title: PB2E

description: Hybridized to 250K_Nsp

value: Euploid


title: P4022

status: Public on Jul 04 2011

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

country: USA

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visulaized and analyzed using DNA Analytics 4.0.85 and the ADM2 step gram algorithm.

molecule: genomic DNA

organism: Homo sapiens

source_name: Frozen tissue biopsy

label_protocol: A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.

growth_protocol: Tumor samples from patients with either pancreatic ductal adenocarcinoma, adrenocortical carcinoma, or prostate carcinoma were flash-frozen and maintaned at -80 degrees C until processed for flow sorting

extract_protocol: 25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care).

tag: tissue

value: Pancreatic Ductal Adenocarcinoma

source_name: Reference pooled 46XX

value: pooled normal (46,XX) reference (Promega)


title: Blastomere7A

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against an in house gDNA reference set of 61 normal females.

label: biotin

label_protocol: Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)

extract_protocol: Biopsied polar body, blastomere and trophectoderm samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

tag: cell type

value: Blastomere

tag: patient number

tag: ploidy

value: Aneuploid

tag: karyotype


title: P1057


title: Blastomere7Ei

description: Hybridized to 250K_Nsp

value: normal


title: Whole Brain ACTH Treated Gratified, Replicate 3

type: RNA

city: Durham

first: Andreas

middle: Robert

last: Pfenning

state: NC

address: Duke University Medical Center, Box 3209, Department of Neurobiology

department: Neurobiology

institute: Duke University

hyb_protocol: Sample and reference RNAs were pooled, mixed with 1X hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS), COT-1 DNA, and poly-dA to limit nonspecific binding, and heated to 95°C for 2 minutes.  This mixture was pipetted onto a microarray slide by use of a Maui Mixer hybridization chamber (BioMicro Systems, Salt Lake City, UT) and hybridized overnight at 42°C on an automated Maui Hybridization Station (BioMicro Systems, Salt Lake City, UT).

scan_protocol: The array was then washed at increasing stringencies, and scanned on a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Within array Loess normalization was performed using the Limma package 3 to remove any bias that the intensity has on log-fold change.  Next, between array variance stabilization normalization was carried out, where both the red and green channel on the arrays are aligned to each other based on the assumption that most of the genes are constant across experiments4.  Spots not reaching the quality criterion were removed from further analysis.  Quality was determined in three ways.  1) There was insufficient red or green intensity to produce a reliable ratio.  2) The consistency of the ratio throughout the spot was low.  3) Other machine-annotated flags indicated the spot was not reliably read.  After filtering, if a particular spot was found only to be present on a small number of arrays (<15), then that spot was filtered for all arrays.  Spots measuring the same gene were combined into a final score for that transcript to avoid bias in a gene set analysis if the correlation between the was greater than 0.5 across all samples.

molecule: total RNA

organism: Mus musculus

source_name: Total RNA from adult mouse whole brain

label_protocol: Add water first, then 1ul of oligo dT primer, then RNA samples.  Incubate at 65 degrees  for 10 mins, followed by 25 degrees for 5 mins.  Add 5x rxn buffer, .1M DTT, dNTP mix, Cy dCTP (3 or 5), Cy cUTP (3 or 5), and Superscript II.

growth_protocol: Adult Male Mice

extract_protocol: Total RNA was isolated from the hypothalamus and remainder of the brain from each animal using the TRIZOL-RNA-easy method, and RNA quality was assessed using spectrophotometry and micro-electrophoresis.

tag: strain

tag: developmental stage

value: adult

tag: gender

value: male

value: Whole Brain minus Hypothalamus

tag: treatment

value: ACTH Gratified

source_name: Universal Mouse Reference RNA, Stratagene

extract_protocol: Reference RNA purchased from Stratagene.

tag: reference rna vendor

value: Stratagene


title: Organoid_day1 Lgr4/5 deleted

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Ratios are given in log10.

source_name: Organoid_day1 Lgr4/5 deleted

label_protocol: 1µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.

tag: tissue type

value: Organoid from VillinCre_Lgr4fl/fl-Lgr5fl/fl mouse small intestine

value: Lgr4_Lgr5 double ko day1 after deletion

source_name: mouse reference RNA (Stratagene)


title: Organoid_day1 Lgr4/5 deleted_biological replicate


title: Blastomere7Eii

description: Hybridized to 250K_Nsp


title: Blastomere8Ai

description: Hybridized to 250K_Nsp


title: P4003.1


title: P1029C1


title: Organoid_day1 wt_biological replicate

source_name: Organoid_day1 wt

value: Organoid from VillinCre_wt mouse small intestine

value: wt Tamoxifen induction for 1 day


title: Whole Brain ACTH Treated Gratified, Replicate 2


title: Whole Brain ACTH Treated Gratified, Replicate 1


title: P3002B


title: Whole Brain ACTH Treated Gratified, Replicate 4


title: Lgr4_Lgr5 double ko day1 biological replicate 2 dye swap 2

source_name: Lgr4_Lgr5 double ko day1 after deletion

extract_protocol: Crypts were isolated from Lgr4/5 double knock-out mice one day after inductino of deletion with P450Cre with 2mM EDTA. RNA was subsequenly isolated using Trizol and purified ones over a RNeasy column (Qiagen)

value: isolated crypts from small intestine

source_name: wt control crypts


title: Whole Brain ACTH Treated, Replicate 4

value: ACTH


title: P1006F


title: Blastomere5Ei

description: Hybridized to 250K_Nsp

value: Euploid


title: Organoid_day1 wt


title: OPM2 DZNep treated

city: Singapore

first: Zhigang

last: Xie

address: 14 Medical Drive, CeLS Building #02-07

department: CSI Singapore

country: Singapore

institute: National University of Singapore

description:
8.OPM-2 DZNep
OPM2-DZNep

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Genespring GX (Agilent Technologies). The data normalization was done using MAS5 algorithm in GeneSpring GX. For each control-treatment comparison, entities that have flagged present or marginal in at least 1 out of 2 samples were retained, and the differentially expressed genes were identified using the fold change function.

source_name: B lymphocyte

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Express Kit Manual, 2009, Affymetrix).

growth_protocol: Human MM cell lines KMS18, MM.1S and OPM-2 were maintained in RPMI 1640, supplemented with 10% fetal calf serum (FCS), 100 U/mL penicillin and 100 ug/mL streptomycin. MM cell line NCI-H929 was cultured in RPMI 1640 with 15% FCS and 0.00036% 2-mercaptoethanol. All cells were grown at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Qiagen RNeasy Mini kit (Germany) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 0.5 μmol/L DZNep for 48 h.

value: Multiple Myeloma Cell Line

tag: cell line

tag: treatment group

value: DZNep treated


title: Blastomere6A

description: Hybridized to 250K_Nsp

value: Blastomere


title: Blastomere5Eii

description: Hybridized to 250K_Nsp


title: Blastomere6E

description: Hybridized to 250K_Nsp


title: Blastomere4E

description: Hybridized to 250K_Nsp


title: Blastomere3Eii

description: Hybridized to 250K_Nsp


title: P1026Z

value: Pancreatic Ductal Adenocarcinoma

value: pooled normal (46,XX) reference (Promega)


title: Whole Brain ACTH Treated, Replicate 3

value: adult


title: Whole Brain ACTH Treated, Replicate 2

value: male


title: KMS18 DZNep treated

description:
6.KMS18 DZNep
KMS18-DZNep


title: OPM2 DMSO Control

description:
7.OPM-2 DMSO
OPM2-DMSO

value: DMSO Control


title: Lgr4_Lgr5 double ko day1 biological replicate 1 dye swap 2


title: Whole Brain ACTH Treated, Replicate 1

value: Whole Brain minus Hypothalamus


title: Blastomere8Ei

description: Hybridized to 250K_Nsp

value: normal


title: Organoid_Control (ENR)

source_name: Control (ENR)

growth_protocol: Intestinal organoids were cultured in vitro in crypt culture medium (EGF, Noggin, R-spondin) according to Sato et al, Nature, 2009.

treatment_protocol: Organoids were cultured with R-spondin after splitting for one day before RNA isolation.

value: Organoid from  small intestine


title: Lgr4_Lgr5 double ko day1 biological replicate 1 dye swap 1


title: KMS18 DMSO Control

description:
5.KMS18 DMSO
KMS18-DMSO


title: Lgr4_Lgr5 double ko day1 biological replicate 2 dye swap 1


title: P1051Y


title: Blastomere3Ei

description: Hybridized to 250K_Nsp


title: Blastomere2E

description: Hybridized to 250K_Nsp


title: MM1.S DZNep treated

description:
4.MM1S DZNep
MM1.S-DZNep


title: Blastomere3A

description: Hybridized to 250K_Nsp

value: Aneuploid

value: complex aneuploid


title: Organoid_R-spondin withdrawal day 1 (EN)

source_name: R-spondin withdrawal for one day (EN)

treatment_protocol: Organoids were cultured without R-spondin after splitting for one day before RNA isolation.


title: Blastomere5A

description: Hybridized to 250K_Nsp


title: Whole Brain Control, Replicate 3

value: Stratagene


title: D20790


title: Whole Brain Control, Replicate 4


title: Whole Brain Control, Replicate 2


title: B. subtilis_NaOCl treated_replicate3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

description: B. subtilis grown in minimal medium

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: B. subtilis cells_before NaOCl treatment

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: The Bacillus subtilis 168 wild type strain was grown under vigorous agitation at 37 °C in a minimal medium described before (Stülke et al., 1993, J Gen Microbiol 139, 2041-2045).

extract_protocol: Total RNA was isolated by the acid phenol method as described (Majumdar et al., 1991, Biotechniques 11: 94-101).

treatment_protocol: At OD500 of 0.4, cells were treated for 10 minutes with 50 µM NaOCl (purchased from Sigma Aldrich).

tag: genotype

value: wild type

value: untreated

source_name: B. subtilis cells_NaOCl treated

value: NaOCl


title: Blastomere1A

description: Hybridized to 250K_Nsp


title: 4050489


title: Blastomere4A

description: Hybridized to 250K_Nsp


title: MM1.S DMSO Control

description:
3.MM1S DMSO
MM1.S-DMSO

value: Multiple Myeloma Cell Line


title: B. subtilis_NaOCl treated_replicate2

description: B. subtilis grown in minimal medium


title: Whole Brain Control, Replicate 1


title: D27712


title: NCI-H929 DMSO Control

description:
1.H929 DMSO
NCI-H929-DMSO


title: B. subtilis_NaOCl treated_replicate1

description: B. subtilis grown in minimal medium


title: NCI-H929 DZNep treated

description:
2.H929 DZNep
NCI-H929-DZNep

value: DZNep treated


title: Blastomere1Eii

description: Hybridized to 250K_Nsp

value: Blastomere

value: Euploid


title: 1061600A8

value: Pancreatic Ductal Adenocarcinoma

value: pooled normal (46,XX) reference (Promega)


title: P1023w1


title: P1024


title: RWPE-1,3D culture for 6day,triplicate data,03

status: Public on Jul 03 2011

city: Tainan city

first: Jimmy

middle: Jiun-Ming

last: Su

address: 1F,No 367,Sheng-Li Rd. North District

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes,Taiwan

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A 2.0 Plus GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.

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

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

source_name: RWPE-1,3D culture for 6day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).

growth_protocol: RWPE-1 cells were maintained in Keratinocyte-SFM and LNCAP cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics

extract_protocol: Total RNA samples were extracted from 2D,3D-2days,and 3D-6days using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).

treatment_protocol: no treatment

value: Prostate

value: RWPE-1 (immortalized prostate epithelial cells)

tag: growth protocol

value: 3D culture

tag: time


title: LNCAP,2D,triplicate data,01

value: LNCaP cells (prostate cancer cells)

value: 2D culture


title: LNCAP,3D culture for 6day,triplicate data,03

source_name: LNCAP,3D culture for 6day


title: LNCAP,2D,triplicate data,03


title: LNCAP,2D,triplicate data,02


title: LNCAP,3D culture for 2day,triplicate data,01

source_name: LNCAP,3D culture for 2day


title: LNCAP,3D culture for 6day,triplicate data,02


title: RWPE-1,3D culture for 2day,triplicate data,03

source_name: RWPE-1,3D culture for 2day


title: LNCAP,3D culture for 6day,triplicate data,01


title: RWPE-1,2D,triplicate data,03


title: RWPE-1,3D culture for 6day,triplicate data,01


title: LNCAP,3D culture for 2day,triplicate data,03


title: RWPE-1,3D culture for 6day,triplicate data,02


title: RWPE-1,3D culture for 2day,triplicate data,01


title: LNCAP,3D culture for 2day,triplicate data,02


title: RWPE-1,2D,triplicate data,02


title: Blastomere2A

description: Hybridized to 250K_Nsp

value: Aneuploid


title: Blastomere1Ei

description: Hybridized to 250K_Nsp

value: normal


title: RWPE-1,2D,triplicate data,01


title: H3K36me3 no TGF-b, array 1

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

scan_protocol: Performed according to standard NimbleGen protocol with NimbleGen software (Signalmap)

data_processing: Briefly, we first quantile normalized Cy3 (Input) intensities from all arrays to a common target. We used a smoothing procedure to improve the signal to noise ratio of the M (log2 ratio Cy5/Cy3) values and fitted a function of M values to the chromosomal location using loess. We then picked the genomic regions with the lowest 20% fitted values as the reference region. The Cy5 intensities in the reference regions should have similar distributions in each sample. We therefore quantile normalized them to the same distribution target. The quantile procedure was used to construct a function to map pre-normalization Cy5 intensities to post-normalization Cy5 intensities. This map was then applied to all the Cy5 intensities. This procedure made the M values comparable from array to array.

source_name: ChIP against H3K36me3

label_protocol: Labels with Cy3 and Cy5 were performed according to standard NimbleGen protocol

growth_protocol: Confluent cultures serum starved for 48hrs before treatment

treatment_protocol: No TGF-β treatment

tag: antibody

tag: vendor

value: Abcam

tag: cat#

tag: sample type

value: input DNA

source_name: Genomic DNA


title: RWPE-1,3D culture for 2day,triplicate data,02

tag: tissue


title: 14162910 - snips A vs Wt A

status: Public on Jul 02 2011

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: Developmental stage: Boyes et al. Plant Cell 2001 (PMID: 11449047).

hyb_protocol: Wt A Cy5 / snips A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Wt

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: stem - media : Loam  hygrometry : 40%  temperature : 22°C  light : 13h

extract_protocol: Wt A:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

value: Columbia

value: wild-type

tag: age

value: 71 days

value: boyes 6.20

source_name: snips mutant

extract_protocol: snips A:10ug. (Qiagen_RNeasy.pdf)

value: lac4g*lac17 in col0


title: H3K4me3 no TGF-b, array 1

hyb_protocol: Performed according to standard NimbleGen protocol

source_name: ChIP against H3K4me3

tag: cell type

tag: lot#


title: H3K4me3 36-hour TGF-b, array 1

extract_protocol: Performed according to standard NimbleGen protocol

treatment_protocol: TGF-β treatment for 36hrs


title: 14162909 - Wt A vs snips A

hyb_protocol: snips A Cy5 / Wt A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: developmental stage


title: H3K9me2 no TGF-b, array 1 replicate

source_name: ChIP against H3K9me2


title: H3K36me3 36-hour TGF-b, array 1


title: H3K9me2 36-hour TGFb, array 1 replicate


title: H3K9me2 36-hour TGFb, array 1


title: 14162861 - Wt A vs kim A

hyb_protocol: kim A Cy5 / Wt A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: kim mutant

extract_protocol: kim A:10ug. (Qiagen_RNeasy.pdf)

value: irx12*lac17 in col0


title: 14162862 - kim A vs Wt A

hyb_protocol: Wt A Cy5 / kim A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Expt10_36hr

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.

source_name: Input fraction from Expt10_36hr

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

tag: time point

value: 36 hours post-TGF-β stimulation

source_name: Methyl-depleted fraction from Expt10_36hr

tag: time poine


title: 14162855 - Wt A vs lac4g A

hyb_protocol: lac4g A Cy5 / Wt A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac4g mutant

extract_protocol: lac4g A:10ug. (Qiagen_RNeasy.pdf)

value: lac4 in col0


title: 14162894 - snips B vs Wt B

hyb_protocol: Wt B Cy5 / snips B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Wt B:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: snips B:10ug. (Qiagen_RNeasy.pdf)


title: 14162858 - lac17 A vs Wt A

hyb_protocol: Wt A Cy5 / lac17 A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac17 mutant

extract_protocol: lac17 A:10ug. (Qiagen_RNeasy.pdf)

value: lac17 in col0


title: 14162857 - Wt A vs lac17 A

hyb_protocol: lac17 A Cy5 / Wt A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162853 - irx12 A vs Wt A

hyb_protocol: Wt A Cy5 / irx12 A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: irx12 mutant

extract_protocol: irx12 A:10ug. (Qiagen_RNeasy.pdf)

value: irx12 in col0


title: 14162666 - Wt B vs snips B

hyb_protocol: snips B Cy5 / Wt B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Expt5_24hr

source_name: Input fraction from Expt5_24hr

value: 24 hours post-TGF-β stimulation

source_name: Methyl-depleted fraction from Expt5_24hr


title: H3K4me3 no TGF-b, array 2


title: H3K36me3 36-hour TGF-b, array 2


title: 14120279 - Wt B vs kim B

hyb_protocol: kim B Cy5 / Wt B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: kim B:10ug. (Qiagen_RNeasy.pdf)


title: 14120278 - lac17 B vs Wt B

hyb_protocol: Wt B Cy5 / lac17 B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: lac17 B:10ug. (Qiagen_RNeasy.pdf)


title: H3K9me2 no TGF-b, array 2 replicate


title: Expt8_36hr

source_name: Input fraction from Expt8_36hr

source_name: Methyl-depleted fraction from Expt8_36hr


title: pSuperior prSET-7 shRNA, 4 days post-transfection, replicate 1

city: Los Angeles

first: Judd

middle: C

last: Rice

state: California

address: 1450 Biggy Street

institute: University of Southern California

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with beadarray in R

source_name: Hela

label_protocol: Biotinylated cRNA were prepared

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit using kit protocol. Quality control was assessed using the Experion RNA analysis kit.

value: Hela cells with pSuperior prSET-7 shRNA, 4 days post transfection


title: 14162664 - kim B vs Wt B

hyb_protocol: Wt B Cy5 / kim B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: H3K9me2 no TGF-b, array 1


title: 14120274 - Wt B vs lac4g B

hyb_protocol: lac4g B Cy5 / Wt B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: lac4g B:10ug. (Qiagen_RNeasy.pdf)


title: 14162665 - Wt A vs irx12 A

hyb_protocol: irx12 A Cy5 / Wt A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Expt2_0hr

source_name: Input fraction from Expt2_0hr

value: timepoint zero

source_name: Methyl-depleted fraction from Expt2_0hr


title: H3K4me3 36-hour TGF-b, array 2

hyb_protocol: Performed according to standard NimbleGen protocol

source_name: Genomic DNA


title: 14120276 - Wt B vs lac17 B

hyb_protocol: lac17 B Cy5 / Wt B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt


title: pSuperior empty shRNA control, 4 days post transfection, replicate 2

description: replicate 1

value: Hela cells with pSuperior empty shRNA control, 4 days post transfection


title: H3K36me3 no TGF-b, array 2

source_name: ChIP against H3K36me3


title: Expt5_36hr

source_name: Input fraction from Expt5_36hr

source_name: Methyl-depleted fraction from Expt5_36hr


title: Expt2_24hr

source_name: Input fraction from Expt2_24hr

source_name: Methyl-depleted fraction from Expt2_24hr


title: pSuperior prSET-7 shRNA, 4 days post-transfection, replicate 2

description: replicate 2


title: 14162856 - lac4g A vs Wt A

hyb_protocol: Wt A Cy5 / lac4g A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac4g mutant


title: Expt2_36hr

source_name: Input fraction from Expt2_36hr

source_name: Methyl-depleted fraction from Expt2_36hr


title: Expt10_0hr

source_name: Input fraction from Expt10_0hr

source_name: Methyl-depleted fraction from Expt10_0hr


title: 'Ercolini' versus 'Rocha'_T24h_rep1

city: Lisbon

first: Vanessa

middle: Tolentino

last: Pereira

address: Ed. ICAT, Campus da FCUL, Campo Grande

department: Unit of Molecular Biology and Plant Biotechnology

country: Portugal

institute: FCUL/ICAT/BioFIG

description: Biological replicate 1 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested 24 hours after sprayed with Stemphylium vesicarium fungus.

hyb_protocol: The hybridization mix consisted of 30μl of labeled cDNAs,15 µg of Poly (A)-DNA (Sigma), 7.5 µg of salmon sperm DNA (Invitrogen), 1.4x Denhardt's solution (Invitrogen ), 3x SSC (Invitrogen) and 0.3% SDS (v/v) . The hybridization mix was denatured at 97°C for 2 min. After cooling to 60°C was added 1µl of 10x DIG blocking buffer (Roche Diagnostic GmbH, Germany). Samples were applied to microarrays and hybridization was carried out at 60 °C for 17 hours in chambers ArrayIt (Telechem International). After hybridization, slides were washed sequentially.

scan_protocol: Slides were scanned using VersArray ChipReader® vs 3.1. build 1.68 (Bio-Rad, USA) and spot and background intensities quantified using VersArray AnalyserTM software vs 4.5.1.46 (Bio-Rad, USA).

data_processing: Data files were imported into GEPAS (http://gepas.bioinfo.cipf.es) and log2-transformed prior to normalization (DNMAD). Print-tip Lowess was used for within-slide normalization considering background subtraction. Impute missing values (median). Patterns with less than 70% removed.

organism: Pyrus communis

source_name: pear tree_'Ercolini'_fungus infection_24 hours

label_protocol: 70 mg of total RNA were reverse transcribed using SuperScript Direct cDNA Labeling System (Invitrogen, Life Technologies) in the presence of (Cy5)-dUTP and (Cy3)-dUTP (Amersham, GE Healthcare).

growth_protocol: Pyrus communis clones of 'Ercolini' and 'Rocha' cultivars were planted into pots containing universal soil and kept outdoors.

extract_protocol: Total RNA was isolated using Hot-Borate method essentially as described by  Wan and Wilkins (1994, Anal. Bioche. 223 ).

treatment_protocol: RNA was extracted from leaves from 'Ercolini' and 'Rocha', no infected and infected with Stemphylium vesicarium.

tag: cultivar

value: Ercolini

tag: inoculation

value: Stemphylium vesicarium

value: leaf

source_name: pear tree_'Rocha'_fungus infection_24 hours

value: Rocha


title: 'Ercolini' versus 'Rocha'_T24h_rep2

description: Biological replicate 2 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested 24 hours after sprayed with Stemphylium vesicarium fungus.


title: 'Ercolini' versus 'Rocha'_T6h_rep2

description: Biological replicate 2 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested 6 hours after sprayed with Stemphylium vesicarium fungus.

source_name: pear tree_'Ercolini'_fungus infection_6 hours

source_name: pear tree_'Rocha'_fungus infection_6 hours


title: 14120272 - Wt B vs irx12 B

hyb_protocol: irx12 B Cy5 / Wt B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: irx12 mutant

extract_protocol: irx12 B:10ug. (Qiagen_RNeasy.pdf)

value: Columbia

tag: genotype

value: wild-type


title: pSuperior empty shRNA control, 4 days post transfection, replicate 1

description: replicate 1

source_name: Hela


title: H3K9me2 36-hour TGFb, array 2 replicate

source_name: ChIP against H3K9me2

value: Abcam

value: input DNA

source_name: Genomic DNA


title: 'Ercolini' versus 'Rocha'_T0h_rep3

description: Biological replicate 3 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested after sprayed with water.

source_name: pear tree_'Ercolini'_no infection

value: water

source_name: pear tree_'Rocha'_no infection


title: H3K9me2 no TGF-b, array 2


title: 'Ercolini' versus 'Rocha'_T6h_rep3

description: Biological replicate 3 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested 6 hours after sprayed with Stemphylium vesicarium fungus.


title: 14120273 - irx12 B vs Wt B

hyb_protocol: Wt B Cy5 / irx12 B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt

value: 71 days

value: boyes 6.20


title: 'Ercolini' versus 'Rocha'_T24h_rep3

description: Biological replicate 3 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested 24 hours after sprayed with Stemphylium vesicarium fungus.


title: Neo Clones of SKOV3 ovarian carcinoma cells - Repeat 1

city: Washington

first: Xin

middle: James

last: Li

state: DC

address: 4000 Reservoir Rd Suite 180

institute: Georgetown University

hyb_protocol: Cenechip Eukaryotic Target Hybridization protocol

scan_protocol: Genechip expression washing, stain and scan user manual,P/N 702731

data_processing: RMA using R/Bioconductor

source_name: Mamalian Cultured cells (ovarian carcinoma)

label_protocol: One-Cycle Target Labeling Assay

extract_protocol:
PROTOCOL:
1. Harvest cells or use cells that are already pelleted before.
Cells grown in suspension or monolayer (1 x 107 cells)
Pellet the cells for 5 min at 300 x g in an RNase-free glass or polypropylene centrifuge tube. Carefully remove all supernatant by aspiration. Use tripsin in case of monolayer. Cells can also be lysed directly on the plate using desired amount of lysis buffer.
Note: Incomplete removal of the cell-culture medium will inhibit lysis and dilute the lysate, affecting the conditions for binding of RNA to the RNeasy membrane.
2. Disrupt cells by addition of Buffer RLT.
Prepared by Tapas Saha
For pelleted cells, loosen the cell pellet thoroughly by flicking the tube. Add the appropriate volume of Buffer RLT according the following table and proceed to step 3.
RNeasy column Number of cells Buffer RLT (μl)
Mini < 5 x 106 350
Mini 5 x 106 – 1 x 107 600
Note: Ensure that β-ME is added to Buffer RLT before use
3. Homogenize cells using homogenizer for at least 30 seconds. Alternatively, vortex the sample for 10 s, and pass the lysate at least 5–10 times through an 18–20-gauge needle fitted to an RNase-free syringe.
Note: Incomplete homogenization will lead to significantly reduced yields and can cause clogging of the RNeasy column. Homogenization with homogenizers generally results in higher total RNA yields than with other homogenization methods.
4. Add 1 volume (350 μl or 600 μl) of 70% ethanol to the homogenized lysate, and mix thoroughly by shaking vigorously. Do not centrifuge.
5. Apply the total sample (up to 700 μl), including any precipitate that may have formed, to an RNeasy mini column placed in a 2 ml collection centrifuge tube. Close the tube gently, and centrifuge for 30-45 second at > 8000 g (> 10000 rpm). Discard the flow-through. If the volume exceeds 700 μl load the column again with the remaining extract solution.
6. Add 700 μl Buffer RW1 to the RNeasy column. Close the centrifuge tube gently, and centrifuge for 30-45 seconds at > 8000 g (> 10000 rpm) to wash the column. Discard the flow-through and the collection tube.
7. Transfer the column to a fresh 2 ml collection tube Add 500 μl Buffer RPE to the RNeasy column. Close the centrifuge tube gently, and centrifuge for 30-45 seconds at > 8000 g (> 10000 rpm) to wash the column. Discard the flow-through.
Note: Buffer RPE is supplied as a concentrate. Ensure that ethanol is added to Buffer RPE before use.
8. Add another 500 μl Buffer RPE to the RNeasy column. Close the centrifuge tube gently, and centrifuge for 5 min at > 8000 g (> 10000 rpm) to dry the RNeasy silica-gel membrane. Transfer the columns in a separate tube and spin it for 1 minute at high speed.
It is important to dry the RNeasy membrane since residual ethanol may interfere with downstream reactions. This centrifugation ensures that no ethanol is carried over during elution.
Prepared by Tapas Saha
9. To elute, transfer the RNeasy column to a new 1.5 ml eppendorf tube. Pipet 30-50 μl of RNase-free water directly onto the RNeasy silica-gel membrane. Close the tube gently. Let it stand for 1 min, and then centrifuge for 1 min at > 8000 g (> 10000 rpm).
10. Repeat the elution step (step 9) as described with a second volume of RNase-free water. To obtain a higher total RNA concentration, this second elution step may be performed by using the first eluate.
11. Load a Formamide/Denatured RNA gel (Different protocol) to visualize the quality of the RNA isolated. At the same time measure the concentration of the RNA by spectrophotometer.

tag: tissue type

value: ovarian tumor

tag: disease type

value: ovarian carcinoma

tag: cell line


title: Neo Clones of SKOV3 ovarian carcinoma cells - Repeat 3


title: 'Ercolini' versus 'Rocha'_T0h_rep2

description: Biological replicate 2 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested after sprayed with water.


title: Neo Clones of SKOV3 ovarian carcinoma cells - Repeat 2


title: Stable expression of BRCA1 in SKOV3 cells - Repeat 3


title: Stable expression of BRCA1 in SKOV3 cells - Repeat 1


title: Stable expression of BRCA1 in SKOV3 cells - Repeat 2


title: 14120275 - lac4g B vs Wt B

hyb_protocol: Wt B Cy5 / lac4g B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac4g mutant

value: lac4 in col0


title: 'Ercolini' versus 'Rocha'_T0h_rep1

description: Biological replicate 1 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy5/Cy3), the leaves of both cultivars were harvested after sprayed with water.


title: 'Ercolini' versus 'Rocha'_T6h_rep1

description: Biological replicate 1 of 3. Comparison of resistant/tolerant 'Ercolini' versus susceptible 'Rocha' (Cy3/Cy5), the leaves of both cultivars were harvested 6 hours after sprayed with Stemphylium vesicarium fungus.


title: Expt8_24hr

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

source_name: Input fraction from Expt8_24hr

value: 24 hours post-TGF-β stimulation

source_name: Methyl-depleted fraction from Expt8_24hr


title: Expt10_24hr

source_name: Input fraction from Expt10_24hr

source_name: Methyl-depleted fraction from Expt10_24hr


title: H3K9me2 36-hour TGFb, array 2

tag: antibody

tag: vendor


title: Bone marrow B220+ cells isolated from kinase dead knockin  IKKαK44A/K44A mice 1

city: Frederick

first: Mumtaz

last: Yaseen

state: Maryland

address: 1050 Boyles Street

institute: NCI

description:
KAFv (IKK alpha  kinase knockin  FVB mice)
Bone marrow B220+ cells isolated from kinase dead knockin  IKKαK44A/K44A mice

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450, with Affymetrix W/S kit 900720, protocol FS450_0001.

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

data_processing: The data were analyzed with Affymetrix GeneExpression Console 1.1 (MAS 5.0). The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

source_name: Bone marrow B220+ cells

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA (GeneChip® 3’ IVT Express Kit Labeling Assay,P/N 702646 Rev. 7, Dec 2009).

growth_protocol: Bone marrow from the tibias and femurs of 4wk old KAKA and WT littermate control mice was flushed out in RPMI medium containing 1% FCS. Cells were RBC lysed and washed thoroughly. B220+ cells were enriched using anti-B220+ magnetic beads and separated through magnetic cell sorter (MACS) columns.

extract_protocol: RNA was extracted from a total of 3×106  B220+ cells. We used a trizol method of RNA extraction.

treatment_protocol: No prior treatment was given to the BM B220+ cells

value: Bone marrow B220+ cells

value: kinase dead knockin  IKKαK44A/K44A

tag: genetic background

value: FVB


title: Bone marrow B220+ cells isolated from WT littermate control mice 2

description:
KAFv (IKK alpha  kinase knockin  FVB mice)
Bone marrow B220+ cells isolated from WT littermate control mice

value: wild type


title: Bone marrow B220+ cells isolated from kinase dead knockin  IKKαK44A/K44A mice 3


title: Bone marrow B220+ cells isolated from kinase dead knockin  IKKαK44A/K44A mice 2


title: RDV-S infected Rice_rep1

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 1 of 3, RDV-S infected rice

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Japonica Group

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media :commercial soil (Bonsol: Sumitomo Chemical, Osaka,Japan)
No of seedling per pot : 14
Light condition: Natural conditions
Temperature: 25±3℃
Growth environment: greenhouse study
Light condition: Natural conditions
Temperature: 25±3℃
Growth length: 21 days past inoculation

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: Qiagen Rneasy maxi kit
manual: Qiagen

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Temperature: 25±3℃
virus inoculation: Rice Dwarf Virus strain S
virus inoculation: five viruliferous green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours
growth stage: two leaves visible

value: Nipponbare

tag: tissue

value: shoot

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
Light condition: continuous light
Temperature: 25±3℃
virus inoculation: mock inoculation
virus inoculation: five virus free green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours


title: RDV-S infected Rice_rep3

description: Biological replication 3 of 3, RDV-S infected rice


title: Expt8_0hr

source_name: Input fraction from Expt8_0hr

value: timepoint zero

source_name: Methyl-depleted fraction from Expt8_0hr


title: RDV-D84 infected Rice_rep2

description: Biological replication 2 of 3, RDV-D84 infected rice

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Temperature: 25±3℃
virus inoculation: Rice Dwarf Virus strain D84
virus inoculation: five viruliferous green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours
growth stage: two leaves visible


title: RDV-D84 infected Rice_rep3

description: Biological replication 3 of 3, RDV-D84 infected rice


title: Murine Thymocytes

status: Public on Jul 01 2011

city: Frankfurt am Main

first: Sebastian

last: Newrzela

state: Hessen

address: Theodor-Stern-Kai 7

department: Pathology

institute: University Clinic Frankfurt

description: Gene expression of murine thymocytes (Pool T)

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65ug Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with preheated 0.06x SSPE buffer (37C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). All Cy3 images are provided.

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.  For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware). This software offers – among other features – the possibility to compare two single intensity profiles in a ratio experiment. All samples were labeled with Cy3, here, the ratio experiments are shown as control versus (vs.) sample experiments [the ratio experiment results are available on Series records]

source_name: Murine Thymocytes

label_protocol: For the linear T7-based amplification step, 0.5 μg of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Immortalized T cells were cultured under standard culture conditions. Medium: RPMI, 10% FCS, 2% Glu, 1%Pe/St, 1% sodium pyruvate, 1% nonessential amino acids, and 0.1% β-mercaptoethanol throughout the entire cultivation time. Culture conditions also included human IL-2 at 100U/ml for stimulation.

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin® RNA II, Macherey-Nagel).

treatment_protocol: Freshly isolated mature murine T lymphocytes from the lymph nodes and freshly isolated thymocytes from the thymus of C57BL/6 mice, as well as cultured immortalized T cells were collected for RNA isolation.

tag: strain

value: C57BL/6 mice.

value: Thymus

value: mononuclear cells


title: Mouse ES cells vs. iPS cells C1

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

institute: University of Minnesota

description: Biological replicate 1 of 2. Mouse iPS cells, harvested 30 days after transduction.

hyb_protocol: Corresponding Cy3 and Cy5 labeled cRNAs were combined in hybridization buffer and samples were and hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

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

data_processing: The Agilent Feature Extraction Software (FES 10.1) was used to read out and process the microarray image files. For data normalization and determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). Normalized log10 ratio (Cy5/Cy3) representing test/reference.

source_name: Total RNA from CGR8.8, labeled with Cyanine-3 (green).

label_protocol: 1 µg of each RNA was used as template to produce Cy3-labeled cRNA. The RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF).

extract_protocol: RNA was extracted using RNA II (Macherey & Nagel) following manufacturer's instructions.

value: ES CGR8.8

source_name: Total RNA from iPS cells, labeled with Cyanine-5 (red).

label_protocol: 1 µg of each RNA was used as template to produce Cy5-labeled cRNA. The RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: iPS cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF).

treatment_protocol: 30 days after transduction iPSC clone was harvested.

value: iPS cells


title: Mouse ES cells vs. MEFs B2

description: Biological replicate 2 of 2. Mouse embryonic fibroblasts, harvested after several passages.

source_name: Total RNA from mouse embryonic fibroblasts, labeled with Cyanine-5 (red).

growth_protocol: ES cells and iPS cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF).

value: MEFs


title: RDV-O infected Rice_rep3

description: Biological replication 3 of 3, RDV-O infected rice

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Temperature: 25±3℃
virus inoculation: Rice Dwarf Virus strain O
virus inoculation: five viruliferous green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours
growth stage: two leaves visible


title: RDV-O infected Rice_rep2

description: Biological replication 2 of 3, RDV-O infected rice


title: RDV-D84 infected Rice_rep1

description: Biological replication 1 of 3, RDV-D84 infected rice


title: Mouse ES cells vs. iPS cells C2

description: Biological replicate 2 of 2. Mouse iPS cells, harvested 30 days after transduction.


title: Murine naive T lymphocytes

description: Gene expression of murine naive T lymphocytes (Pool L)

source_name: Murine naive T lymphocytes

value: Lymph nodes


title: RDV-S infected Rice_rep2

description: Biological replication 2 of 3, RDV-S infected rice


title: Immortalized murine T lymphocytes

description: Gene expression of immortalized murine T lymphocytes (Pool IM)

source_name: Immortalized murine T lymphocytes


title: RDV-O infected Rice_rep1

description: Biological replication 1 of 3, RDV-O infected rice


title: 146a Overexpressed LPS stimulated (10 ng/ml) 24 hrs vs scrambled LPS stimulated (10 ng/ml) 24 hrs rep 5

city: Winnipeg

first: Rhiannon

middle: LCH

last: Huzarewich

state: MB

address: 1015 Arlington St.

department: Molecular PathoBiology

country: Canada

institute: Public Health Agency of Canada

hyb_protocol: Hybridization and washing was performed according to the Two-Color Microarray-Based Gene Expression Analysis protocol for a 4x44K microarray format (Agilent technologies) following manufacturer's instructions.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3) following the scan settings for a 4x44K microarray format according to manufacturer's instructions.

data_processing: The .TIFF images were uploaded into Feature Extraction (Agilent technologies, G2567AA FE software, v.9.1), the spots were identified, and the grids constructed using the GE2-v5_91_0806 protocol and the 014868_D_20060807 grid file for the whole mouse genome 4x44K expression arrays which were downloaded from the Agilent technologies website. Background calculations were performed by the feature extraction software using spatial and multiplicative detrending and normalization was performed using linear and lowess. The p-value to determine differential expression was 0.01 and the resulting log10 ratios from the feature extraction software were provided as the red (AlexaFlour 647)/green (AlexaFlour 555) channel.

label: AlexaFluor 555

source_name: Microglia cells 146a overexpressed LPS stimulated 24 hrs

label_protocol: Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Ambion) following manufacturer's instructions. Each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen).

extract_protocol: Total RNA extracted using the mirVanaTM miRNA Isolation kit (Ambion cat.# AM1560) following manufacturer's instructions.

value: EOC 13.31 microglia cells

label: AlexaFluor 647

source_name: Microglia cells scrambled LPS stimulated 24 hrs


title: Mouse ES cells vs. MEFs B1

description: Biological replicate 1 of 2. Mouse embryonic fibroblasts, harvested after several passages.


title: 146a Overexpressed LPS stimulated (10 ng/ml) 24 hrs vs scrambled LPS stimulated (10 ng/ml) 24 hrs rep 6


title: Expt5_0hr

source_name: Input fraction from Expt5_0hr

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

source_name: Methyl-depleted fraction from Expt5_0hr


title: 146a Overexpressed LPS stimulated (10 ng/ml) 24 hrs vs scrambled LPS stimulated (10 ng/ml) 24 hrs rep 4


title: 146a Overexpressed LPS stimulated (10 ng/ml) 24 hrs vs scrambled LPS stimulated (10 ng/ml) 24 hrs rep 3


title: 146a Overexpressed LPS stimulated (10 ng/ml) 8 hrs vs scrambled LPS stimulated (10 ng/ml) 8 hrs rep 6

source_name: Microglia cells 146a overexpressed LPS stimulated 8 hrs

source_name: Microglia cells scrambled LPS stimulated 8 hrs


title: 146a Overexpressed LPS stimulated (10 ng/ml) 24 hrs vs scrambled LPS stimulated (10 ng/ml) 24 hrs rep 2


title: 146a Overexpressed LPS stimulated (10 ng/ml) 24 hrs vs scrambled LPS stimulated (10 ng/ml) 24 hrs rep 1


title: 146a Overexpressed LPS stimulated (10 ng/ml) 8 hrs vs scrambled LPS stimulated (10 ng/ml) 8 hrs rep 5


title: 146a Overexpressed LPS stimulated (10 ng/ml) 8 hrs vs scrambled LPS stimulated (10 ng/ml) 8 hrs rep 1


title: LPS stimulated 100 ng/ml vs PBS rep4

source_name: Microglia cells LPS stimulated 100 ng/ml

source_name: Microglia cells PBS


title: 146a Overexpressed LPS stimulated (10 ng/ml) 8 hrs vs scrambled LPS stimulated (10 ng/ml) 8 hrs rep 4


title: 146a Overexpressed LPS stimulated (10 ng/ml) 8 hrs vs scrambled LPS stimulated (10 ng/ml) 8 hrs rep 2


title: LPS stimulated 100 ng/ml vs PBS rep3


title: LPS stimulated 100 ng/ml vs PBS rep1


title: 146a Overexpressed LPS stimulated (10 ng/ml) 8 hrs vs scrambled LPS stimulated (10 ng/ml) 8 hrs rep 3


title: LPS stimulated 10 ng/ml vs PBS rep1

source_name: Microglia cells LPS stimulated 10 ng/ml


title: LPS stimulated 10 ng/ml vs PBS rep2


title: LPS stimulated 10 ng/ml vs PBS rep3


title: LPS stimulated 10 ng/ml vs PBS rep4


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep12

description: 251486817764_146a_KO_LPS_stimln_3_24_hrs(647)_scr(555)_1_4

source_name: Microglia cells srambled then LPS stimulation

source_name: Microglia cells 146a knockout then LPS stimulation


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep10

description: 251486817764_146a_KO_LPS_stimln_2_24_hrs(647)_scr(555)_1_2


title: LPS stimulated 100 ng/ml vs PBS rep2


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep7

description: 251486817763_146a_KO_LPS_stimln_1_24_hrs_(555)_scr(647)_1_3


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep11

description: 251486817764_146a_KO_LPS_stimln_3_24_hrs(555)_scr(647)_1_3


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep8

description: 251486817763_146a_KO_LPS_stimln_1_24_hrs_(647)_scr(555)_1_4


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep6

description: 251486817763_146a_KO_LPS_stimln_3_8_hrs_(647)_scr(555)_1_2


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep9

description: 251486817764_146a_KO_LPS_stimln_2_24_hrs_(555)_scr(647)_1_1


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep4

description: 251486817762_146a_KO_LPS_stimln_2_8_hrs_(647)_scr(555)_1_4


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep3

description: 251486817762_146a_KO_LPS_stimln_2_8_hrs_(555)_scr(647)_1_3


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep2

description: 251486817762_146a_KO_LPS_stimln_1_8_hrs_(647)_scr(555)_1_2


title: 146a knockout vs scrambled rep7

description: 251486811763_146a-3_KO_(555)_scr_(647)_1_3

source_name: Microglia cells 146a knockout

source_name: Microglia cells scrambled


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep1

description: 251486817762_146a_KO_LPS_stimln_1_8_hrs_(555)_scr(647)_1_1


title: 146a knockout vs scrambled rep5

description: 251486811763_146a-3_KO_(555)_scr_(647)_1_1


title: 146a knockout then LPS stimulation vs scrambled then LPS stimulation rep5

description: 251486817763_146a_KO_LPS_stimln_3_8_hrs_(555)_scr(647)_1_1


title: 146a knockout vs scrambled rep4

description: 251486811762_146a-2_KO_(647)_scr_(555)_1_4


title: 146a knockout vs scrambled rep8

description: 251486811763_146a-3_KO_(647)_scr_(555)_1_4


title: 146a knockout vs scrambled rep6

description: 251486811763_146a-3_KO_(647)_scr_(555)_1_2


title: 146a knockout vs scrambled rep3

description: 251486811762_146a-2_KO(555)_scr_(647)_1_3


title: LPS stimulated vs PBS rep3

description: 251486812087_LPS_2_555_PBS_647_48_hrs_1_3

source_name: Microglia cells LPS stimulated


title: LPS stimulated then 146a knockout vs LPS stimulated plus scrambled rep5

description: 251486811761_LPS_48_hrs_KO_1_555_LPS_scr_647_1_3

source_name: Microglia cells LPS stimulated then 146a knockout

source_name: Microglia cells LPS stimulated then scrambled


title: LPS stimulated then 146a knockout vs LPS stimulated plus scrambled rep1

description: 251486811760_LPS_48_hrs_KO_1_555_LPS_scr_647_1_3


title: LPS stimulated vs PBS rep5

description: 251486811760_LPS_3_555_PBS_647_48_hrs_1_1


title: 146a knockout vs scrambled rep1

description: 251486811762_146a-1_KO_(555)_scr_(647)_1_1


title: LPS stimulated vs PBS rep1

description: 251486812087_LPS_1_555_PBS_647_48_hrs_1_1


title: 146a overexpressed vs scrambled rep6

description: 251486812050_146a_OE_3_555_scr_647_8_hrs_1_2

source_name: Microglia cells 146a Overexpressed

source_name: Microglia cells Scrambled


title: LPS stimulated then 146a knockout vs LPS stimulated plus scrambled rep3

description: 251486811761_LPS_48_hrs_KO_2_555_LPS_scr_647_1_1


title: 146b overexpressed vs scrambled rep4

description: 251486812053_146b_OE_3_555_scr_647_24_hrs_1_2

source_name: Microglia cells 146b Overexpressed


title: 146b overexpressed vs scrambled rep1

description: 251486812050_146b_OE_2_647_scr_555_24_hrs_1_3


title: LPS stimulated then 146a knockout vs LPS stimulated plus scrambled rep2

description: 251486811760_LPS_48_hrs_KO_1_647_LPS_scr_555_1_4


title: 146a overexpressed vs scrambled rep4

description: 251486812049_146a_OE_2_555_scr_647_8_hrs_1_4


title: LPS stimulated then 146a knockout vs LPS stimulated plus scrambled rep6

description: 251486811761_LPS_48_hrs_KO_1_647_LPS_scr_555_1_4


title: LPS stimulated vs PBS rep2

description: 251486812087_LPS_1_647_PBS_555_48_hrs_1_2


title: LPS stimulated vs PBS rep4

description: 251486812087_LPS_2_647_PBS_555_48_hrs_1_4


title: LPS stimulated vs PBS rep6

description: 251486811760_LPS_3_647_PBS_555_48_hrs_1_2


title: 146b overexpressed vs scrambled rep2

description: 251486812050_146b_OE_2_555_scr_647_24_hrs_1_4


title: 146a knockout vs scrambled rep2

description: 251486811762_146a-1_KO_(647)_scr_(555)_1_2


title: 146a overexpressed vs scrambled rep2

description: 251486812049_146a_OE_1_555_scr_647_8_hrs_1_2


title: 146a overexpressed vs scrambled rep5

description: 251486812050_146a_OE_3_647_scr_555_8_hrs_1_1


title: enriched normal vs depleted normal, rep4 (Agilent)

source_name: Normal depleted splenic cells

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer's instructions.

tag: strain of mouse

source_name: Normal enriched splenic cells


title: 146a overexpressed vs scrambled rep3

description: 251486812049_146a_OE_2_647_scr_555_8_hrs_1_3

tag: cell type


title: 146a overexpressed vs scrambled rep1

description: 251486812049_146a_OE_1_647_scr_555_8_hrs_1_1


title: prion infected vs normal endpoint, rep5 (Agilent)

description: 251486810143_Pooled#8,9,10(647)_C#2(555)_1_1

source_name: Normal splenic cells, endpoint

value: VM

tag: inoculum

value: PBS

tag: inoculation type

value: IP

tag: date of inoculation

source_name: Prion infected splenic cells, endpoint


title: prion infected vs normal endpoint, rep3 (Agilent)

value: 22A (scrapie)


title: prion infected vs normal endpoint, rep7 (Agilent)


title: enriched normal vs depleted normal, rep1 (Agilent)


title: enriched normal vs depleted normal, rep2 (Agilent)


title: prion infected vs normal endpoint, rep8 (Agilent)


title: prion infected vs normal endpoint, rep2 (Agilent)


title: Ovine oocyte from primordial follicle PDO

city: Castanet-Tolosan Cedex

first: Agnes

last: Bonnet

address: Chemin de Borde-Rouge  BP 52627

description: Gene expression data generated to identify a global gene expression for each follicular compartment during early developmental stages

hyb_protocol: Standard Affymetrix procedures at a concentration of 40 ng Biotin-labeled cRNA /µl hybridization mix

scan_protocol: Affymetrix microarrays were processed in the Microarray Core Facility of the Institute of Research of Biotherapy, CHRU-INSERM-UM1 Montpellier  Scan : standard Affymetrix procedures

data_processing: Images were interpreted using Microarray Suite version 5.0 (MAS 5.0) in GCOS with scaling (100).

organism: Ovis aries

source_name: oocyte from primordial follicle

label_protocol: LCM-derived RNA sample was subject to the two round of T7 amplification using  the RiboAmp®HS PLUS Amplification kit. Fifteen micrograms of aRNA were labeled using the Arcturus biotin turboTM labeling kit (Arcturus, ref KIT0608) .  Affymetrix microarrays were processed in the Microarray Core Facility of the Institute of Research of Biotherapy, CHRU-INSERM-UM1 Montpellier.

extract_protocol: RNA was extracted following the manufacturer's protocol using PicoPure RNA Isolation Kit (Arcturus, ref: KIT0202)  including on-column DNase treatment (Qiagen, Ref 79254)

value: oocyte from primordial follicle

tag: age

value: new-born lamb ovaries (<1 day)


title: Ovine oocyte from primary follicle PMO

source_name: oocyte from primary follicle

value: oocyte from primary follicle


title: prion infected vs normal endpoint, rep1 (Agilent)

description: 251486810142_Pooled#8,9,10(555)_C#2(647)_1_1


title: Ovine oocyte from secondary follicle SECO

source_name: oocyte from secondary follicle

value: oocyte from secondary follicle


title: Ovine granulosa cells from primordial follicle PDG


title: Ovine fetal ovary-P1

description: Gene expression data generated to assess heterologous hybridization (bovine and ovine fetal gonad on bovine Affymetrix chip) and labeling protocol comparisons

source_name: fetal ovary

label_protocol: RNA was amplified using Affymetrix One-cycle protocol with approximately 3  micrograms of total RNA as described in the GeneChip® Expression Analysis Technical Manual.  Affymetrix microarrays were processed in the Microarray Core Facility of the Institute of Research of Biotherapy, CHRU-INSERM-UM1 Montpellier.

extract_protocol: RNA was extracted following the manufacturer's protocol using RNeasy  Mini Kit  (Qiagen, Ref 74104) column including on-column DNase treatment (Qiagen, Ref 79254)

value: fetal ovary

value: 132 days post coïtum


title: Ovine fetal ovary-P2

description: Gene expression data generated to assess labeling protocols comparisons

label_protocol: RNA was subject to two-round of T7 amplification using the RiboAmp®HS PLUS kit until the second-round cDNA synthesis. Biotin-labeled cRNAs were synthesized following Affymetrix protocol using the second-round cDNAs as templates (440 ng / 8µl).  Affymetrix microarrays were processed in the Microarray Core Facility of the Institute of Research of Biotherapy, CHRU-INSERM-UM1 Montpellier.


title: prion infected vs normal endpoint, rep4 (Agilent)


title: prion infected vs normal endpoint, rep6 (Agilent)


title: Ovine granulosa cells from primary follicle PMG

source_name: granulosa cells from primary follicle

value: granulosa cells from primary follicle


title: Ovine granulosa cells from secondary follicle SECG

source_name: granulosa cells from secondary follicle

value: granulosa cells from secondary follicle


title: Ovine fetal ovary-P3

label_protocol: RNA was subject to the two round of T7 amplification using  the RiboAmp®HS PLUS Amplification kit. Fifteen micrograms of aRNA were labeled using the Arcturus biotin turboTM labeling kit (Arcturus, ref KIT0608) .  Affymetrix microarrays were processed in the Microarray Core Facility of the Institute of Research of Biotherapy, CHRU-INSERM-UM1 Montpellier.


title: Bone marrow B220+ cells isolated from WT littermate control mice 1

description:
KAFv (IKK alpha  kinase knockin  FVB mice)
Bone marrow B220+ cells isolated from WT littermate control mice

source_name: Bone marrow B220+ cells

value: Bone marrow B220+ cells

value: wild type

value: FVB


title: SG200Dpit2 4dpi rep 1

city: Marburg

first: Gunther

last: Doehlemann

address: Karl von Frisch Str.

department: Organismic Interactions

institute: Max Planck Institue for Terrestiral Microbiology

description: Zea mays after infection with Ustilago maydisstrain SG200Dpit2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol Midi_Euk2V3.

scan_protocol: GeneChips were scanned on a Affymetrix GSC3000G scanner

data_processing: Date were analyzed with the GeneChip operating software (GCOS) 1.4 to generate CEL files.

organism: Zea mays

source_name: maize seedling leave (leaf 3), 4 days after infection

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

growth_protocol: Maize plants (Early Golden Bantam) were grown in a phytochamber in a 15/9 hour light/dark cycle. Temerature was 28°c and 20°c, relative humudity 40% and 60% during light and dark periods, respectively, with 1 hour ramping for both parameters.

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

treatment_protocol: Seedlings were inoculated 7 days after sawing with the respective U. maydis strains, resulting in an infection of the third seedling leaf. Samples were taken 4 days after fungal infection.

tag: variety

value: Early Golden Bantam

value: leaf

tag: disease state


title: SG200Dpit2 4dpi rep 3

value: infection with Ustilago maydisstrain SG200Dpit2


title: Bovine fetal ovary-P1

description: Gene expression data generated to assess heterologous hybridization (bovine and ovine fetal gonad on bovine Affymetrix chip)

organism: Bos taurus

value: eight months post coïtum


title: SG200Dpit2 4dpi rep 2


title: SG200Dpit1 4dpi rep 2

description: Zea mays after infection with Ustilago maydisstrain SG200Dpit1


title: SG200Dpit1 4dpi rep 3

value: infection with Ustilago maydisstrain SG200Dpit1


title: 1114_014_20 wt pre-treatment 0 vs. wt KCl 20

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

hyb_protocol: Competitive hybridization at 65oC for 15h

scan_protocol: images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 5.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

organism: Saccharomyces cerevisiae

label_protocol: aa-dUTP incorporation during cDNA synthesis

extract_protocol: Acid phenol

tag: genotype

value: wild-type

tag: treatment

value: 1M KCl

tag: time (min)

value: pretreatment sample


title: 1114_010_20 wt rapamycin 5 vs. rrp6 rapamycin 5

value: rrp6 ORF deletion

value: 200ng/mL Rapamycin


title: 1114_011_20 wt rapamycin 10 vs. rrp6 rapamycin 10


title: 1114_015_20 wt pre-treatment 0 vs. wt LiCl 20

value: 300mM LiCl


title: 1114_013_20 wt rapamycin 40 vs. rrp6 rapamycin 40


title: 1114_016_20 wt pre-treatment 0 vs. wt rapamycin 20


title: 1114_006_20 wt LiCl 10 vs. rrp6 LiCl 10


title: 1114_003_20 wt KCl 20 vs. rrp6 KCl 20


title: 1114_005_20 wt LiCl 5 vs. rrp6 LiCl 5


title: 1114_004_20 wt KCl 40 vs. rrp6 KCl 40


title: 1114_009_20 wt pre-treatment 0 vs. rrp6 pre-treatment 0


title: 1114_007_20 wt LiCl 20 vs. rrp6 LiCl 20


title: 1114_008_20 wt LiCl 40 vs. rrp6 LiCl 40


title: SG200Dpit1 4dpi rep 1


title: HEK293-Hace1 normoxia replicate 2

city: Vancouver

first: Tony

last: Ng

state: BC

department: Molecular Oncology

institute: BC Cancer Research Centre

description: HEK293-MSCV-Hace1 control subconfluent cultures in 10% serum

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with the Genetrix SB (64-bit) software, version 3.40 using ITERPLIER-sketch as normalization method for CORE annotation-level analysis.
probe group file HuEx-1_0-st-v2
meta-probeset file HuEx-1_0-st-probeset_annot

source_name: HEK293-Hace1 normoxia replicate 2

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).

growth_protocol: Low-passage HEK293 cells stably overexpressing HA-Hace1 or MSCV vector-alone

treatment_protocol: Placement in 1% O2, 5% CO2, 37oC hypoxia tissue culture chamber for 2 hours

tag: cell line

value: 21% Oxygen

tag: transfection


title: 1114_002_20 wt KCl 10 vs. rrp6 KCl 10


title: 1114_012_20 wt rapamycin 20 vs. rrp6 rapamycin 20


title: 1114_001_20 wt KCl 5 vs. rrp6 KCl 5


title: HEK293-MSCV hypoxia replicate 1

description: HEK293-MSCV subconfluent cultures subjected to 1% O2 tension for 2 hours in 10% serum

source_name: HEK293-MSCV hypoxia replicate 1

value: 1% Oxygen

value: MSCV


title: HEK293-Hace1 hypoxia replicate 1

description: HEK293-MSCV-Hace1 subconfluent cultures subjected to 1% O2 tension for 2 hours in 10% serum

source_name: HEK293-Hace1 hypoxia replicate 1


title: HEK293-Hace1 hypoxia replicate 2

source_name: HEK293-Hace1 hypoxia replicate 2


title: HEK293-MSCV hypoxia replicate 2

source_name: HEK293-MSCV hypoxia replicate 2


title: HEK293-MSCV normoxia replicate 2

description: HEK293-MSCV control subconfluent cultures in 10% serum

source_name: HEK293-MSCV normoxia replicate 2


title: HEK293-Hace1 normoxia replicate 1

source_name: HEK293-Hace1 normoxia replicate 1


title: LPS stimulated then 146a knockout vs LPS stimulated plus scrambled rep4

description: 251486811761_LPS_48_hrs_KO_2_647_LPS_scr_555_1_2

source_name: Microglia cells LPS stimulated then scrambled

value: EOC 13.31 microglia cells

source_name: Microglia cells LPS stimulated then 146a knockout


title: 0527_013_20 wt pre-treatment 0 vs. wt 3AT_rap 20

value: 50mM 3-Amino-1,2,4-triazole (3-AT) + 200ng/mL Rapamycin


title: 0527_011_20 wt pre-treatment 0 vs. wt 3AT_rap 5


title: 0527_012_20 wt pre-treatment 0 vs. wt 3AT_rap 10


title: 0412_037_20 wt pre-treatment 0 vs. ckb1 pre-treatment 0

value: ckb1 ORF deletion


title: HEK293-MSCV normoxia replicate 1

source_name: HEK293-MSCV normoxia replicate 1


title: 0825_043_20 wt mock treated 20 vs. wt LiCl 20

value: untreated control


title: 1103_074_20 wt mock treated 40 vs. wt LiCl 40


title: 1103_071_20 wt mock treated 5 vs. wt LiCl 5


title: 0527_020_20 wt mock treated 10 vs. wt 3AT_KCl 10

value: 50mM 3-Amino-1,2,4-triazole (3-AT) + 1M KCl


title: 1103_072_20 wt mock treated 10 vs. wt LiCl 10


title: 0825_041_20 wt mock treated 5 vs. wt LiCl 5


title: 0825_042_20 wt mock treated 10 vs. wt LiCl 10


title: enriched normal vs depleted normal, rep3 (Agilent)

source_name: Normal enriched splenic cells

source_name: Normal depleted splenic cells


title: 0527_021_20 wt mock treated 20 vs. wt 3AT_KCl 20


title: 0527_019_20 wt mock treated 5 vs. wt 3AT_KCl 5


title: 1103_037_20 wt mock treated 20 vs. wt LiCl 20


title: 1103_035_20 wt mock treated 5 vs. wt LiCl 5


title: 146b overexpressed vs scrambled rep3

description: 251486812053_146b_OE_3_647_scr_555_24_hrs_1_1

source_name: Microglia cells Scrambled

source_name: Microglia cells 146b Overexpressed


title: 1103_073_20 wt mock treated 20 vs. wt LiCl 20


title: 0527_014_20 wt pre-treatment 0 vs. wt 3AT_rap 40


title: 0825_047_20 wt mock treated 20 vs. wt carbon 20

value: Glucose depletion


title: 0527_022_20 wt mock treated 40 vs. wt 3AT_KCl 40


title: 0825_048_20 wt mock treated 40 vs. wt carbon 40


title: 0825_044_20 wt mock treated 40 vs. wt LiCl 40


title: 0825_046_20 wt mock treated 10 vs. wt carbon 10


title: 1103_052_20 edc2 mock treated 20 vs. edc2 kcl 20

value: edc2 ORF deletion


title: 0825_045_20 wt mock treated 5 vs. wt carbon 5


title: 1103_038_20 wt mock treated 40 vs. wt LiCl 40


title: 1103_044_20 edc2 mock treated 5 vs. edc2 kcl 5


title: 0527_030_20 wt pre-treatment 0 vs. wt TBB 40


title: 1103_050_20 edc2 mock treated 10 vs. edc2 kcl 10