title: Mock IP, 8/11/10 #2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89260.gif

source_name: Total RNA from lysate after IP

value: Total RNA from lysate after IP

source_name: RNA that co-purified with an RBP

value: RNA that co-purified with an RBP


title: PBMC_naive_PPD_unvaccinated.progressor_rep3b

status: Public on Nov 15 2012

type: RNA

city: Salisbury

first: Alice

last: Hicks

address: Porton Down

department: TB research

country: United Kingdom

institute: Health Protection Agency

description: Gene expression in PPD-stimulated PBMCs isolated from a naive animal

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 1.65 µg Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rhesus Macaque Gene Expression Microarrays (015421) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.cDNA in hybridization buffer was hybridized overnight (17 hours, 65°C, 10 rpm)

scan_protocol: Slides were scanned immediately after washing using the Agilent’s High-Resolution C Scanner at a resolution of 5 µm using one color scan setting for 4x44k array slides (Profile AgilentHD_GX_1Color) for 4x44k array slides (Scan Area 61 x 21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software v10.7 (Agilent) using the default settings for 1-colour gene expression analysis (protocol GE1_107_Sep09). Data underwent quantile normalisation and was baseline transformed to the median of the naive time-points for each individual animal (e.g. stimulated post-vacc and stimulated post-challenge expression levels baseline transformed to stimulated naive expression level in each animal).

molecule: total RNA

organism: Macaca fascicularis

source_name: PBMCs, PPD-stimulated, naive

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Low Input Quick Amplification and Labelling kit (one-color) (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated from PBMC samples by adding Trizol reagent (Invitrogen, Paisley, UK). The RNA was harvested from the Trizol as described in the manufacturer's protocol and RNA cleaned up using RNeasy spin columns (Qiagen, Crawley, UK) including an on-column DNA digest step (Qiagen, Crawley, UK), as described in the manufacturer's protocol.RNA was quantified using a NanoDrop ND1000 UV-vis Spectrophotometer (NanoDrop Technologies, Cambridge, UK), and the quality determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Stockport, UK). Only RNA with RIN>7.0 was used for microarray

treatment_protocol: PBMCs were isolated from heparin-anticoagulated blood and cryopreserved on the day of collection. PBMCs were resuscitated and washed in medium (R10) consisting of RPMI 1640 supplemented with L-glutamine (2 mM), penicillin (50 U/ml)/streptomycin (50µg/ml) and 10% heat-inactivated foetal bovine serum with 50 U/ml Benzonase pre-warmed to 37°C and “rested” for 2 hours at 37°C in 5% CO2. After resting cells were washed again, and cell concentrations adjusted to 2 x 106 cells/ml in R10. PBMCs were stimulated with 30 µg/ml PPD for 16 hours at 37°C in the presence of 5% CO2

tag: experimental group

value: Unvaccinated Progressor

tag: animal name

tag: cell stimulation

value: PPD

tag: immune status

value: Naive


title: 9_15_2010_Mock(1)

city: Durham

first: Nikoleta

middle: G

last: Tsvetanova

state: NC

address: 308 Research Drive

department: Pharmacology & Cancer Biology

country: USA

institute: Duke University

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89675.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Saccharomyces cerevisiae

source_name: Reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: channel 1

value: Reference RNA

source_name: IP RNA

tag: channel 2

value: IP RNA

tag: geneticmodification

value: untagged

tag: media

value: absent


title: PBMC_post.challenge_PPD_unvaccinated.progressor_rep3

description: Gene expression in PPD-stimulated PBMCs isolated from a unvaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to develop TB disease

source_name: PBMCs, PPD-stimulated, post-challenge

value: Post challenge


title: UPR_Mock_1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91960.gif

source_name: Reference

value: Reference

source_name: IP

value: IP

value: present


title: PBMC_naive_unstimulated_unvaccinated.progressor_rep3a

description: Gene expression in unstimulated PBMCs isolated from a naive animal

source_name: PBMCs, unstimulated, naive


title: HAC1-d3'UTR #2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89254.gif

value: HAC1-3' utr deletion


title: UPR_Ypt1_1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91958.gif

value: tagged


title: 9_15_2010_Mock(2)

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89680.gif


title: HAC1-d3'UTR #1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89253.gif


title: YER102W-TAP ("WT") #2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89252.gif

value: no deletion control


title: UPR_Ypt1_2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91959.gif


title: PBMC_post.challenge_PPD_vaccinated.controller_rep6

description: Gene expression in PPD-stimulated PBMCs isolated from a BCG-vaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to control infection for duration of study

value: Vaccinated Controller


title: YER102W-TAP ("WT") #1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89251.gif

value: Total RNA from lysate after IP


title: PBMC_naive_PPD_unvaccinated.progressor_rep3a


title: ada5-d  #2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89258.gif

value: RNA that co-purified with an RBP


title: Mock IP, 8/11/10 #1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89259.gif


title: Ypt1 normalmedium (1)

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88196.gif


title: ire1-d #2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89256.gif


title: PBMC_18wkpost-vacc_PPD_vaccinated.controller_rep6

description: Gene expression in PPD-stimulated PBMCs isolated 18 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge

source_name: PBMCs, PPD-stimulated, 18wks post BCG-vaccination

value: 18 wks post-BCG


title: ada5-d #1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89257.gif


title: PBMC_post.challenge_unstimulated_vaccinated.controller_rep6

description: Gene expression in unstimulated PBMCs isolated from a BCG-vaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to control infection for duration of study

source_name: PBMCs, unstimulated, post-challenge


title: PBMC_18wkpost-vacc_unstimulated_vaccinated.controller_rep6

description: Gene expression in unstimulated PBMCs isolated 18 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge

source_name: PBMCs, unstimulated, 18wks post BCG-vaccination


title: PBMC_8wkpost-vacc_PPD_vaccinated.controller_rep6

description: Gene expression in PPD-stimulated PBMCs isolated 8 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge

source_name: PBMCs, PPD-stimulated, 8wks post BCG-vaccination

value: PPD

value: 8 wks post-BCG


title: PBMC_8wkpost-vacc_unstimulated_vaccinated.controller_rep6

description: Gene expression in unstimulated PBMCs isolated 8 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge

source_name: PBMCs, unstimulated, 8wks post BCG-vaccination


title: Cartilage, Sham, 8 weeks, rep3

city: London

first: Tom

last: Appleton

state: ON

address: Rm 0061 DSB The University of Western Ontario

department: Physiology & Pharmacology

country: Canada

institute: The University of Western Ontario

description: Gene expression data from knee articular cartilage chondrocytes 8 weeks after Sham surgery

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.

label: biotin

organism: Rattus norvegicus

source_name: knee articular cartilage

label_protocol: Affymetrix protocol

extract_protocol: Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).

treatment_protocol: See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13

tag: surgery

value: Sham

tag: time after surgery

value: 8 weeks


title: PBMC_post.challenge_unstimulated_unvaccinated.progressor_rep3

description: Gene expression in unstimulated PBMCs isolated from a unvaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to develop TB disease

value: Unvaccinated Progressor


title: Ypt1 normalmedium (2)

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88197.gif

value: Reference RNA

value: IP RNA

value: absent


title: ire1-d #1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-08/89255.gif


title: PBMC_naive_unstimulated_unvaccinated.progressor_rep3b

description: Gene expression in unstimulated PBMCs isolated from a naive animal

value: Naive


title: PBMC_naive_PPD_vaccinated.controller_rep6a

description: Gene expression in PPD-stimulated PBMCs isolated from a naive animal


title: PBMC_naive_unstimulated_vaccinated.controller_rep6b


title: PBMC_naive_PPD_vaccinated.controller_rep6b


title: Cartilage, OA, 8 weeks, rep1

description: Gene expression data from knee articular cartilage chondrocytes 8 weeks after induction of OA

value: OA


title: Cartilage, Sham, 8 weeks, rep2


title: Cartilage, OA, 8 weeks, rep2


title: PBMC_naive_unstimulated_vaccinated.controller_rep6a


title: HAC1complete sequence  in Cy5 (1)

description:
Simple annotation: mRNA vs Total RNA Comparison, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81025.gif
is_reverse: no

source_name: Total yeast mRNA

value: Total yeast mRNA

source_name: HAC1 mRNA (complete sequence)

value: HAC1 mRNA (complete sequence)


title: Cartilage, Sham, 8 weeks, rep1


title: PBMC_post.challenge_PPD_unvaccinated.controller_rep3

description: Gene expression in PPD-stimulated PBMCs isolated from a unvaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to control infection for duration of study

value: Unvaccinated Controller

value: Post challenge


title: PBMC_post.challenge_unstimulated_unvaccinated.progressor_rep2


title: PBMC_naive_PPD_unvaccinated.controller_rep3a


title: PBMC_post.challenge_PPD_unvaccinated.progressor_rep2

description: Gene expression in PPD-stimulated PBMCs isolated from a unvaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to develop TB disease


title: PBMC_naive_PPD_unvaccinated.progressor_rep2b


title: Cartilage, Sham, 2 weeks, rep3

description: Gene expression data from knee articular cartilage chondrocytes 2 weeks after Sham surgery

value: 2 weeks


title: PBMC_naive_unstimulated_unvaccinated.controller_rep3a


title: PBMC_post.challenge_unstimulated_unvaccinated.controller_rep3

description: Gene expression in unstimulated PBMCs isolated from a unvaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to control infection for duration of study


title: Cartilage, OA, 2 weeks, rep3

description: Gene expression data from knee articular cartilage chondrocytes 2 weeks after induction of OA


title: Cartilage, OA, 8 weeks, rep3


title: Cartilage, OA, 2 weeks, rep2


title: PBMC_naive_unstimulated_unvaccinated.controller_rep3b


title: Cartilage, Sham, 2 weeks, rep1


title: PBMC_naive_PPD_unvaccinated.controller_rep3b


title: Cartilage, OA, 2 weeks, rep1


title: PBMC_naive_unstimulated_unvaccinated.progressor_rep2b


title: TR.PD1.late#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools (apt v.1.10.2) on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

organism: Mus musculus

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: strain background

tag: age

tag: gender

value: male

tag: tissue

value: spleen, lymph node

tag: exclusion markers

tag: cell type

value: regulatory T cells (Treg)

tag: phenotype markers

value: CD4+, GFP+

tag: separation method

value: FACSAria


title: TR.PD1.late#2

value: 8 weeks


title: TR.PD1.early#3


title: TR.PD1.early#1


title: PBMC_naive_PPD_unvaccinated.progressor_rep2a

tag: experimental group

value: Unvaccinated Progressor

tag: animal name

value: PPD


title: TR.ICOS.late#1


title: PBMC_naive_unstimulated_unvaccinated.progressor_rep2a

tag: cell stimulation

tag: immune status


title: TR.ICOS.late#2


title: PBMC_post.challenge_unstimulated_vaccinated.controller_rep5

description: Gene expression in unstimulated PBMCs isolated from a BCG-vaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to control infection for duration of study

value: Vaccinated Controller


title: TR.CTLA4.late#3


title: TR.ICOS.early#1


title: TR.PD1.late#3


title: PBMC_18wkpost-vacc_PPD_vaccinated.controller_rep5

description: Gene expression in PPD-stimulated PBMCs isolated 18 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge

value: 18 wks post-BCG


title: TR.CTLA4.late#1


title: TR.CTLA4.early#1


title: PBMC_18wkpost-vacc_unstimulated_vaccinated.controller_rep5

description: Gene expression in unstimulated PBMCs isolated 18 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge


title: TR.CD80.late#2


title: TR.CTLA4.early#2


title: TR.CD80.late#1


title: TR.CTLA4.early#3


title: TR.ICOS.early#2


title: PBMC_8wkpost-vacc_PPD_vaccinated.controller_rep5

description: Gene expression in PPD-stimulated PBMCs isolated 8 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge

value: 8 wks post-BCG


title: PBMC_8wkpost-vacc_unstimulated_vaccinated.controller_rep5

description: Gene expression in unstimulated PBMCs isolated 8 weeks post BCG-vaccination from an animal that would go on to control TB infection after challenge


title: PBMC_naive_unstimulated_vaccinated.controller_rep5b

value: Naive


title: TR.CD80.early#2


title: TR.CD3.late#4


title: TR.CTLA4.late#2


title: PBMC_naive_PPD_vaccinated.controller_rep5a


title: PBMC_naive_PPD_vaccinated.controller_rep5b


title: PBMC_post.challenge_unstimulated_vaccinated.controller_rep4


title: TR.CD80.early#1


title: PBMC_naive_unstimulated_vaccinated.controller_rep5a


title: PBMC_18wkpost-vacc_unstimulated_vaccinated.controller_rep4


title: PBMC_18wkpost-vacc_PPD_vaccinated.controller_rep4


title: TR.CD3.late#3


title: TR.CD3.late#2


title: PBMC_8wkpost-vacc_PPD_vaccinated.controller_rep4


title: TR.CD3.late#1


title: TR.CD3.early#2


title: TR.CD3.early#1


title: TR.CD3.early#3


title: TR.CD3.early#4


title: PBMC_naive_PPD_vaccinated.controller_rep4a


title: Cartilage, Sham, 2 weeks, rep2

value: Sham


title: PBMC_8wkpost-vacc_unstimulated_vaccinated.controller_rep4


title: PBMC_post.challenge_PPD_vaccinated.controller_rep4

description: Gene expression in PPD-stimulated PBMCs isolated from a BCG-vaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to control infection for duration of study


title: TR.CD3-28.late#3


title: PBMC_naive_PPD_vaccinated.controller_rep4b


title: PBMC_naive_unstimulated_vaccinated.controller_rep4b


title: TR.CD3-28.late#2


title: TR.CD3-28.late#1


title: TR.CD3-28.early#3


title: TR.CD3-28.early#2


title: TR.BTLA.late#3


title: TR.CD3-28.early#1


title: TR.BTLA.late#2


title: PBMC_post.challenge_PPD_vaccinated.controller_rep3


title: PBMC_post.challenge_unstimulated_vaccinated.controller_rep3


title: TR.BTLA.late#1


title: PBMC_naive_unstimulated_vaccinated.controller_rep4a


title: PBMC_naive_unstimulated_vaccinated.controller_rep3b


title: TR.BTLA.early#3


title: PBMC_8wkpost-vacc_PPD_vaccinated.controller_rep3


title: TR.BTLA.early#2


title: PBMC_naive_PPD_vaccinated.controller_rep3b


title: TR.BTLA.early#1


title: PBMC_8wkpost-vacc_unstimulated_vaccinated.controller_rep3


title: TR.0hr#5


title: PBMC_naive_PPD_vaccinated.controller_rep3a


title: TR.0hr#3


title: TR.0hr#4


title: PBMC_post.challenge_unstimulated_vaccinated.controller_rep2


title: PBMC_18wkpost-vacc_PPD_vaccinated.controller_rep3


title: PBMC_post.challenge_PPD_vaccinated.controller_rep2


title: PBMC_18wkpost-vacc_unstimulated_vaccinated.controller_rep3


title: TC.PD1.late#2

value: CD11b, CD11c, B220, CD8, GFP

value: conventional T cells (Tconv)


title: PBMC_naive_unstimulated_vaccinated.controller_rep3a


title: PBMC_8wkpost-vacc_PPD_vaccinated.controller_rep2


title: PBMC_18wkpost-vacc_unstimulated_vaccinated.controller_rep2


title: PBMC_18wkpost-vacc_PPD_vaccinated.controller_rep2


title: PBMC_8wkpost-vacc_unstimulated_vaccinated.controller_rep2


title: TC.PD1.early#2


title: PBMC_naive_PPD_vaccinated.controller_rep2b


title: PBMC_naive_unstimulated_vaccinated.controller_rep2b


title: TC.ICOS.late#2


title: TC.PD1.early#1


title: PBMC_naive_unstimulated_vaccinated.controller_rep2a

source_name: PBMCs, unstimulated,naive


title: PBMC_post.challenge_PPD_vaccinated.controller_rep1

value: Post challenge


title: TC.PD1.late#3


title: TC.ICOS.late#1


title: TC.PD1.late#1


title: PBMC_post.challenge_unstimulated_vaccinated.controller_rep1


title: PBMC_post.challenge_PPD_vaccinated.controller_rep5


title: TC.PD1.early#3


title: TC.CTLA4.late#3


title: PBMC_18wkpost-vacc_unstimulated_vaccinated.controller_rep1


title: TC.CTLA4.late#2


title: PBMC_8wkpost-vacc_PPD_vaccinated.controller_rep1


title: TC.CTLA4.late#1


title: PBMC_18wkpost-vacc_PPD_vaccinated.controller_rep1


title: PBMC_naive_PPD_vaccinated.controller_rep1a


title: TC.ICOS.early#2


title: PBMC_naive_PPD_vaccinated.controller_rep1b


title: PBMC_naive_unstimulated_vaccinated.controller_rep1b


title: PBMC_naive_unstimulated_vaccinated.controller_rep1a


title: PBMC_8wkpost-vacc_unstimulated_vaccinated.controller_rep1


title: TC.CTLA4.early#3


title: PBMC_post.challenge_PPD_unvaccinated.progressor_rep1


title: TC.CD80.late#2


title: TC.CTLA4.early#1


title: TC.CD80.early#2


title: TC.CTLA4.early#2


title: PBMC_post.challenge_unstimulated_unvaccinated.progressor_rep1

description: Gene expression in unstimulated PBMCs isolated from a unvaccinated chinese cynomolgus 6 weeks after challenge with M.tuberculosis. The animal went on to develop TB disease


title: TC.CD80.early#1


title: TC.CD3.late#2


title: TC.CD3.late#3


title: TC.CD3.late#4


title: PBMC_naive_unstimulated_unvaccinated.progressor_rep1b


title: TC.CD80.late#1


title: PBMC_naive_PPD_unvaccinated.progressor_rep1b


title: PBMC_naive_PPD_unvaccinated.progressor_rep1a


title: PBMC_naive_PPD_unvaccinated.controller_rep2b

value: Unvaccinated Controller


title: PBMC_naive_unstimulated_unvaccinated.controller_rep2b


title: TC.CD3.late#1

value: male


title: PBMC_post.challenge_unstimulated_unvaccinated.controller_rep2


title: TC.CD3.early#4

value: spleen, lymph node


title: PBMC_naive_PPD_unvaccinated.controller_rep2a


title: PBMC_naive_unstimulated_unvaccinated.progressor_rep1a


title: PBMC_post.challenge_PPD_unvaccinated.controller_rep2


title: PBMC_naive_unstimulated_unvaccinated.controller_rep2a


title: TC.CD3.early#2


title: Embryonic Lrrc10-/-, rep3

city: Madison

first: Matt

last: Brody

state: WI

address: 1300 University Ave.

institute: UW-Madison

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis. 17hrs at 65 deg Celsius, Surehyb chamber.

scan_protocol: Agilent Technologies Scanner G2505B, US22502567 5um 16bit.

data_processing: Agilent Feature Extraction Software version 9.5 for background subtraction - localbackground and normalization Linear LOWESS. Goodspots were designated as those features with both channels r and g where controltype=0, issaturated=0, isfeatnonunifol=0, isfeatpopnol=0, iswellabovebg=1 in 80% of arrays.

source_name: Lrrc10 KO heart

label_protocol: Total RNA was amplified and labeled according to the manufacturer's instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent Low RNA Input Linear Amplification Kit, PLUS.

growth_protocol: Ad lib feeding and drinking. 12hours light:12hours dark.

extract_protocol: Polytron 10 seconds and processed with a Qiagen RNeasy Mini kit.

treatment_protocol: Sacrificed and dissected at E15.5, and placed in Trizol, flash frozen and stored at -80C.

tag: strain/background

tag: genotype

value: heart

tag: sample composition

value: pooled heart RNA from two Lrrc10 KO (Lrrc10-/-) mice

source_name: Wildtype heart reference

tag: time of sacrifice

value: two months

value: pooled heart RNA from two wildtype (Lrrc10+/+) mice


title: PBMC_post.challenge_PPD_unvaccinated.controller_rep1


title: TC.CD3.early#1

value: 8 weeks

value: FACSAria


title: Embryonic Lrrc10-/-, rep2


title: 5388438026_H

city: Woolloongabba

first: Gethin

last: Thomas

state: QLD

address: Princess Alexandra Hospital

country: Australia

institute: University of Queensland Diamantina Institute

description: RNA extracted from flash frozen mice spines using Trizol

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data were processed using the Illumina BeadStudio software then the processed data were assessed for quality control and normalised in Lumi. Analysis of gene expression patterns was performed in BRB-ArrayTools. For quality control scanned images of the arrays were visually inspected for artefacts in Illumina BeadStudio followed by the graphical analysis of density plots in Lumi.  The microarray data were transformed by variance stabilization transformation (VST) then normalized by robust spline normalization (RSN). Post-normalization quality control was carried out using density plots to ensure all samples had similar distribution and variance. To reduce background noise in the data analysis all probes that were not expressed in any of the samples, i.e. whose intensity was below background in all samples, were excluded from the analysis. This did not exclude probes for genes whose expression was either “switched-on” or “switched-off”.

source_name: Dissected spine

label_protocol: 500ng of RNA was used in the Illumina TotalPrep cRNA Amplification Kit according to the standard protocol. Samples were hybridised to Mouse Ref-8 Expression BeadChips.

extract_protocol:
Spines were dissected from 4 control and 4 PGISp-affected mice and flash frozen in liquid nitrogen. For the PGISp mice, only mice showing severe peripheral arthritis were selected.
RNA was extracted from the spines using Trizol as per the manufacturers protocol with the extra spin step included as recommended for bone samples then cleaned up using RNAeasy columns.

tag: strain

value: BALB/c

tag: genotype/variation

value: IL4 knockout

tag: treatment

value: none (Control)


title: 5388438026_F


title: 5388438026_G

value: proteoglycan-induced spondylitis


title: TC.CD3.early#3

tag: strain background

tag: age

tag: gender


title: PBMC_post.challenge_unstimulated_unvaccinated.controller_rep1


title: Embryonic Lrrc10-/-, rep1

tag: tissue


title: PBMC_naive_PPD_unvaccinated.controller_rep1a

source_name: PBMCs, PPD-stimulated, naive

value: PPD

value: Naive


title: PBMC_naive_unstimulated_unvaccinated.controller_rep1b

description: Gene expression in unstimulated PBMCs isolated from a naive animal


title: PBMC_naive_PPD_unvaccinated.controller_rep1b

description: Gene expression in PPD-stimulated PBMCs isolated from a naive animal


title: TC.CD3-28.late#2

tag: exclusion markers

value: CD11b, CD11c, B220, CD8, GFP

tag: cell type

value: conventional T cells (Tconv)

tag: phenotype markers


title: 5388438026_D


title: TC.CD3-28.late#1

tag: separation method


title: TC.CD3-28.early#3


title: 5388438026_E


title: 5388438026_C


title: MMSET DeltSET overexpression in HME Cell Replicate 2

city: Atlanta

first: Meng

last: Zhao

state: GA

address: 1518 Clifton Rd, #369

department: BIOS

institute: Emory University

description: Sample 6

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Homo sapiens

source_name: MMSET DeltSET overexpression_HME

label_protocol: 1 µg of total RNA were primed with 2 µl of 100 µM T7-oligo-dT DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 400 U MMLV RTase (Agilent), and labeled with T7 polymerase with 100 µM each of dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

growth_protocol: Cells were grown in MEBM with supplements (Lonza) and Zeocin antibiotic for selection.

extract_protocol: Total RNA was isolated using Trizol and an miRNeasy Kit (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Cells were plated in 100mM plates at a desired concentration and transduced with lacZ control or MMSET or MMSET DeltaSET lentivirus. Cells were selected in Zeocin selection media to generate stable lines.

tag: cell line

value: HME

value: benign breast cells

value: MMSET DeltSET overexpression

tag: transduced with

value: MMSET DeltaSET lentivirus

source_name: Total RNA from LacZ control cells

value: LacZ vector control

tag: tranduced with

value: lacZ control lentivirus


title: TC.BTLA.late#3

value: male

value: spleen, lymph node


title: TC.CD3-28.early#1

value: 8 weeks

value: FACSAria


title: TC.CD3-28.late#3


title: TC.BTLA.late#2


title: TC.CD3-28.early#2


title: 5388438026_B

value: BALB/c

value: IL4 knockout


title: MMSET overexpression in H16N2 Cell Replicate 2

description: Sample 2

source_name: MMSET overexpression_H16N2

value: MMSET overexpression

value: MMSET lentivirus


title: MMSET DeltSET overexpression in HME Cell Replicate 1

description: Sample 5


title: MMSET overexpression in HME Cell Replicate 2

description: Sample 4

source_name: MMSET overexpression_HME


title: 5388438026_A

value: proteoglycan-induced spondylitis


title: PBMC_naive_unstimulated_unvaccinated.controller_rep1a

source_name: PBMCs, unstimulated, naive

tag: experimental group

value: Unvaccinated Controller

tag: animal name

tag: cell stimulation

tag: immune status

value: Naive


title: MMSET overexpression in HME Cell Replicate 1

description: Sample 3

value: HME

tag: genotype/variation


title: TC.BTLA.late#1

value: CD11b, CD11c, B220, CD8, GFP

value: conventional T cells (Tconv)


title: MMSET overexpression in H16N2 Cell Replicate 1

description: Sample 1

value: benign breast cells


title: HAC1 complete in Cy3

description:
Simple annotation: mRNA vs Total RNA Comparison, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81628.gif
is_reverse: yes

source_name: HAC1 mRNA

tag: channel 1

value: HAC1 mRNA

source_name: Total mRNA

tag: channel 2

value: Total mRNA


title: HAC1complete sequence in Cy5 (2)

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81026.gif
is_reverse: no

value: Total yeast mRNA

value: HAC1 mRNA (complete sequence)


title: TC.BTLA.early#3

tag: strain background

tag: age

value: 8 weeks

value: male

value: spleen, lymph node


title: HAC1 complete in Cy3(2)

description:
Simple annotation: mRNA vs Total RNA Comparison, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82620.gif
is_reverse: yes


title: Synthecon (4849520026_G)

city: Austin

first: Irina

last: Fernandez

state: TX

address: 107 West Dean Keeton st

department: Biomedical Engineering

institute: University of Texas at Austin

description: biological_replicates:  Synthecon replicate 8

hyb_protocol: Labeled cRNA was used to probe MouseRef-8 v2 Expression beadchips using Standard Illumina hybridization protocol

data_processing:
Raw data were extracted using an Illumina BeadArray Reader
Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction.
The background subtraction, expression summary, normalization, and log base 2 transformation of gene signals were carried out using Quantile Normalization

source_name: embryonic stem cells

label_protocol: Total RNA (100ng per sample) was used for preparation of biotin-labeled targets (cRNA) using  a MessageAmpTM II-based protocol (Ambion,Inc Austin TX) and one round of amplification

extract_protocol: RNA was extracted  with QIAGEN RNeasy mini kit  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser by Asuragen Inc.

tag: strain

value: day 7 differentiation

value: embryonic stem cell


title: Synthecon (4849520026_E)

description: biological_replicates:  Synthecon replicate 6


title: HAC1 complete sequence in Cy5 (3)

description:
Simple annotation: mRNA vs Total RNA Comparison, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81625.gif
is_reverse: no

source_name: HAC1 complete sequence mRNA

value: HAC1 complete sequence mRNA


title: HAC1 complete in Cy3 (3)

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82622.gif
is_reverse: yes


title: TC.BTLA.early#2

tag: gender

tag: tissue

tag: exclusion markers

value: FACSAria


title: TC.BTLA.early#1

tag: cell type

tag: phenotype markers

tag: separation method


title: Synthecon (4849520026_F)

description: biological_replicates:  Synthecon replicate 7


title: TC.0hr#5


title: Synthecon (4849520026_C)

description: biological_replicates:  Synthecon replicate 4


title: Static (4849520026_A)

description: biological_replicates:  Static replicate 3


title: Synthecon (4849520026_D)

description: biological_replicates:  Synthecon replicate 5


title: TC.0hr#4


title: Synthecon (4849520026_B)

description: biological_replicates:  Synthecon replicate 3


title: antiHA_Mock_2

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95188.gif
GeneticModification: ADA5 control

source_name: Total RNA from lysate after IP

value: Total RNA from lysate after IP

source_name: IPed RNA

value: IPed RNA

tag: simple annotation

tag: image

tag: geneticmodification

value: ADA5 control


title: TC.0hr#3

value: CD11b, CD11c, B220, CD8, GFP


title: TC.ICOS.early#1

value: conventional T cells (Tconv)


title: Synthecon (5091212022_H)

description: biological_replicates:  Synthecon replicate 2


title: BM (5091212022_F)

description: biological_replicates:  bone marrow replicate 3

source_name: bone marrow cells

value: 10 weeks old mice

value: bone marrow


title: BM (5091212022_E)

description: biological_replicates:  bone marrow replicate 2


title: Spinner (5091212022_A)

description: biological_replicates:  Spinner replicate 3


title: FL (5091212022_B)

description: biological_replicates:  fetal liver replicate 1

source_name: fetal liver cells

value: E15 embryos

value: fetal liver


title: FL (5091212022_C)

description: biological_replicates:  fetal liver replicate 2


title: HA-Ada5_1

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95184.gif
GeneticModification: ADA5


title: Synthecon (5091212022_G)

description: biological_replicates:  Synthecon replicate 1


title: antiHA_Mock_1

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95187.gif
GeneticModification: ADA5 control


title: CD15+ from mice 7

city: San Diego

first: Lei

last: Bao

state: CA

address: 3855 Health Sciences Drive

department: Cancer Center

institute: UCSD

hyb_protocol: RNA was hybridized to Affymetrix Mouse Genome 1.0 ST  arrays using affymetryx instruction manual. The hybridization cocktail containing fragmented and labeled RNA, hybridization mix and hybridization controls were heated at  95°C for 5 min, and was allowed to hybridize for 16 hrs.

scan_protocol: Scanning was performed on Affymetryx gene chip scanner 7G

data_processing: bioconductor/RMA

source_name: CD15+ cancer stem like cells

label_protocol: Invitro  transcription was performed to label RNA, using IVT mastermix according to Affimetryx instructions.This reaction mixture was incubated for 16 hrs at 40°C using the program for IVT.

extract_protocol: SmoA1 Tg MB tumor cells were sorted into CD15+ and CD15- populations, and RNA was extracted using RNeasy Kit (Qiagen, Germantown, MD). RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Samples showing RNA integrity (RIN) greater than 8.0 were used for microarray analysis.

value: FACS sorted CD15+ CSCs isolated from cerebellum

value: Smo A1 Tg medulloblastoma mouse model


title: FL (5091212022_D)

description: biological_replicates:  fetal liver replicate 3


title: Static (5091212009_H)

description: biological_replicates:  Static replicate 2


title: CD15+ from mice 5


title: CD15- from mice 5

value: FACS sorted CD15- CSCs isolated from cerebellum


title: TAP_Mock_2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91967.gif
GeneticModification: DGI1 control

source_name: Reference

value: Reference

source_name: IP

value: IP

value: DGI1 control


title: Gdi1_2

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91963.gif
GeneticModification: DGI1


title: HA-Ada5_3

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95186.gif
GeneticModification: ADA5


title: Cy3:12C7A X Cy5:013C7A

city: Rotorua

first: Joseph

middle: Gogo

last: Dubouzet

address: 49 Sala St

department: Biotransformation

country: New Zealand

institute: Scion

description: biological replicate 2 of 2

hyb_protocol: After labelling, unincorporated dye was removed using a Qiagen RNeasy mini spin column. Purified samples were assessed for yield and specific activity using a NanoDrop ND-1000 UV-VIS spectrophotometer. Samples that gave yields of >0.8 µg cRNA and specific activity (Concentration of Cy3/ Concentration of cRNA x1000) >10 were used for arrays. Labelled samples were hybridized to arrays at 65°C for 17 hours at 10 rpm in an Agilent G2545A Hybridization oven using 2x GEx Agilent hybridization buffer. Slides were washed using Agilent wash buffers.

scan_protocol: Array scanning and feature extraction was performed using the Agilent G2565CA Microarray Scanner as outlined in the Agilent protocol for Two-colour Microarray-Based Gene Expression Analysis, Version 6.5, May 2010

data_processing: Data were transformed into log (base 2), followed by Loess normalization with no background correction. Data were imported into R using the limma package (Smyth, 2005). Statistical analysis of data was performed using the linear models approach implemented in limma, using the M values for each array as the dependent data. The empirical Bayes shrinkage-based approach to per-probe variance estimation was used to generate a moderated t-statistic for each probe. This statistic was then used to determine the statistical significance of the differences for each gene at each time/tissue combination (Smyth, 2005). P-values were calculated for each comparison, and adjusted to control for the False Discovery Rate using the Benjamin-Hochberg method (Benjamini and Hochberg, 1995).

organism: Pinus radiata

source_name: developing xylem

label_protocol: Paired hybridization for each microarray was between treatment versus control of each tissue from the same experimental duration, e.g., bark, 0 mg Ehephon, 1 WAT versus bark, 1 mg Ethephon, 1 WAT, and so forth (see sample description). Total RNA of 50-100 ng was used for labelling.  Samples were labelled with Cy3 or Cy5 using the Agilent Low input Quick Amp labelling kit (see above sample description

growth_protocol: One-year-old rooted clonal saplings of a single genotype were purchased from ArborGen Australasia (Whakatane, New Zealand) for this experiment. These were placed in 500 ml pots containing standard potting mix that were then arrayed on an unroofed concrete pavement for another year prior to their use in this research.

extract_protocol: RNA was obtained from bark, cambial layer and xylem. Bark refers to the outermost layer of tissues of the stem immediately above the mucilaginous cambial layer. The cambial region (aka “xylem scrapings” or “developing xylem”) includes the undifferentiated cambium layer, expanding cells and a few early secondary walls classifiable as xylem but no phloem (Cato et al., 2006). The xylem refers to the woody fibrous tissue left after scraping off the cambial region. Samples from the 0 and 1 mg treatments were processed for RNA extraction. Three replicates consisting of 5 saplings per replicate were destructively sampled 1 week after Ethephon treatment and an identical batch was sampled 7 weeks later. After wiping off the residual lanolin from the bark surface with tissue paper, the bark was cut and peeled off, the cambial region was scraped off with the blunt edge of a box cutter, and the remaining woody xylem was cut off from the rest of the plant. The respective tissues were wrapped in water-proof paper, flash-frozen in liquid nitrogen and stored at -80oC prior to RNA extraction. Total RNA was extracted using Invitrogen’s Concert reagent (xylem) whilst RNA extracted from bark was obtained using Invitrogen’s Concert reagent followed by purification with Agilent’s Plant RNA Isolation kit. RNA from the cambial region was extracted using Agilent’s Plant RNA Isolation kit.

treatment_protocol: Ethrel (48% Ethephon or 2-Chloroethylphosphonic acid, Bayer Crop Science, NZ) releases ethylene in plant tissues. Lanolin pastes containing 0, 1, 5 and 25 mg Ethephon were dispensed onto 3x6 cm aluminium foil sheets. One paste-laden sheet was wrapped around the basal stem of each experimental sapling, 5-7.5 cm from the soil level. The 1 mg/plant dosage corresponded to the 1% in lanolin dose used in P. halepensis (Yamamoto and Kozlowski, 1987).

value: developing xylem

tag: mg ethephon

tag: weeks after treatment


title: antiHA_Mock_3

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95189.gif
GeneticModification: ADA5 control


title: CD15+ from mice 6

tag: genotype/variation


title: CD15- from mice 6


title: CD15- from mice 4


title: BM (5091212009_G)

description: biological_replicates:  bone marrow replicate 1


title: Gdi1_1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91962.gif
GeneticModification: DGI1

tag: channel 1


title: HA-Ada5_2

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95185.gif
GeneticModification: ADA5

tag: channel 2


title: Cy3:11B7CA X Cy5:012B7CA

description: biological replicate 2 of 2

source_name: bark

value: bark


title: Spinner (5091212009_F)

description: biological_replicates:  Spinner replicate 2

value: day 7 differentiation

value: embryonic stem cell


title: TAP_Mock_1

description:
Simple annotation: mRNA vs Total RNA Comparison, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2011-01/91966.gif
GeneticModification: DGI1 control


title: Spinner (5091212009_E)

description: biological_replicates:  Spinner replicate 1


title: CD15- from mice 2


title: Cy3:11X7C1 X Cy5:023X7C

description: biological replicate 2 of 2

source_name: xylem

value: xylem


title: Cy3:12X7C X Cy5:023X7C

description: biological replicate 1 of 2


title: CD15+ from mice 2


title: Sec12-DamP_BY4741#1

description:
Simple annotation: Drug_treatment, DTT
Image: http://smd.stanford.edu/MicroArray/gifs/2010-12/91555.gif

source_name: Sec12-DamP 0min

value: Sec12-DamP 0min

tag: genotype

source_name: WT untreated (0min)

value: WT untreated (0min)


title: undiff (5091212009_C)

description: biological_replicates:  undifferentiated replicate 3

tag: age

value: day 0 differentiation


title: Cy3:13B7CA X Cy5:012B7CA

description: biological replicate 1 of 2


title: Static (5091212009_D)

description: biological_replicates:  Static replicate 1

tag: strain


title: undiff (5091212009_B)

description: biological_replicates:  undifferentiated replicate 2


title: Cy3:11X56C X Cy5:013X56C

description: biological replicate 1 of 2


title: CD15+ from mice 4


title: CD15- from mice 3


title: CD15+ from mice 3


title: Cy3:13X56C X Cy5:013X56C

description: biological replicate 2 of 2


title: CD15+ from mice 1


title: Cy3:013B56CA X Cy5:13B56CA

description: biological replicate 2 of 2


title: Sec12-DamP_BY4741#2

description:
Simple annotation: Drug_treatment, DTT
Image: http://smd.stanford.edu/MicroArray/gifs/2010-12/91556.gif


title: Cy3:023C56A X Cy5:12C56A

description: biological replicate 2 of 2


title: Cy3:013B56CA X Cy5:12B56CA

description: biological replicate 1 of 2


title: Ypt1-DamP_BY4741 #1

description:
Simple annotation: Drug_treatment, DTT
Image: http://smd.stanford.edu/MicroArray/gifs/2010-12/91554.gif

source_name: Ypt1-DamP 0min

value: Ypt1-DamP 0min


title: wt-matA-htp152-b

status: Public on Nov 14 2012

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

description: Strains were streaked from -80C stocks onto plates and grown for 3-5 days depending on growth rate. Liquid cultures were inoculated with independent colonies and grown overnight in Synthetic Complete (SC) medium: 2gr/l Drop out mix Complete and 6.71gr/l Yeast Nitrogen Base without AA, Carbohydrate and w/AS (YNB) from US Biologicals (Swampscott, USA) with 2percent   D-glucose. Overnight cultures were diluted to an OD600 of 0.15 in 1.5 ml fresh medium and grown at 30C in a 24 well plate in a Tecan Infinite F200 under continuous shaking. Growth curves were made for the mutant cultures (two cultures from two isolates) as well as for two wildtype (wt) inoculates, grown in parallel. Mutant and wt cells were harvested by centrifugation (6100 rpm, 3 min) at mid-log phase at an OD600 of 0.6, and pellets were immediately frozen in liquid nitrogen after removal of supernatant. S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2percent   D-glucose)under agitation (230rpm), at 30C. The cells were collected at midlog.

hyb_protocol: Hybridization protocol v2.2

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

molecule: nuclear RNA

source_name: wt-matA

label_protocol: robot amplification and labeling v1.0

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.0

extract_protocol: yeast HTP RNA isolation for robot v2.0

value: wt-matA

source_name: refpool

value: refpool


title: undiff (5091212009_A)

description: biological_replicates:  undifferentiated replicate 1

source_name: embryonic stem cells


title: wt-matA-htp117-b

hyb_protocol: Tecan HS4800 hybridization

growth_protocol: yeast-deleteome[grow]

extract_protocol: yeast RNA isolation for robotic amplification v1.0


title: wt-matA-htp92-b


title: DamP/WT #2

description:
Simple annotation: Drug_treatment, DTT
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91374.gif

source_name: BY4741 strain RNA

value: BY4741 strain RNA

source_name: Ypt1-DamP strain

value: Ypt1-DamP strain


title: wt-matA-htp115-b


title: wt-matA-htp116-b


title: Cy3:13C7A X Cy5:013C7A

description: biological replicate 1 of 2


title: Cy3:023C56A X Cy5:13C56A

description: biological replicate 1 of 2


title: wt-matA-htp152-a


title: wt-matA-htp114-d


title: wt-matA-THM019-b


title: wt_matA-htp92-a


title: wt-matA-htp114-a


title: wt-matA-htp117-a


title: wt-matA-htp114-c


title: wt-matA-htp115-a


title: wt-matA-htp114-b


title: wt-matA-tl002-2-b

label_protocol: aminoallyl labeling v2.1.1


title: wt-matA-THM019-a


title: wt-matA-htp116-a


title: wt-matA-sv071-b


title: wt-HTP154-matA-a


title: wt-matA-1-a.1


title: wt-matA-1-b.1


title: wt-HTP154-matA-b


title: wt-matA-nbr022-b


title: wt-matA-THM012-a


title: wt-matA-THM022-a


title: wt-matA-tl002-2-a


title: wt-matA-THM012-b


title: wt-matA-sv071-a


title: wt-jb015-k3-a

value: wt


title: wt-jb015-k3-b


title: wt-jb015-k2-b


title: wt-jb-15-k1-d


title: wt-jb015-k1-b


title: wt-jb015-k1-c


title: wt-jb015-k2-a


title: wt-htp97-b


title: wt-htp99-b


title: wt-htp95-d


title: wt-htp99-a


title: wt-jb015-k1-a


title: wt-htp94-d


title: wt-htp95-b


title: wt-htp94-b


title: wt-htp95-c


title: wt-htp93-b


title: wt-htp93-a


title: wt-htp91-b


title: wt-htp94-a


title: wt-htp88-a


title: wt-htp90-b


title: wt-htp85-b


title: wt-htp88-b


title: wt-htp95-a


title: wt-htp86-a


title: wt-htp86-b


title: wt-htp91-a


title: wt-htp89-a


title: wt-htp90-a


title: wt-htp85-a


title: wt-htp84-b


title: wt-htp83-b


title: wt-htp82-b


title: wt-htp81-b


title: wt-htp82-a


title: wt-htp84-a


title: wt-htp81-a


title: wt-htp80-a


title: wt-htp76-a


title: wt-htp75-a


title: wt-htp74-c


title: wt-htp75-b


title: wt-htp77-b


title: wt-htp72-c


title: wt-htp72-b


title: wt-htp79-b


title: wt-htp67-a


title: wt-htp79-a


title: wt-htp74-b


title: wt-htp76-b


title: wt-htp66-a


title: wt-htp66-b


title: wt-htp60-1-a


title: wt-htp59-b


title: wt-htp58-a


title: wt-htp57-b


title: wt-htp62-a


title: wt-htp62-b


title: wt-htp56-b


title: wt-htp60-1-b


title: wt-htp56-a


title: wt-htp53-b


title: wt-htp57-a


title: wt-htp53-c


title: wt-htp58-b


title: wt-htp55-a


title: wt-htp53-a


title: wt-htp50-b


title: wt-htp54-b


title: wt-htp54-d


title: wt-htp50-a


title: wt-htp44-a


title: wt-htp54-a


title: wt-htp67-b


title: wt-htp49-b


title: wt-htp52-b


title: wt-htp42-a


title: wt-htp42-b


title: wt-htp43-b


title: wt-htp49-a


title: wt-htp43-a


title: wt-htp40-1-a


title: wt-htp41-b


title: wt-htp51-b


title: wt-htp41-a


title: wt-htp44-b


title: wt-htp52-a


title: wt-htp38-b


title: wt-htp39-b


title: wt-htp38-a


title: wt-htp34-a


title: wt-htp32-c


title: wt-htp51-a


title: wt-htp29-a


title: wt-htp36-1-a


title: wt-htp31-a


title: wt-htp33-a


title: wt-htp31-b


title: wt-htp34-b


title: wt-htp30-b


title: wt-htp37-1-b


title: wt-htp33-b


title: wt-htp29-b


title: wt-htp27-d


title: wt-htp32-a


title: wt-htp28-a


title: wt-htp28-d


title: wt-htp30-a


title: wt-htp36-b


title: wt-htp26-a


title: wt-htp27-a


title: wt-htp28-b


title: wt-htp26-b


title: wt-htp25-b


title: wt-htp25-a


title: wt-htp32-b


title: wt-htp24-b


title: wt-htp24-a


title: wt-htp20-a


title: wt-htp23-a


title: wt-htp21-a


title: wt-htp23-b


title: wt-htp18-d


title: wt-htp22-a


title: wt-htp21-b


title: wt-htp19-b


title: wt-htp20-b


title: wt-htp18-a


title: wt-htp19-a


title: wt-htp22-b


title: wt-htp17-a


title: wt-htp12-b


title: wt-htp14-b


title: wt-htp16-b


title: wt-htp27-b


title: wt-htp18-b


title: wt-htp12-c


title: wt-htp110-b


title: wt-htp13-a


title: wt-htp16-a


title: wt-htp110-a


title: wt-htp11-a


title: wt-htp11-d


title: wt-htp12-a


title: wt-htp113-a


title: wt-htp111-a


title: wt-htp103-b


title: wt-htp112-a


title: wt-htp105


title: wt-htp104-b


title: wt-htp107-b


title: wt-htp109-a


title: wt-htp108-a


title: wt-htp106-b


title: wt-htp14-a


title: wt-htp102-d


title: wt-htp09-b


title: wt-htp11-b


title: wt-htp106-a


title: wt-htp107-a


title: wt-htp100-a


title: wt-htp104-a


title: wt-htp105-a


title: wt-htp100-b


title: wt-htp09-a


title: wt-htp102-c


title: wt-htp103-a


title: wt-htp101-a


title: wt-htp08-c


title: wt-htp08-b


title: wt-htp05-a


title: wt-htp06-a


title: wt-htp06-b


title: wt-htp05-b


title: wt-htp-d1-16-b


title: wt-htp08-d


title: wt-htp-35-b


title: wt-htp08-a


title: wt-htp-01-b


title: wt-hpr1-b


title: wt-htp-03-b


title: wt-htp-13-b


title: wt-JB013-1-b


title: wt-htp-d1-10-a


title: wt-htp-02-a


title: wt-JB013-1-a


title: wt-tls004-b

scan_protocol: standard Agilent protocol Imagene feature extraction

source_name: wt

extract_protocol: yeast mRNA extraction v1.3


title: wt-htp-02-b


title: wt-tls014-b


title: wt-tls009-a


title: wt-htp-1-c


title: wt-hpr1-a


title: wt-htp05-d


title: wt-htp-01-a


title: wt-htp-35-a


title: wt-tm011-a


title: wt-tls042-b


title: wt-tl047-b


title: wt-tl045-b


title: wt-tl043-b


title: wt-tl030-b


title: wt-tl041-a


title: wt-tl029-a


title: wt-tl035-a


title: wt-tl040-a


title: wt-tl045-a


title: wt-tl041-b


title: wt-tl040-b


title: wt-tl021-a


title: wt-tl035-b


title: wt-tl033-b


title: wt-tl025-b


title: wt-tl022-a


title: wt-tl027-b


title: wt-tl030-a


title: wt-tl026-b


title: wt-tl034-a


title: wt-tl024-b


title: wt-tl044-a


title: wt-tl023-b


title: wt-tl028-a


title: wt-tl018-b


title: wt-tl025-a


title: wt-tl019-b


title: wt-tl019-a


title: wt-tl022-b


title: wt-tl013-a


title: wt-tl008-b


title: wt-tl005-a


title: wt-tl012-a


title: wt-thm010-b


title: wt-tl002-2-b


title: wt-thm005-b


title: wt-tl011-a


title: wt-nbr043-a


title: wt-sv065-a


title: wt-thm007-b


title: wt-nbr025-a


title: wt-nbr023-b


title: wt-thm006-a


title: wt-sv066-a


title: wt-thm004-a


title: wt-thm007-a


title: wt-thm006-b


title: wt-nbr043-b


title: wt-nbr022-a


title: wt-tl012-b


title: wt-sv065-b


title: wt-tl006-b


title: GM0637+ATM-IN at T'4

city: Houston

first: Guohui

last: Wan

address: 7777 Knight Road

department: Cancer Biology

institute: The University of Texas M.D. Anderson Cancer Center

description:
F635 Median, indirect labeling of aRNA
F532 Median, direct labeling of aRNA
635/532 Ratio formation
Gene expression data from MCFs after DNA damage

hyb_protocol: Labelled miRNAs were hybridized by miRNA OneArray™ Hybridization (OneArray) according to the manufacturer's instruction.

scan_protocol: MiRNAs-Chips were scanned using the Molecular Devixes™ GenePix™ Scanner.

data_processing: The data were analyzed with Array Studio Analysis Software by Rosetta Resolver.

label: Cy5 and Cy3

source_name: GM0637 Fibroblast

label_protocol: MicroRNA were prepared and labelled according to Kreatech ULS™ miRNA Labeling Kit (Standard, Phalanxbiotech) from 4 ug total RNA.

growth_protocol: The GM0637 cells were plated on multiple 100-mm dishes for each line in 10% fetal calf serum and Dulbecco's modified Eagle's medium (DMEM) in 37℃ with 5% CO2.

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

treatment_protocol: GM0637 cells were pretreated with ATM inhibitor (ATM-IN) before treatment with a radiomimetic drug, neocarzinostatin (NCS) that generates DSBs. Cells were harvested at varying time points (0-4 h).

value: Human Fibroblast

value: ATM+

tag: treatment

value: ATM inhibitor + neocarzinostatin

tag: time

value: 4 h

tag: cell line


title: wt-nbr021-a


title: wt-nbr019-1-b


title: GM0637+ATM-IN at T'0

tag: cell type

value: 0 h


title: wt-tl007-a


title: wt-nbr023-a


title: wt-nbr019-1-a


title: GM0637 at T0

value: neocarzinostatin


title: GM0637 at T4


title: wt-tl011-b


title: wt-nbr004-b


title: wt-nbr003-b


title: wt-nbr004-a


title: wt-mt004-b


title: wt-mt004-a


title: wt-mmk030-b


title: wt-mmk031-a


title: wt-nbr003-a


title: wt-mmk029-a


title: wt-mt006-b


title: wt-tl031-b


title: wt-mt007-b


title: wt-mmk025-b


title: wt-mmk024-a


title: wt-mmk026-b


title: wt-mmk020-b


title: wt-mmk023-b


title: wt-mmk014-b


title: wt-mmk017-a


title: wt-mmk024-b


title: wt-mmk022-a


title: wt-mmk015-b


title: wt-mmk013-a


title: wt-mmk009-b


title: wt-mmk021-b


title: wt-mmk029-b


title: wt-mmk020-a


title: wt-mmk011-b


title: wt-mmk018-b


title: wt-mmk012-b


title: wt-mmk019-b


title: wt-mmk002-a


title: wt-mmk011-a


title: wt-mmk007-a


title: wt-mmk007-b


title: wt-mmk006-a


title: wt-mbr002-b


title: wt-lpa021-a


title: wt-jb005-a


title: wt-lpa018-b


title: wt-lpa008_1-a


title: wt-lpa008_1-b


title: wt-lpa021-b


title: wt-gam005-a


title: wt-gam003-a


title: wt-gam001-b


title: wt-jb001-a


title: Slide25 4

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

description: Array 8

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: PowerScanner with 2 lasers in auto-gain configuration was used to extract the signal from cye3 and cye 5 labbeled probed for each arrays.

data_processing:
Data were processed by ArrayPro to mesure the intensity of scanned images. Using FlexArray, Intensities were corrected, normalized (Loess) then compared using limma statistical test between BSO and CTL samples.
VALUEs below represent normalized log2 (test/control) ratios.

organism: Bos taurus

source_name: blastocysts, Control-Oxid

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries. For more information, please refer to: Cagnone et al. 2012 Biol Reprod.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: In vitro culture used a 3 step synthetic oviductal fluid system. First step of culture spread from day 0 to day 3. 2nd step of culture spread from day 3 to day 5 in control SOF medium supplemented or not with 0.4 mM BSO. 3rd step of culture spread form days 5 to 7 in SOF (3) and was supplemented or not with BSO 0.01 mM (following the SOF2)

tag: sample type

value: in vitro

tag: developmental stage

value: pooled blastocysts

tag: time of embryo collection

value: 196 hpf (hours post-in-vitro fertilization)

tag: agent (compound added)

tag: number per pool

tag: in vitro production

value: Yes

source_name: blastocysts, BSO

value: BSO


title: wt-lpa013-b


title: wt-ea032-1-a


title: wt-ea019-1-b


title: Slide114 4

description: Array 2


title: Slide25 1

description: Array 5


title: wt-gam001-a


title: wt-ea019-1-a


title: wt-gam003-b


title: Slide115 4

description: Array 4


title: Slide25 3

description: Array 7


title: wt-SEL02-a


title: wt-tl018-a


title: wt-ea004-1-b


title: wt-SEL007-a


title: wt-dl003-b


title: Slide25 2

description: Array 6


title: Slide114 3

description: Array 1


title: Slide115 3

description: Array 3


title: wt-LPA022-b


title: Slide78 4

description: Array 6

data_processing:
Data were processed by ArrayPro to mesure the intensity of scanned images. Using FlexArray, Intensities were corrected, normalized (Loess) then compared using limma statistical test between AAPH and CTL samples.
VALUEs below represent normalized log2 (test/control) ratios.

treatment_protocol: In vitro culture used a 3 step synthetic oviductal fluid system. First step of culture spread from day 0 to day 3. 2nd step of culture spread from day 3 to day 5 in control SOF medium supplemented or not with 0.01 mM AAPH. 3rd step of culture spread form days 5 to 7 in SOF (3) and was supplemented or not with AAPH 0.01 mM (following the SOF2)

source_name: blastocysts, AAPH

value: AAPH


title: Slide78 3

description: Array 5


title: wt-MBr003-b


title: Slide79 4

description: Array 8


title: wt-EA040-a


title: Slide26 4

description: Array 4


title: Slide26 3

description: Array 3


title: Slide26 2

description: Array 2


title: wt-LPA020-a


title: Strain p17 isolated from murine tumor rep2

city: Braunschweig

first: Piotr

last: Bielecki

address: Inhoffenstr 7

department: Cell Biology

country: Germany

institute: Helmholtz Centre for Infection Research

description:
Ex vivo P. aeruginosa gene expression from murine tumor infection
p17 tumor 2
p17T34a_Pae_G1a.CEL
Re-analysis of Sample GSM567693

hyb_protocol: Standard affymetrix

scan_protocol: Standard affymetrix

data_processing: R version 2.6.0, Bioconductor 2.1. The quality of all chips was assessed by fitting a linear model to the probe level data using the function “fitPLM” from the “affyPLM” package. Subsequently, the distribution (boxplots) of RLE (Relative Log Expression) and NUSE (Normalised Unscaled Standard Errors) was manually analysed.

organism: Pseudomonas aeruginosa

source_name: Strain p17 isolated from murine tumor rep. 2

label_protocol: Biotin incorporation during amplification

growth_protocol: Burn wound and CF sputum - collection and stabilization in RNAprotect (QIAGEN), Murine tumore - 3 mice with tumor per strain infected intravenously with P. aeruginosa, Tumors extracted after 24h homogenized with stabilization of the RNA, Planktonic LB - early stationary phase - RNAprotect

extract_protocol: QIAGEN RNAmini, Ambion MicrobEnrich, Ambion MessageAMP

treatment_protocol: RNAprotect QIAGEN, burn wound sample collected with sterile swab which was deepen in RNAprotect, CF mucuse sample mixed with RNAprotect

tag: strain(s)

tag: initial p. aeruginosa isolate source

value: burn wound

tag: rna extracted from

value: murine tumor


title: Strain p17 isolated from murine tumor rep1

description:
Ex vivo P. aeruginosa gene expression from murine tumor infection
p17 tumor 1
p17T34_Pae_G1a.CEL
Re-analysis of Sample GSM567692

source_name: Strain p17 isolated from murine tumor rep. 1


title: Strain p11 isolated from murine tumor rep2

description:
Ex vivo P. aeruginosa gene expression from murine tumor infection
p11 tumor 2
HZI1559 p11_tumor_b.CEL
Re-analysis of Sample GSM567683

source_name: Strain p11 isolated from murine tumor rep. 2


title: Strain CFCZ isolated from CF patient sputum rep2

description:
Ex vivo P. aeruginosa gene expression from CF lung infection
CFCZ CF 2
HZI2392_Pae_G1a.CEL

source_name: Strain CFCZ isolated from CF patient sputum rep. 2

value: CFCZ

value: CF patient sputum


title: Strain p11 isolated from murine tumor rep1

description:
Ex vivo P. aeruginosa gene expression from murine tumor infection
p11 tumor 1
HZI1558 p11_tumor_a.CEL
Re-analysis of Sample GSM567682

source_name: Strain p11 isolated from murine tumor rep. 1


title: Strain p10 isolated from murine tumor rep1

description:
Ex vivo P. aeruginosa gene expression from murine tumor infection
p10 tumor 1
p10T23_Pae_G1a.CEL
Re-analysis of Sample GSM567672

source_name: Strain p10 isolated from murine tumor rep. 1


title: Strain p10 isolated from murine tumor rep2

description:
Ex vivo P. aeruginosa gene expression from murine tumor infection
p10 tumor 2
p10T23a_Pae_G1a.CEL
Re-analysis of Sample GSM567673

source_name: Strain p10 isolated from murine tumor rep. 2


title: Uninfected NT at 5 d.p.i., rep4

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

description:
MO-WT U4
Gene expression data from PBS-injected NT mice brain at 5 d.p.i.

hyb_protocol: Samples were hybridized using Herring sperm DNA, acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences); heat 65C for 5 min, 90C for 5 min, 45C for 5 min, centrifuge top speed for 5 min; hybridize 16 h at 45C, 60rpm; Fluidics script EukGE-WS2v4_450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G using GCOS (GeneChip Operating Software).

data_processing: Raw data were analyzed through Bioconductor package affy. The RMA method was used as the background-correction, normalization, and probe summarization method.

source_name: Uninfected NT mouse brain at 5 d.p.i.

label_protocol: 2ug RNA was enzymatically labeled using the BioArray High Yield RNA Transcript Labeling kit (Enzo).

growth_protocol: H-2(d) congenic C57BL/6 mice, with (TG) or without (NT) the human hsp70 transgene driven by the neuron-specific enolase promoter, were used in these studies.

extract_protocol: Total brain RNA was isolated from the right cerebral hemisphere, 5 or 10 d.p.i., using the RNeasy lipid tissue mini-kit (Qiagen).

treatment_protocol: Mice 42 h of age received an intracranial inoculation of 4x10(4) PFU Edmonston MeV (infected) or an equivalent volume of phosphate-buffered saline (uninfected) in the left cerebral hemisphere.

tag: strain/background

tag: genotype/variation

value: non-transgenic

tag: tissue

value: brain (right cerebral hemisphere)

value: 7 days

value: PBS control

tag: time post-infection


title: Uninfected NT at 5 d.p.i., rep2

description:
MO-WT U2
Gene expression data from PBS-injected NT mice brain at 5 d.p.i.

tag: age

tag: treatment


title: wt-LPA019-b

tag: strain

tag: genotype

value: wt

source_name: refpool

value: refpool


title: Pool of strains CF1, CF2, CF3, CF4 isolated from CF pateint sputum rep1

description:
Ex vivo P. aeruginosa gene expression from CF lung infection
CF1-4 CF 1
HZI1734_Pae_G1a.CEL

source_name: Pool of strains CF1, CF2, CF3, CF4 isolated from CF pateint sputum rep. 1

value: CF1, CF2, CF3, CF4


title: Pool of strains CF1, CF2, CF3, CF4 isolated from CF patient sputum rep2

description:
Ex vivo P. aeruginosa gene expression from CF lung infection
CF1-4 CF 2
HZI1738_Pae_G1a.CEL

source_name: Pool of strains CF1, CF2, CF3, CF4 isolated from CF patient sputum rep. 2


title: Uninfected NT at 5 d.p.i., rep3

description:
MO-WT U3
Gene expression data from PBS-injected NT mice brain at 5 d.p.i.


title: Uninfected TG at 5 d.p.i., rep3

description:
MO-Tg U3
Gene expression data from PBS-injected TG mice brain at 5 d.p.i.

source_name: Uninfected TG mouse brain at 5 d.p.i.

value: hsp70 transgenic


title: Strain CFCZ isolated from CF patient sputum rep1

description:
Ex vivo P. aeruginosa gene expression from CF lung infection
CFCZ CF 1
HZI2391_Pae_G1a.CEL

source_name: Strain CFCZ isolated from CF patient sputum rep. 1


title: Uninfected TG at 5 d.p.i., rep4

description:
MO-Tg U4
Gene expression data from PBS-injected TG mice brain at 5 d.p.i.


title: Strain p17 isolated from burn wound rep2

description:
Ex vivo P. aeruginosa gene expression from burn wound
p17 burn 2
HZI1545 p17_clinic_B.CEL
Re-analysis of Sample GSM567689

source_name: Strain p17 isolated from burn wound rep. 2


title: Strain p17 isolated from burn wound rep1

description:
Ex vivo P. aeruginosa gene expression from burn wound
p17 burn 1
HZI1544 p17_clinicA.CEL
Re-analysis of Sample GSM567688

source_name: Strain p17 isolated from burn wound rep. 1


title: Strain p11 isolated from burn wound rep2

description:
Ex vivo P. aeruginosa gene expression from burn wound
p11 burn 2
GBF0931 p11_clinical_b.CEL
Re-analysis of Sample GSM567679

source_name: Strain p11 isolated from burn wound rep. 2


title: Uninfected TG at 5 d.p.i., rep1

description:
MO-Tg U1
Gene expression data from PBS-injected TG mice brain at 5 d.p.i.


title: Infected NT 10 d.p.i., rep9

description:
MO-B10-WT 9
Gene expression data from MeV-infected NT mice brain at 10 d.p.i.

source_name: MeV-infected NT mouse brain at 10 d.p.i.

value: 12 days

value: measles virus (MeV)


title: Strain p11 isolated from burn wound rep1

description:
Ex vivo P. aeruginosa gene expression from burn wound
p11 burn 1
GBF0930 p11_clinical_a.CEL
Re-analysis of Sample GSM567678

source_name: Strain p11 isolated from burn wound rep. 1


title: Strain p10 isolated from burn wound rep2

description:
Ex vivo P. aeruginosa gene expression from burn wound
p10 burn 2
HZI1053 p10_clinical_b.CEL
Re-analysis of Sample GSM567669

source_name: Strain p10 isolated from burn wound rep. 2


title: Infected NT 10 d.p.i., rep8

description:
MO-B10-WT 8
Gene expression data from MeV-infected NT mice brain at 10 d.p.i.


title: Infected NT 10 d.p.i., rep7

description:
MO-B10-WT 7
Gene expression data from MeV-infected NT mice brain at 10 d.p.i.


title: wt-lpa018-c

description: Strains were streaked from -80C stocks onto plates and grown for 3-5 days depending on growth rate. Liquid cultures were inoculated with independent colonies and grown overnight in Synthetic Complete (SC) medium: 2gr/l Drop out mix Complete and 6.71gr/l Yeast Nitrogen Base without AA, Carbohydrate and w/AS (YNB) from US Biologicals (Swampscott, USA) with 2percent   D-glucose. Overnight cultures were diluted to an OD600 of 0.15 in 1.5 ml fresh medium and grown at 30C in a 24 well plate in a Tecan Infinite F200 under continuous shaking. Growth curves were made for the mutant cultures (two cultures from two isolates) as well as for two wildtype (wt) inoculates, grown in parallel. Mutant and wt cells were harvested by centrifugation (6100 rpm, 3 min) at mid-log phase at an OD600 of 0.6, and pellets were immediately frozen in liquid nitrogen after removal of supernatant. S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2percent   D-glucose)under agitation (230rpm), at 30C. The cells were collected at midlog.

source_name: wt


title: wt-lpa018-a


title: Strain CFCZ isolated from in vitro planktonic culture rep2

description:
In vitro P. aeruginosa gene expression from sessile growth
CFCZ LB 2
HZI2437_Pae_G1a.CEL

source_name: Strain CFCZ isolated from in vitro planktonic culture rep. 2

value: in vitro planktonic culture


title: Infected NT 5 d.p.i., rep4

description:
MO-B10-WT 4
Gene expression data from MeV-infected NT mice brain at 5 d.p.i.

source_name: MeV-infected NT mouse brain at 5 d.p.i.


title: Strain p10 isolated from burn wound rep1

description:
Ex vivo P. aeruginosa gene expression from burn wound
p10 burn 1
HZI1051 p10_clinical_a.CEL
Re-analysis of Sample GSM567668

source_name: Strain p10 isolated from burn wound rep. 1


title: Infected NT 10 d.p.i., rep5

description:
MO-B10-WT 5
Gene expression data from MeV-infected NT mice brain at 10 d.p.i.


title: Infected NT 10 d.p.i., rep6

description:
MO-B10-WT 6
Gene expression data from MeV-infected NT mice brain at 10 d.p.i.


title: Strain CFCZ isolated from in vitro planktonic culture rep1

description:
In vitro P. aeruginosa gene expression from sessile growth
CFCZ LB 1
HZI2436_Pae_G1a.CEL

source_name: Strain CFCZ isolated from in vitro planktonic culture rep. 1


title: wt-mmk002-b


title: Infected NT 5 d.p.i., rep2

description:
MO-B10-WT 2
Gene expression data from MeV-infected NT mice brain at 5 d.p.i.


title: Strain p17 isolated from in vitro planktonic culture rep2

description:
In vitro P. aeruginosa gene expression from sessile growth
p17 LB 2
HZI1549 p17_lb_b.CEL
Re-analysis of Sample GSM567687

source_name: Strain p17 isolated from in vitro planktonic culture rep. 2


title: Pool of strains CF1, CF2, CF3, CF4 isolated from in vitro planktonic culture rep1

description:
In vitro P. aeruginosa gene expression from sessile growth
CF1-4 LB 1
HZI1733_Pae_G1a.CEL

source_name: Pool of strains CF1, CF2, CF3, CF4 isolated from in vitro planktonic culturte rep. 1


title: Infected NT 5 d.p.i., rep1

description:
MO-B10-WT 1
Gene expression data from MeV-infected NT mice brain at 5 d.p.i.


title: Pool of strains CF1, CF2, CF3, CF4 isolated from in vitro planktonic culture rep2

description:
In vitro P. aeruginosa gene expression from sessile growth
CF1-4 LB 2
HZI1737_Pae_G1a.CEL

source_name: Pool of strains CF1, CF2, CF3, CF4 isolated from in vitro planktonic culturte rep. 2


title: Strain p17 isolated from in vitro planktonic culture rep1

description:
In vitro P. aeruginosa gene expression from sessile growth
p17 LB 1
HZI1548 p17_lb_a.CEL
Re-analysis of Sample GSM567686

source_name: Strain p17 isolated from in vitro planktonic culture rep. 1


title: Infected NT 5 d.p.i., rep3

description:
MO-B10-WT 3
Gene expression data from MeV-infected NT mice brain at 5 d.p.i.


title: Infected TG 10 d.p.i., rep9

description:
MO-B10-Tg 9
Gene expression data from MeV-infected TG mice brain at 10 d.p.i.

source_name: MeV-infected TG mouse brain at 10 d.p.i.


title: Strain p11 isolated from in vitro planktonic culture rep1

description:
In vitro P. aeruginosa gene expression from sessile growth
p11 LB 1
GBF0928 p11_LB_a.CEL
Re-analysis of Sample GSM567676

source_name: Strain p11 isolated from in vitro planktonic culture rep. 1


title: Infected TG 10 d.p.i., rep8

description:
MO-B10-Tg 8
Gene expression data from MeV-infected TG mice brain at 10 d.p.i.


title: Infected TG 10 d.p.i., rep7

description:
MO-B10-Tg 7
Gene expression data from MeV-infected TG mice brain at 10 d.p.i.


title: Infected TG 5 d.p.i., rep4

description:
MO-B10-Tg 4
Gene expression data from MeV-infected TG mice brain at 5 d.p.i.

source_name: MeV-infected TG mouse brain at 5 d.p.i.


title: Infected TG 10 d.p.i., rep6

description:
MO-B10-Tg 6
Gene expression data from MeV-infected TG mice brain at 10 d.p.i.


title: Infected TG 10 d.p.i., rep5

description:
MO-B10-Tg 5
Gene expression data from MeV-infected TG mice brain at 10 d.p.i.


title: Strain p11 isolated from in vitro planktonic culture rep2

description:
In vitro P. aeruginosa gene expression from sessile growth
p11 LB 2
GBF0929 p11_LB_b.CEL
Re-analysis of Sample GSM567677

source_name: Strain p11 isolated from in vitro planktonic culture rep. 2


title: Strain p10 isolated from in vitro planktonic culture rep2

description:
In vitro P. aeruginosa gene expression from sessile growth
p10 LB 2
HZI1052 p10_LB_b.CEL
Re-analysis of Sample GSM567667

source_name: Strain p10 isolated from in vitro planktonic culture rep. 2


title: Strain p10 isolated from in vitro planktonic culture rep1

description:
In vitro P. aeruginosa gene expression from sessile growth
p10 LB 1
HZI1050 p10_LB_a.CEL
Re-analysis of Sample GSM567666

source_name: Strain p10 isolated from in vitro planktonic culture rep. 1


title: Infected TG 5 d.p.i., rep1

description:
MO-B10-Tg 1
Gene expression data from MeV-infected TG mice brain at 5 d.p.i.


title: Untreated NK cells

first: Aditya

middle: A

last: Munshi

address: 44 Binney St

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

description:
JB5
Gene expression data from untreated NK cells.

hyb_protocol: Fragmented cRNA were hybridized to Affymetrix Human Genome U133 Plus 2.0 chips overnight at 45°C.

scan_protocol: The chips were scanned using an Affymetrix GeneChip scanner.

data_processing: dChip software was used for normalization and expression computation.

source_name: Untreated NK cells

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

growth_protocol: The cells were grown in RPMI media with 10% human AB serum.

extract_protocol: The RNA was extracted using RNeasy technology by Qiagen.

tag: cell type

value: NK cells


title: Hsp90 inhibitor-treated CD8 T cells

description:
JB4
Gene expression data from CD8 cells treated with Hsp90 inhibitor.

source_name: Hsp90 inhibitor-treated CD8 T cells

treatment_protocol: HSP90 inhibitor (Geldanamycin) treatment.

value: CD8 T cells

value: Hsp90 inhibitor


title: C/EBPa KO SLAM+KSLs on D21, rep3

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

hyb_protocol: Following fragmentation, 4.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using RMA in the bioconducter and normalized using cross correlation.  The trimmed mean target intensity of each array was set to 16.

source_name: C/EBPa KO SLAM+KSLs Day 21 after pIpC injection

label_protocol: Total RNA was amplified using the Ovation Pico WTA System V2 (Nugen), and biotinylated with the FL-Ovation Biotin Module Version 2 (Nugen), according to the supplied protocol

growth_protocol: All mice were kept in a sterile barrier facility approved by the Beth Israel Deaconess Medical Center Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was isolated using an RNeasy microkit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Adult HSCs using the markers (lin-sca1+ckit+CD150+CD48-) and fetal liver HSCs (lin-Mac-1 low  sca1+ckit+CD150+CD48-) using were collected after sorting and placed on ice in the Trizol solution (GibcoBRL).

value: sorted  HSCs (lin-sca1+ckit+CD150+CD48-)

value: Pu.1 knock-in (PU.1ki/ki)

tag: developmental stage

value: adult


title: C/EBPa KO SLAM+KSLs on D21, rep2


title: Hsp90 inhibitor-treated NK cells

description:
JB6
Gene expression data from NK cells treated with Hsp90 inhibitor.

source_name: Hsp90 inhibitor-treated NK cells


title: Control SLAM+KSLs on Day 21, rep4

source_name: Control SLAM+KSLs Day 21 after pIpC injection

value: wild type


title: Donor 7 p8

city: Enschede

first: Jeroen

last: Leijten

address: Drienerlolaan 5

institute: University of Twente

description:
Isolated RNA from human chondrocytes after 8 passages
Donor 7 p8

hyb_protocol: Hybridization was processed according to the standard Illumina protocol.

scan_protocol: Beadchips were scanned according to standard protocol using a Illumina iScan array scanner

data_processing:
The data were analyzed with Illumina's Genomestudio v. 2010,1 software with the default settings adviced by Illumina.
All sample probe profiles were exported from Genomestudio and imported into Genespring v11.

source_name: articular chondrocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol.

growth_protocol: human chondrocytes were seeded at 25,000 cells/cm2 after isolation and splitting. Cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Total RNA was isolated using NucleoSpin RNA II kit (Macherey-Nagel).

treatment_protocol: Cells were split, reseeded at 25,000 cells/cm2 and continued to be cultured in identical fresh culture medium up until passage 8

value: Dedifferentiating chondrocytes

tag: donor

tag: passage


title: Control SLAM+KSLs on Day 21, rep3


title: Hsp90 inhibitor-treated CD4 T cells

description:
JB2
Gene expression data from CD4 cells treated with Hsp90 inhibitor.

source_name: Hsp90 inhibitor-treated CD4 T cells

value: CD4 T cells


title: Untreated CD4 T cells

description:
JB1
Gene expression data from untreated CD4 cells.

source_name: Untreated CD4 T cells


title: C/EBPa KO SLAM+KSLs on D21, rep4


title: Donor 7 p4

description:
Isolated RNA from human chondrocytes after 4 passages
Donor 7 p4


title: Slide79 3

description: Array 7

source_name: blastocysts, AAPH

tag: sample type

value: in vitro

value: pooled blastocysts

tag: time of embryo collection

value: 196 hpf (hours post-in-vitro fertilization)

tag: agent (compound added)

value: AAPH

tag: number per pool

value: Yes

source_name: blastocysts, Control-Oxid


title: C/EBPa KO SLAM+KSLs on D7, rep2

source_name: C/EBPa KO SLAM+KSLs Day 7 after pIpC injection


title: Control SLAM+KSLs on Day 21, rep1


title: Donor 7 p6

description:
Isolated RNA from human chondrocytes after 6 passages
Donor 7 p6


title: wt-ea033-1-b

description: Strains were streaked from -80C stocks onto plates and grown for 3-5 days depending on growth rate. Liquid cultures were inoculated with independent colonies and grown overnight in Synthetic Complete (SC) medium: 2gr/l Drop out mix Complete and 6.71gr/l Yeast Nitrogen Base without AA, Carbohydrate and w/AS (YNB) from US Biologicals (Swampscott, USA) with 2percent   D-glucose. Overnight cultures were diluted to an OD600 of 0.15 in 1.5 ml fresh medium and grown at 30C in a 24 well plate in a Tecan Infinite F200 under continuous shaking. Growth curves were made for the mutant cultures (two cultures from two isolates) as well as for two wildtype (wt) inoculates, grown in parallel. Mutant and wt cells were harvested by centrifugation (6100 rpm, 3 min) at mid-log phase at an OD600 of 0.6, and pellets were immediately frozen in liquid nitrogen after removal of supernatant. S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2percent   D-glucose)under agitation (230rpm), at 30C. The cells were collected at midlog.

source_name: wt

value: wt

source_name: refpool

value: refpool


title: Donor 7 p0

description:
Isolated RNA from human chondrocytes after 0 passages
Donor 7 p0


title: C/EBPa KO SLAM+KSLs on D7, rep3


title: Infected TG 5 d.p.i., rep2

description:
MO-B10-Tg 2
Gene expression data from MeV-infected TG mice brain at 5 d.p.i.

source_name: MeV-infected TG mouse brain at 5 d.p.i.

value: hsp70 transgenic

value: brain (right cerebral hemisphere)

value: 7 days

value: measles virus (MeV)


title: Donor 7 p2

description:
Isolated RNA from human chondrocytes after 2 passages
Donor 7 p2


title: Control SLAM+KSLs on Day 21, rep2

value: sorted  HSCs (lin-sca1+ckit+CD150+CD48-)


title: Untreated CD8 T cells

description:
JB3
Gene expression data from untreated CD8 cells.

source_name: Untreated CD8 T cells

value: CD8 T cells


title: C/EBPa KO SLAM+KSLs on D21, rep1

value: Pu.1 knock-in (PU.1ki/ki)

value: adult


title: Slide26 1

description: Array 1

tag: in vitro production


title: Donor 5 p8

description:
Isolated RNA from human chondrocytes after 8 passages
Donor 5 p8

value: Dedifferentiating chondrocytes


title: Flag_P3

first: Ahmed

last: Sayadi

state: Singapore

address: 61 biopolis

institute: Genome Institute of Singapore

description:
AFGE1132-9.CEL
Reanalysis of GSM833402

hyb_protocol: GeneChip Hybridization Control Kit and GeneChip Hybridization, Wash, Stain Kit (Affymetrix) were used to hybidize Human Gene 1.0ST arrays.

scan_protocol: Standard Affymetrix Scan protocol was followed.

data_processing: The data were analyzed with Partek Genomics Suite version 6.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Flag plasmid, passage #9

label_protocol: Biotinylated ss-cDNA were prepared with GeneChip WT cDNA synthesis and Amplification Kit, GeneChip WT terminal Labeling Kit and GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: HeLa cells (ATCC, CCL-2) were grown at 37degres in 10%FBS DMEM. They were passaged every 2 days. P1, P2, P3, P4 in the sample names refer to the cell passage number.

extract_protocol: total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HeLa cells were seeded one day before transfection with pCMV-Flag-EVI1Δ324 plasmid or pCMV-Flag-Evi1 plasmid or pCMV-Flag plasmid. The cells were used for RNA extraction 24hr after transfection.

tag: cell line

value: HeLa


title: Flag-Evi1_P4

description:
AFGE1132-10.CEL
Reanalysis of GSM833399

source_name: Flag-Evi1 plasmid, passage #10


title: C/EBPa KO SLAM+KSLs on D7, rep1

tag: genotype/variation


title: Uninfected TG at 5 d.p.i., rep2

description:
MO-Tg U2
Gene expression data from PBS-injected TG mice brain at 5 d.p.i.

source_name: Uninfected TG mouse brain at 5 d.p.i.

tag: strain/background

tag: tissue

value: PBS control


title: Donor 5 p4

description:
Isolated RNA from human chondrocytes after 4 passages
Donor 5 p4


title: Flag_P4

description:
AFGE1132-12.CEL
Reanalysis of GSM833403

source_name: Flag plasmid, passage #12


title: Control SLAM+KSLs on Day 7, rep3

source_name: Control SLAM+KSLs Day 7 after pIpC injection

value: wild type


title: Flag-Evi1Δ324_P3

source_name: Flag-Evi1Δ324 plasmid, passage #8


title: Flag-Evi1Δ324_P1

source_name: Flag-Evi1Δ324 plasmid, passage #2


title: Control SLAM+KSLs on Day 7, rep2


title: Donor 5 p0

description:
Isolated RNA from human chondrocytes after 0 passages
Donor 5 p0

source_name: articular chondrocytes


title: E15.5 fetal liver, rep1

source_name: E15.5 fetal liver

value: sorted  HSCs (lin-Mac-1 low  sca1+ckit+CD150+CD48-)

value: fetal


title: Flag_P1

description:
AFGE1132-3.CEL
Reanalysis of GSM833400

source_name: Flag plasmid, passage #3


title: Flag-Evi1Δ324_P4

source_name: Flag-Evi1Δ324 plasmid, passage #11


title: Flag_P2

description:
AFGE1132-6.CEL
Reanalysis of GSM833401

source_name: Flag plasmid, passage #6


title: Flag-Evi1Δ324_P2

source_name: Flag-Evi1Δ324 plasmid, passage #5


title: Control SLAM+KSLs on Day 7, rep1


title: Flag-Evi1_P3

description:
AFGE1132-7.CEL
Reanalysis of GSM833398

source_name: Flag-Evi1 plasmid, passage #7


title: Donor 4 p4

description:
Isolated RNA from human chondrocytes after 4 passages
Donor 4 p4


title: Donor 4 p8

description:
Isolated RNA from human chondrocytes after 8 passages
Donor 4 p8


title: Flag-Evi1_P2

description:
AFGE1132-4.CEL
Reanalysis of GSM833397

source_name: Flag-Evi1 plasmid, passage #4


title: Donor 4 p6

description:
Isolated RNA from human chondrocytes after 6 passages
Donor 4 p6


title: E15.5 fetal liver, rep2

value: sorted  HSCs (lin-Mac-1 low sca1+ckit+CD150+CD48-)


title: E15.5 fetal liver, rep3


title: EAS7 vs. Cholesteatoma 7

city: Bielefeld

first: Jörn

last: Kalinowski

address: Universitätsstr. 27

department: Centrum für Biotechnologie

institute: Universität Bielefeld

hyb_protocol: Hybridization to whole human genome microarray gene expression chips (Agilent) and dye swaps (Cy3 and Cy5) were performed for RNA amplified from each specimen.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization. The protocol used was GE2_107_Sep09.

molecule: polyA RNA

source_name: middle ear, auditory canal skin

label_protocol: 500ng of the purified total RNA was subjected to T7-based amplifications using Agilent Amp Labeling Kit to generate fluorescent cRNA. The method uses T7 RNA polymerase, which at the same time amplifies target material and incorporates cyanin 3- or cyanin 5-labeled CTP.

growth_protocol: Acquired cholesteatomas and external auditory canal skin specimens were obtained from patients undergoing middle ear surgery at Klinikum Bielefeld Mitte (Bielefeld, Germany).

extract_protocol: RNA was extracted from cholesteatoma and external auditory canal skin using RNasy Mini Kits (Qiagen, Mississauga, ON, Canada) according to manufacturer’s instructions.

treatment_protocol: All samples (skin and cholesteatoma) were directly placed into liquid nitrogen in the surgical theatre and stored at -80°Cprior to RNA extraction.

value: middle ear, auditory canal skin

tag: disease state

value: cholesteatoma

value: normal


title: vacht KD 3

first: David

middle: E

last: Carter

address: 1151 Richmond Street North

department: London Regional Genomics Centre

institute: Robarts Research Institute

description: gene expression data from hearts

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomcis Suite using the RMA normalization method

source_name: heart tissue from KD mouse

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: WT and VAChT KD mice were aged to 3 months of age before hearts were excised for RNA extraction.

extract_protocol: RNA was extracted using the Fatty and Fibrous Tissue RNA Extraction Kit (Bio-rad)

treatment_protocol: No treatments were applied to the animals or tissue.

value: heart

tag: gender

value: male

value: VAChT KD

tag: age

value: 3 months


title: Donor 3 p8 MK

description:
Isolated RNA from human chondrocytes after 8 passages
Donor 3 p8 MK


title: EAS6 vs. Cholesteatoma 6


title: vacht KD 2

description: gene expression data from hearts

tag: genotype

tag: strain


title: vacht KD 1

description: gene expression data from hearts


title: Donor 3 p4 MK

description:
Isolated RNA from human chondrocytes after 4 passages
Donor 3 p4 MK

tag: cell type


title: EAS2 vs. Cholesteatoma 2


title: Flag-Evi1_P1

description:
AFGE1132-1.CEL
Reanalysis of GSM833396

source_name: Flag-Evi1 plasmid, passage #1


title: EAS3 vs. Cholesteatoma 3


title: Uninfected NT at 5 d.p.i., rep1

description:
MO-WT U1
Gene expression data from PBS-injected NT mice brain at 5 d.p.i.

source_name: Uninfected NT mouse brain at 5 d.p.i.

value: non-transgenic

value: brain (right cerebral hemisphere)

value: 7 days

tag: treatment

tag: time post-infection


title: Donor 3 p2 MK

description:
Isolated RNA from human chondrocytes after 2 passages
Donor 3 p2 MK

value: Dedifferentiating chondrocytes

tag: donor

tag: passage


title: wild-type 3

description: gene expression data from hearts

source_name: heart tissue from WT mouse

value: WT


title: EAS5 vs. Cholesteatoma 5


title: Donor 4 p0

description:
Isolated RNA from human chondrocytes after 0 passages
Donor 4 p0


title: Donor 3 p6 MK

description:
Isolated RNA from human chondrocytes after 6 passages
Donor 3 p6 MK


title: Ifit2KObrain-VSV-6d-rep1

city: Cleveland

first: Ganes

middle: C.

last: Sen

address: 9500 Euclid Avenue NE-20

institute: Cleveland Clinic

description: 6 days after intrasal VSV infection

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI

source_name: brain

label_protocol: biotinylated cRNAs prepared using Ambion’s Illumina TotalPrep-96 RNA Amplification kit

extract_protocol: RNA was extracted with Trizol reagent, followed DNase I treatment and clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: 2 months

tag: time point

value: 6 days

tag: agent

value: vesicular stomatitis virus (VSV)


title: wild-type 1

city: London

description: gene expression data from hearts


title: wild-type 2

description: gene expression data from hearts


title: Donor 3 p0 MK

description:
Isolated RNA from human chondrocytes after 0 passages
Donor 3 p0 MK


title: Ifit2KObrain-VSV-2d-rep1

description: 2 days after intrasal VSV infection

value: 2 days


title: wtbrain-VSV-6d-rep1

description: 6 days after intrasal VSV infection

value: wt


title: EAS1 vs. Cholesteatoma 1

value: middle ear, auditory canal skin


title: wtbrain-VSV-2d-rep1

description: 2 days after intrasal VSV infection


title: spore of evo39 rep7

status: Public on Nov 13 2012

city: Rehovot

first: Avihu

last: Yona

address: Hertzel 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institue of Science

data_processing: RMA algorithm in the Matlab bioinformatix toolbox

source_name: spore of evo39 rep7

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacture instructions.

growth_protocol: 18 generations of growth in stress-free conditions

extract_protocol: Total RNA using EPICENTER yeast RNA purification

treatment_protocol: before extraction samples were grown to mid log phase

tag: condition

value: spore of evo39

tag: replicate


title: spore of evo39 rep8

hyb_protocol: GeneChip system according to manufacture instructions.

source_name: spore of evo39 rep8


title: spore of evo39 rep5

scan_protocol: GeneChip system according to manufacture instructions.

source_name: spore of evo39 rep5


title: spore of evo39 rep3

source_name: spore of evo39 rep3


title: spore of evo39 rep6

source_name: spore of evo39 rep6


title: spore of evo39 rep2

source_name: spore of evo39 rep2


title: spore of evo39 rep1

source_name: spore of evo39 rep1


title: EvoHigh-pH after another 600 generations on high-pH (8.6) rep 4

source_name: EvoHigh-pH total 750 gen. rep 4

value: EvoHigh-pH total 750 gen.


title: EvoHigh-pH after another 600 generations on high-pH (8.6) rep 2

source_name: EvoHigh-pH total 750 gen. rep 2


title: EvoHigh-pH after another 600 generations on high-pH (8.6) rep 3

source_name: EvoHigh-pH total 750 gen. rep 3


title: EvoHigh-pH after another 600 generations on high-pH (8.6) rep 1

source_name: EvoHigh-pH total 750 gen. rep 1


title: Haploid ancestor after 150 generations on high-pH (8.6)

source_name: haploid wt after 150 gen. on ph 8.6

value: haploid wt after 150 gen. on ph 8.6


title: EvoHigh-pH euploid spore

source_name: EvoHigh-pH euploid spore

value: EvoHigh-pH euploid spore


title: haplid WT

source_name: haplid WT

value: haplid WT


title: WTtrisomeIII  after 1000 generations on 39°C and minimal medium rep 2

source_name: chrIII trisomic after 1000 gen. of minimal medium and heat rep2


title: haploid ancestor


title: EvoHigh-pH disomic spore

source_name: EvoHigh-pH disomic spore

value: EvoHigh-pH disomic spore


title: diploid WT control on minimal medium

source_name: diploid WT control on minimal medium

value: diploid WT control on minimal medium


title: H2 after another 600 generations on 30°C rep 3

source_name: abrupt heat for 450 gen. + 600 gen. of normal temp rep 3


title: WTtrisomeIII  after 1000 generations on 39°C and minimal medium rep 1

source_name: chrIII trisomic after 1000 gen. of minimal medium and heat rep1


title: H2 after another 1000 generations on 39°C and on minimal medium rep 1

source_name: abrupt heat for 450 gen. + 1000 gen. of heat and minimal medium rep 1


title: H2 after another 600 generations on 30°C rep 2

source_name: abrupt heat for 450 gen. + 600 gen. of normal temp rep 2


title: diploid ancestor after 450 generations of gradually applied heat from 30°C to 39°C rep 2

source_name: Gradual heat after 450 gen. rep2

value: Gradual heat after 450 gen.


title: Infected TG 5 d.p.i., rep3

description:
MO-B10-Tg 3
Gene expression data from MeV-infected TG mice brain at 5 d.p.i.

source_name: MeV-infected TG mouse brain at 5 d.p.i.

tag: genotype/variation

value: hsp70 transgenic

value: brain (right cerebral hemisphere)

value: 7 days

value: measles virus (MeV)


title: diploid ancestor after 450 generations of gradually applied heat from 30°C to 39°C rep 3

source_name: Gradual heat after 450 gen. rep3


title: H2 after another 600 generations on 30°C rep 1

source_name: abrupt heat for 450 gen. + 600 gen. of normal temp rep 1


title: diploid ancestor after 450 generations of gradually applied heat from 30°C to 39°C rep 1

source_name: Gradual heat after 450 gen. rep1


title: H2 after another 1000 generations on 39°C and on minimal medium rep 2

source_name: abrupt heat for 450 gen. + 1000 gen. of heat and minimal medium rep 2


title: H2 after another 600 generations on 30°C rep 4

source_name: abrupt heat for 450 gen. + 600 gen. of normal temp rep 4


title: dipliod ancestor after 450 genrations on 30°C rep 2

source_name: optimal conditions after 450 gen. rep2

value: optimal conditions after 450 gen.


title: diploid WT control

source_name: diploid WT control

value: diploid WT control


title: diploid ancestor after 450 generations of gradually applied heat from 30°C to 39°C rep 4

source_name: Gradual heat after 450 gen. rep4


title: dipliod ancestor after 450 genrations on 39°C rep 4

source_name: abrupt heat after 450 gen. rep4

value: abrupt heat after 450 gen.


title: dipliod ancestor after 450 genrations on 39°C rep 3

source_name: abrupt heat after 450 gen. rep3


title: dipliod WT

source_name: Wt diploid

value: Wt diploid


title: dipliod ancestor after 450 genrations on 39°C rep 1

source_name: abrupt heat after 450 gen. rep1


title: dipliod ancestor after 450 genrations on 30°C rep 1

source_name: optimal conditions after 450 gen. rep1


title: ChromosomeIII trisomic mono-clonal  (unevolved)

source_name: WTtrisomeIII

value: WTtrisomeIII


title: ChromosomeIII monosomic mono-clonal  (unevolved)

source_name: WTmonosomeIII

value: WTmonosomeIII


title: dipliod ancestor after 450 genrations on 39°C rep 2

source_name: abrupt heat after 450 gen. rep2