in-utero exposure to air, adult exposure to OVA

source_name: Left lung, in-utero exposure to air, adult exposure to OVA, male offspring


title: Lung_EM_biological rep4


title: Lung_EF_biological rep4


title: LIX11LS rep2 VM29_Cy3 vs. RvLS-rep2 VM27_Cy5 (DS): Stationary phase

description: Biological replicate 2 LIX11 LS vs H37Rv LS Dye Swap

source_name: ΔpknK mutant in stationary phase (day 30

tag: genotype/variation

value: ΔpknK mutant

tag: growth stage

value: stationary phase (day 30)

source_name: H37Rv wild type in stationary phase (day 30)

value: H37Rv wild type


title: Dilp Rescue3 vs Mutant3

description: Dilp Rescue3 vs Mutant3

source_name: Drosophila itpr mutant heteroallelic combination sv35/ug3 rescued by ectopic expression of itpr gene in dilp cells


title: Lynch Syndrome_AH37

source_name: Colorectal cancer

value: MLH1 mutation

value: Hepatic flexure

source_name: Promega Male reference

value: Promega Male reference


title: dermal_exvivoLECs_ nondiabetic_rep1


title: Slide 8 Suicide

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

institute: INSERM U675

hyb_protocol: The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes.

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Reference Sample labeled with Hy5

label_protocol: One µg total RNA from sample and reference were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 10.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse and rat registered in the miRBASE version 11 at the Sanger Institute.

extract_protocol: RNA was extracted using miRNeasy kit (Qiagen Inc.,Mississauga,Canada) following procedures suggested by the manufacturer.

tag: reference sample

value: Mix of human frontal cortex of the eight RNA samples

source_name: Brain sample from suicide completers labeled with Hy3

value: Frontal cortex

tag: individual

value: Suicide completer


title: Dilp Rescue2 vs Mutant2

description: Dilp Rescue2 vs Mutant2

value: itpr mutant heteroallelic combination sv35/ug3


title: Slide 6 Suicide


title: Dilp Rescue1 vs Mutant1

description: Dilp Rescue1 vs Mutant1

value: 60hr larvae


title: Slide 7 Suicide


title: LIX11LS rep1 VM28_Cy5 vs. RvLS-rep1 VM26_Cy3: Stationary phase

description: Biological replicate 1 LIX11 LS vs H37Rv LS

source_name: ΔpknK mutant in stationary phase (day 30)


title: Lung_AM_biological rep1

value: Left Lung

value: male

value: Balb/c

value: lungs from 23 weeks old mice


title: Lung_AM_biological rep2


title: Slide 5 Control

source_name: Brain sample from control labeled with Hy3

value: control


title: Lung_AM_biological rep3


title: dermal_exvivoLECs_ type2diabetic_rep3

value: Human dermal microvascular lymphatic endothelial cells (HDLEC)

value: type 2 diabetic adult undergoing leg amputation


title: Lung_AF_biological rep3

description: Left lung from 23 weeks female Balb/c mouse in-utero exposure to air, adult exposure to OVA

source_name: Left lung, in-utero exposure to air, adult exposure to OVA, female offspring

value: female


title: Mutant2 vs CS2 (Wild Type2)

description: Mutant2 vs CS2(Wild Type2)

source_name: Drosophila Wild Type (CS) larvae

value: Canton-S (Wild Type)


title: Mutant1 vs CS1 (Wild Type1)

description: Mutant1 vs CS1(Wild Type1)


title: Lung_AF_biological rep4


title: dermal_exvivoLECs_ type2diabetic_rep2


title: Oleanolic acid treatment-rep2

city: Shanghai

first: Huang

last: Jianhua

address: Wulumuqi Middle Road

country: China

institute: Institute of Integrated Chinese and Western Medicine, Huashan Hospital, Fudan University

description: This sample is of oleanolic acid treated neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the second of four drug-treated biological replicates used in this experiment, each from separate cultures and pregnant mouse.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

source_name: Neural stem cells from brains of Kunming mouse at embrynic 14 day were treated with Oleanolic acid

label_protocol: About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

growth_protocol: Mice embryos at embryonic day 14 (E14) were collected from timed-pregnant Kunming mice and placed in D-PBS (Invitrogen, CA, USA). The forebrain neuroepithelium was removed from embryos under a dissection microscope. The resultant tissue was dissociated by mechanical dissociation into a single cell suspension with a small-bore, fire-polished Pasteur pipette. The cells were filtered through a sterile nylon mesh and washed twice with a DMEM/F12 medium (Invitrogen, CA, USA) containing 100 units/ml penicillin and 100 µg/ml streptomycin. Numbers of viable cells were determined by staining with trypan blue. Neurosphere culture was initiated by seeding cells at a density of 1×105 to 2×105 viable cells/ml in the basal medium supplemented with 20 ng/ml human recombinant fibroblast growth factor-2 (hrFGF2, Invitrogen, CA, USA), 20 ng/ml human recombinant endothelial growth factor (hrEGF, Invitrogen, CA, USA) and Stempro NSC supplement (Invitrogen, CA, USA).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), in accordance with the manufacturer’s protocol.Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Single neural stem cells were cultured in differentiaion medium containing no growth factors for 2 days. Then 10 nM oleanolic acid was added. Control neural stem cells received no treatment.48 h later, cells were harvested for extraction of total RNA.

value: Kunming

tag: treatment

value: Oleanolic acid


title: Mutant3 vs CS3 (Wild Type3)

description: Mutant3 vs CS3(Wild Type3)


title: Lung_AF_biological rep1


title: Slide 4 Control


title: Oleanolic acid treatment-rep4

description: This sample is of oleanolic acid treated neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the forth of four drug-treated biological replicates used in this experiment, each from separate cultures and pregnant mouse.


title: dermal_exvivoLECs_ type2diabetic_rep1


title: Oleanolic acid treatment-rep3

description: This sample is of oleanolic acid treated neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the third of four drug-treated biological replicates used in this experiment, each from separate cultures and pregnant mouse.


title: Slide 2 Control

extract_protocol: RNA was extracted using miRNeasy kit (Qiagen Inc.,Mississauga,Canada) following procedures suggested by the manufacturer


title: Slide 3 Control


title: Slide 1 Suicide


title: Lung_AF_biological rep2


title: H1 v H2

city: Seattle

first: Andy

last: Itsara

state: WA

address: Foege Building S-250, Box 355065, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

hyb_protocol: For array hybridization, 25 ng each of labeled test and reference DNA was then brought to 158 uL volume water. Subsequently, the labeled DNA was hybridized to a custom Agilent array following the Agilent hybridization protocol. Briefly, the recommended hybridization master mix for a 1X microarray was prepared and added to the labeled DNA followed by hybridization at 65°C on a rotator rack (20 rpm) for 72 hr. Array wash proceeded according to the manufacturer's protocol.

scan_protocol: Scanned on Agilent G2505C scanner Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1).

data_processing: Feature extraction was carried out with Agilent Feature Extraction Software (v 10.5.1.1) according to the manufacturer's protocol with the exception of using probes on human chromosome 17 outside of 17q21.31 as the normalization set. The normalization set is specified in "chr17_60K_no17q21_TDT_06092010.txt".

organism:
Homo sapiens
Mus musculus

source_name: Fam 1 Father

label_protocol: Sample labeling was achieved using Roche NimbleGen Dual-Color DNA Labeling kits following the manufacturer’s protocol but using half (500 ng) the input DNA without sonication and scaling the protocol appropriately.

growth_protocol:
Hybrid cell lines were cultured under selective pressure using the following medium: 86% DMEM, 1% 50X HAT supplement, 1% Geneticin, 1% Penicillin-Streptomycin, 1% MEM-NEAA (all Gibco), and 10% FBS (Irvine Scientific).
After electrofusion of Epstein-Barr Virus (EBV) cells with E2 cells, mouse/human hybrid colonies were observed at 18 days. Subsequently, 88 clones were selected for initial expansion and genotyping. Six A and six B chromosome 17 homologues were selected for additional subculture. At pass three, all 12 hybrid clones were tested for chromosome 17 by FISH. Based on the FISH results, two A and two B hybrid clones were selected and for confirmatory genotyping and all cases confirmed retention of the appropriate A or B genotype.

extract_protocol: Cells were dissociated using TrypLE EXpress (Gibco). Genomic DNA was extracted using standard techniques.

tag: chr17 homologue

value: A

tag: cell line

value: B


title: H2 v H2

source_name: Fam 3 Mother

source_name: Fam 2 Mother


title: GS3-NCB2-FRB-r-b

status: Public on Jun 01 2012

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: genes, no bg corr, dye corr

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strain or line


title: GS3-WT-b


title: Control-rep2

description: This sample is of normal control neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the second of four control biological replicates used in this experiment, each from separate cultures and pregnant mouse.

source_name: Neural stem cells from brains of Kunming mouse at embrynic 14 day

value: Control


title: GS3-NCB2-FRB-r-a


title: GS3-WT-a


title: Oleanolic acid treatment-rep1

description: This sample is of oleanolic acid treated neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the first of four drug-treated biological replicates used in this experiment, each from separate cultures and pregnant mouse.


title: LIX11LS rep1 VM28_Cy3  vs. RvLS-rep1 VM26_Cy5_DS: Stationary phase

description: Biological replicate 1 LIX11 LS vs H37Rv LS Dye Swap

value: ΔpknK mutant

value: stationary phase (day 30)

value: H37Rv wild type


title: Control-rep1

description: This sample is of normal control neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the first of four control biological replicates used in this experiment, each from separate cultures and pregnant mouse.


title: Control-rep4

description: This sample is of normal control neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the forth of four control biological replicates used in this experiment, each from separate cultures and pregnant mouse.


title: IMR376


title: H2del v H1

source_name: Fam 1 proband


title: IMR103


title: GS3-WT-r-b


title: GS3-Mot1-FRB-r-b


title: GS3-NCB2-FRB-a


title: GS3-NCB2-FRB-b


title: GS3-Mot1-FRB-r-a


title: GS3-WT-r-a


title: GS3-Mot1-FRB-a