title: LEC MAF-siRNA, rep3

description: Biological replicate 3 of 3.

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA') .

source_name: lymphatic endothelial cells, MAF siRNA

label_protocol: 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)

growth_protocol: Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. Transfected LEC were grown under the same conditions. All cells were mycoplasma free.

treatment_protocol: Lymphatic endothelial cells (LECs) were plated in six well plates (5x10^4cells/well) overnight. The cells were transfected with siRNA against MAF or non-targeting control siRNA (Dharmacon). Two days after transfection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.

value: MAF-siRNA


title: SHEP21N_hypoxia

status: Public on Sep 30 2009

type: RNA

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

country: Italy

institute: Istiuto Giannina Gaslini

description: The cell lines were cultured in RPMI 16140 (Euroclone Ltd., Celbio, Milan, Italy), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, Milan Italy), 2 mmol/L L-glutamine, 10 mM Hepes, 100 units/mL penicillin, 100 ug/mL streptomycin (Euroclone Ltd), and 50 ng/mL tetracycline (Sigma, St. Louis, MO)at 37° C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2. Hypoxic conditions (1% O2) were achieved by culturing the cells in an anaerobic workstation incubator (BUG BOX, Jouan, ALC International S.r.l., Cologno Monzese, Milano, Italy) flushed with a gas mixture containing 1% O2, 5% CO2, and balanced N2 at 37°C in a humidified atmosphere. Oxygen tension in the medium was measured with a portable, trace oxygen analyzer (Oxi 315i/set, WTW; VWR International, Milano, Italy).

hyb_protocol: Fragmented cRNA was used for hybridization to Affymetrix HG-U133 plus 2.0 arrays according to the Affymetrix’s instructions.

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

data_processing: Expression values were quantified and array quality control was performed with the statistical algorithms implemented in Affymetrix Microarray Suite 5.0.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: neuroblastoma cell line under hypoxic conditions

label_protocol: The RNA was reverse-transcribed into cDNA and biotin labeled according to the Affymetrix’s instructions.

extract_protocol: Total RNA was extracted from cell lines using Trizol (Invitrogen Life technologies, Irvine, CA) according to the manufacturer's instructions.

tag: cell line

tag: mycn

value: without overexpression

tag: condition

value: hypoxia


title: LEC pSIN-MCS, rep1

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

country: United Kingdom

institute: UCL

description: Biological replicate 1 of 3.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').

source_name: lymphatic endothelial cells

label_protocol: 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)

growth_protocol: Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.

extract_protocol: TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).

treatment_protocol: Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.

tag: cell type

value: lymphatic endothelial cells

tag: vector

value: pSIN-MCS


title: DT40 (- IAA control)

status: Public on Oct 01 2009

city: Toyonaka

first: Masato

last: Kanemaki

state: Osaka

address: Machikaneyama 1-1,

department: Department of Biological Sciences,

country: Japan

institute: Osaka University

description: Gene expression after 6 hours

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

organism: Gallus gallus

source_name: DT40 cells

label_protocol: standard Agilent protocol

growth_protocol: DT40 cells were grown in DMEM containing 10% FCS, 1% chicken serum and 10nM beta-ME at 38.5oC.

extract_protocol: Following the Qiagen RNeasy Midi Kit protocol.

treatment_protocol: 1/1000 vomume of 0.5M Indole-3-acetic acid (IAA) dissolved in EtOH was added to make final concentration at 500µM.  Cells were maintained at 38.5oC for 6 hours before harvest.


title: DT40 (+500µM IAA)

description: Gene expression after 6 hours


title: LEC pSIN-MCS, rep2

description: Biological replicate 2 of 3.


title: LEC pSIN-MCS, rep3

description: Biological replicate 3 of 3.


title: LEC non-target-siRNA, rep1

description: Biological replicate 1 of 3.

source_name: lymphatic endothelial cells, control siRNA

value: non-targeted-siRNA


title: LEC MAF-siRNA, rep1

description: Biological replicate 1 of 3.


title: LEC MAF-siRNA, rep2

description: Biological replicate 2 of 3.


title: 25% human universal reference+75% human brain RNA_sample D_rep2 (D2)

status: Public on Oct 05 2009

city: Gaithersburg

first: Michael

middle: Ian

last: Brenner

state: MD

address: 217 Perry Parkway bld 5

country: USA

institute: ExonHit Therapeutics

hyb_protocol: Standard hybridization methods of the labeled samples to the Affymetrix-formatted SpliceArrayTM were used following the manufacturer’s recommendations for the 49-format (Affymetrix - Expression analysis technical manual).  The arrays were stained and washed using the Affymetrix FS450-0001 fluidics protocol.

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G.  DAT and CEL images were visually inspected for anomalies and accurate grid placement.

data_processing: Data processing was performed using Partek® software (http://www.partek.com/). 12 .CEL files were imported into Partek® software.  All array data was pre-processed which included probe level RMA background correction, quantile normalization across all arrays, and Log2 transformation followed by median polish to summarize probes to obtain the overall score for each probe set.

label: Biotin

source_name: A mixture of sample A and B – 25% sample A + 75% sample B

label_protocol: Fragmentation and biotin-labeling of the amplified cDNA was performed using the FL-Ovation™ cDNA Biotin Module V2 (NuGen product #4200; Santa Clara, CA, USA) as per manufacturer’s instructions.

extract_protocol: Amplified cDNA was prepared using the WT-Ovation™ Pico RNA Amplification System (NuGen product #3300; Santa Clara, CA, USA) starting with 50 ng of each total RNA sample (A, B, C, D), as described by the manufacturer.  Briefly, the RNA is synthesized into double-stranded cDNA using a SPIA™ DNA/RNA primer.  The DNA portion of the primer binds poly (A) sequence or randomly across the transcript, and the RNA portion of the primer is incorporated into an unique DNA/RNA heteroduplex at one end of the cDNA.  RNase H degrades the RNA portion of the DNA/RNA heteroduplex allowing for additional SPIA™ primer to bind and initiate replication by DNA polymerase.  The process of SPIA™ DNA/RNA primer binding, DNA replication, strand displacement and RNA cleavage is repeated resulting in isothermal linear amplification of the cDNA.  On average, the cDNA yield from 50 ng of high quality total RNA ranges from 6 to 10 micrograms.

tag: maqc sample

value: D [25% sample A (Universal Human Reference RNA)+ 75% sample:B (Human Brain Total RNA)]


title: LEC KSHV_Cluster, rep2

description: Biological replicate 2 of 3.

source_name: lymphatic endothelial cells, KSHV microRNA cluster

value: pSIN-MCS-KSCluster


title: AIDS_KS-biopsy-patient8-repA

hyb_protocol: Cy3 labelled total RNA was hybridised to Agilent Human miRNA Microarray v1.0 as per manufacturer's instructions.

scan_protocol: The Agilent Human miRNA Microarray was scanned using the Agilent scanner as per manufacturer's instructions.

data_processing: Summary expression text files were created using Agilent  Feature Extraction Software. From the summary text files we extracted the median (gMedianSignal) and background signal-(gBGUsed). The arrays were then background corrected using the 'normexp' function of the limma package and quantile normalized to each other.

source_name: AIDS KS lesion biopsy

label_protocol: Total RNA was labelled with Cy3 using the Agilent miRNA labelling and reagent kit as per manufacturer's instructions.

growth_protocol: Fresh frozen KS and skin biopsies were obtained from the NIH AIDS Cancer Specimen Resource Bank (USA) and from Chelsea and Westminster Hospital (UK).  All participants were male, HIV–infected and between the ages of 26 and 58. Three out of five biopsies were collected in London in 2008. The remaining biopsies were nodular stage KS and collected in the U.S.A in 2003. All participants were undergoing anti-retroviral treatment at the time of collection.

extract_protocol: Tissue was disrupted and homogenized using a mechanical rotor and RNA subsequently extracted using the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. The small RNA fraction was assessed using the Agilent small RNA Kit. Quality and integrity of the RNA fraction between 6 and 150 nucleotides was quantified using the Agilent 2100 bioanalyzer (Agilent).

tag: gender

value: male

tag: tissue

value: Kaposi sarcoma lesion

value: A


title: AIDS_KS-biopsy-patient7-repA


title: AIDS_KS-biopsy-patient7-repB

value: B


title: AIDS_KS-biopsy-patient4-repA


title: AIDS_KS-biopsy-patient4-repB


title: skin-biopsy-patient2-repA

source_name: normal skin biopsy

value: skin


title: skin-biopsy-patient3-repA


title: AIDS_KS-biopsy-patient6-repB


title: AIDS_KS-biopsy-patient5-repA


title: skin-biopsy-patient1-repA


title: AIDS_KS-biopsy-patient6-repA


title: BEC KSHV 72h, rep6

description: Biological replicate 6 of 6.

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm  ('RMA') .

source_name: blood vessel endothelial cells, KSHV-infected, 72h

growth_protocol: Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV-infected LEC and BEC were grown under the same conditions. All cells were mycoplasma free.

treatment_protocol: Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.

value: blood vessel endothelial cell

tag: infection

value: KSHV


title: BEC KSHV 72h, rep5

description: Biological replicate 5 of 6.


title: BEC control, rep6

description: Biological replicate 6 of 6.

source_name: blood vessel endothelial cells


title: BEC control, rep5

description: Biological replicate 5 of 6.


title: LEC KSHV 72h, rep6

description: Biological replicate 6 of 6.

source_name: lymphatic endothelial cells, KSHV-infected, 72h

value: lymphatic endothelial cell


title: 430 European wild boar infected sample with Brucella suis

status: Public on Sep 29 2009

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

country: Spain

institute: Instituto de Investigacion en Recursos Cinegéticos

description: Infected sample, RNA extracted from European wild boar naturally infected with Brucella suis, from Navarra Spain.

hyb_protocol: GeneChip® HT IVT Labeling Kit (Affymetrix)

scan_protocol: Microarray Analysis Suite 5.0

data_processing: RMA normalization and statistical analyses were done using the free statistical language R and the libraries developed by the Bioconductor Project (www.bioconductor.org).

organism: Sus scrofa

source_name: Spleen cells

label_protocol: Standard Affymetrix labeling protocol

extract_protocol: Qiagen RNeasy extraction and purification

tag: strain

value: European wild boar

value: spleen cells

tag: disease status

value: naturally infected with Brucella suis


title: P43_TGFB_T24 (24 hours TGFB treatment, SSc FBs)

status: Public on Sep 15 2009

city: Hanover

first: Jennifer

middle: L

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

institute: Dartmouth Medical School

description: Comparison of dermal fibroblasts from healthy and dSSc patients treated and untreated with TGFB.

hyb_protocol: Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to stripped 4 x 44K Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.

scan_protocol: Microarrays were scanned using a dual laser GenePix 4000B scanner (Axon Instruments). The pixel intensities of the acquired images were then quantified using GenePix Pro 5.1 software.

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both Cy3- Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.

label_protocol: Agilent Low RNA Input Linear Amplification protocol: 200 ng of total RNA from each time point sample was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).

growth_protocol:
Plated at 4x10e4 - grown for 48 hours in DMEM + Pen/Strep + 10% FBS (37C 5% CO2)
Grown for 24 hours in low serum conditions (DMEM + Pen/Strep + 0.1%FBS, 37C 5%CO2)
 - then either treated with 50pM TGFB or sample taken for baseline measurement.

extract_protocol: RNeasy mini columns with on column DNaseI digestion (Qiagen)

treatment_protocol: 24 hours of 24 hour timecourse of 50pM TGFB treatment

tag: primary fibroblasts from 41yo male, 1 year diagnosed with dSSc, forearm biopsy taken in 2000

source_name: Universal Human Reference RNA

extract_protocol: Stratagene's protocol

tag: pool of RNA from 10 different human cell lines, commercially available from Stratagene.


title: 355 Brucella suis infected sample from European wild boar


title: LEC KSHV 72h, rep5

description: Biological replicate 5 of 6.


title: LEC KSHV_Cluster, rep1

description: Biological replicate 1 of 3.


title: 535 uninfected European wild boar sample

description: Uninfected sample, RNA extracted from European wild from Navarra Spain.

label_protocol: Affymetrix standard labeling protocol

extract_protocol: Standard protocols from Qiagen extraction and purification kits

value: uninfected (negative to ELISA test and culture for Brucella suis)


title: P43_TGFB_T8 (8 hours TGFB treatment, SSc FBs)

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both  Cy3- Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.

treatment_protocol: 8 hours of 24 hour timecourse of 50pM TGFB treatment

tag: pool of RNA from 10 different human cell lines, commercially available from Stratagene


title: 487 European wild boar sample infected with Brucella suis


title: P43_TGFB_T03 (baseline, SSc FBs)

source_name: P43_TGFB_T01 (baseline)

treatment_protocol: Baseline measurement (3 of 3 triplicates in 24 hour TGFB timecourse)


title: P43_TGFB_T2 (2 hours TGFB treatment, SSc FBs)

treatment_protocol: 2 hours of 24 hour timecourse of 50pM TGFB treatment


title: P43_TGFB_T12 (12 hours TGFB treatment, SSc FBs)

treatment_protocol: 12 hours of 24 hour timecourse of 50pM TGFB treatment


title: Negative control sample 283


title: P43_TGFB_T4 (4 hours TGFB treatment, SSc FBs)

treatment_protocol: 4 hours of 24 hour timecourse of 50pM TGFB treatment


title: C17_TGFB_T4 (4 hour TGFB treatment)

treatment_protocol: 4 hour of 24 hour time course with 50pM TGFB treatment

tag: 58yo female, healthy control, forearm biopsy taken in 2000


title: C17_TGFB_T03 (baseline)

hyb_protocol: Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to Stripped 4 x 44K Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.

source_name: C17_TGFB_T03 (baseline)


title: P43_TGFB_T01 (baseline, SSc FBs)

treatment_protocol: Baseline measurement (1 of 3 triplicates in 24 hour TGFB timecourse)


title: C17_TGFB_T12 (12 hour TGFB treatment)

treatment_protocol: 12 hour of 24 hour time course with 50pM TGFB treatment


title: P43_TGFB_T02 (baseline, SSc FBs)

source_name: P43_TGFB_T02 (baseline)

treatment_protocol: Baseline measurement (2 of 3 triplicates in 24 hour TGFB timecourse)


title: C17_TGFB_T24 (24 hour TGFB treatment)

treatment_protocol: 24 hour of 24 hour time course with 50pM TGFB treatment


title: C17_TGFB_T8 (8 hour TGFB treatment)

treatment_protocol: 8 hour of 24 hour time course with 50pM TGFB treatment


title: C17_TGFB_T02 (baseline)

source_name: C17_TGFB_T02 (baseline)


title: C17_TGFB_T2 (2 hour TGFB treatment)

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both Cy3-  Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.

treatment_protocol: 2 hour of 24 hour time course with 50pM TGFB treatment


title: NHDF_MOCK_T24 (24 hours MOCK treatment, healthy FBs)

hyb_protocol: Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to stripped Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both Cy3-  Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,913 probes that passed the filtering criteria.

growth_protocol:
Plated at 4x10e4 - grown for 48 hours in DMEM + Pen/Strep + 10% FBS (37C 5% CO2)
Grown for 24 hours in low serum conditions (DMEM + Pen/Strep + 0.1%FBS, 37C 5%CO2)
- then either treated with 50pM TGFB or sample taken for baseline measurement.

treatment_protocol:
24 hours of 24 hour timecourse of MOCK treatment.
Cells treated identically to those in timecourse with the exception of no addition of TGFB.

tag: Normal adult dermal fibroblasts, purchased from Clonetics. From 47 yr old, caucasion male, Bx site unknown


title: NHDF_MOCK_T4 (4 hours MOCK treatment, healthy FBs)

treatment_protocol:
4 hours of 24 hour timecourse of MOCK treatment.
Cells treated identically to those in timecourse with the exception of no addition of TGFB.


title: NHDF_MOCK_T12 (12 hours MOCK treatment, healthy FBs)

treatment_protocol:
12 hours of 24 hour timecourse of MOCK treatment.
Cells treated identically to those in timecourse with the exception of no addition of TGFB.


title: NHDF_MOCK_T2 (2 hours MOCK treatment, healthy FBs)

treatment_protocol:
2 hours of 24 hour timecourse of MOCK treatment.
Cells treated identically to those in timecourse with the exception of no addition of TGFB.


title: NHDF_MOCK_T0-3 (baseline, healthy FBs)

treatment_protocol:
0 hours of 24 hour timecourse of MOCK treatment.
Baseline measurement (3 of 3 triplicates in 24 hour TGFB/MOCK treatment timecourse)
Cells treated identically to those in timecourse with the exception of no addition of TGFB.


title: NHDF_MOCK_T0-2 (baseline, healthy FBs)

treatment_protocol:
0 hours of 24 hour timecourse of MOCK treatment.
Baseline measurement (2 of 3 triplicates in 24 hour TGFB/MOCK treatment timecourse)
Cells treated identically to those in timecourse with the exception of no addition of TGFB.


title: NHDF_MOCK_T8 (8 hours MOCK treatment, healthy FBs)

treatment_protocol:
8 hours of 24 hour timecourse of MOCK treatment.
Cells treated identically to those in timecourse with the exception of no addition of TGFB.


title: NHDF_TGFB_T4 (4 hours TGFB treatment, healthy FBs)

treatment_protocol: 4 hours of 24 hour timecourse of 50pM TGFB treatment.


title: NHDF_TGFB_T8 (8 hours TGFB treatment, healthy FBs)

treatment_protocol: 8 hours of 24 hour timecourse of 50pM TGFB treatment.


title: NHDF_TGFB_T24 (24 hours TGFB treatment, healthy FBs)

treatment_protocol: 24 hours of 24 hour timecourse of 50pM TGFB treatment.


title: NHDF_TGFB_T0-2 (baseline, healthy FBs)

treatment_protocol:
0 hours of 24 hour timecourse of 50pM TGFB treatment.
Baseline measurement (2 of 3 triplicates in 24 hour TGFB treatment timecourse)


title: P42_TGFB_T4 (4 hours TGFB treatment, SSc FBs)

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in   both Cy3- Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.

tag: primary fibroblasts from 62yo FEmale, 1 year diagnosed with dSSc, forearm biopsy taken in 2000


title: Brucella suis uninfected 353 European wild boar sample


title: NHDF_TGFB_T2 (2 hours TGFB treatment, healthy FBs)

treatment_protocol: 2 hours of 24 hour timecourse of 50pM TGFB treatment.


title: NHDF_TGFB_T03 (baseline, healthy FBs)

treatment_protocol:
0 hours of 24 hour timecourse of 50pM TGFB treatment.
Baseline measurement (3 of 3 triplicates in 24 hour TGFB treatment timecourse)


title: NHDF_TGFB_T0-1 (baseline, healthy FBs)

treatment_protocol:
0 hours of 24 hour timecourse of 50pM TGFB treatment.
Baseline measurement (1 of 3 triplicates in 24 hour TGFB treatment timecourse)

tag: Normal adult dermal fibroblasts, purchased from Clonetics.  From 47 yr old, caucasion male, Bx site unknown


title: P42_TGFB_T24 (24 hours TGFB treatment, SSc FBs)


title: NHDF_TGFB_T12 (12 hours TGFB treatment, healthy FBs)

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both Cy3-Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.

treatment_protocol: 12 hours of 24 hour timecourse of 50pM TGFB treatment.


title: P42_TGFB_T8 (8 hours TGFB treatment, SSc FBs)


title: P42_TGFB_T03 (baseline, SSc FBs)

treatment_protocol:
0 hours of 24 hour timecourse of 50pM TGFB treatment
baseline measurement (3 of 3 triplicates in 24 hour TGFB timecourse)


title: P42_TGFB_T2 (2 hours TGFB treatment, SSc FBs)


title: P42_TGFB_T02 (baseline, SSc FBs)

treatment_protocol:
0 hours of 24 hour timecourse of 50pM TGFB treatment
baseline measurement (2 of 3 triplicates in 24 hour TGFB timecourse)


title: P42_TGFB_T12 (12 hours TGFB treatment, SSc FBs)


title: P42_TGFB_T01 (baseline, SSc FBs)

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both  Cy3-Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.

source_name: P42_TGFB_T01 (baseline)

treatment_protocol:
0 hours of 24 hour timecourse of 50pM TGFB treatment
baseline measurement (1 of 3 triplicates in 24 hour TGFB timecourse)


title: C17_TGFB_T01 (baseline)

hyb_protocol: Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to stripped Agilent 4 x 44K Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both  Cy3-  Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.

source_name: C17_TGFB_T01 (baseline)

treatment_protocol: Baseline measurement (1 of 3 triplicates in 24 hour TGFB timecourse)


title: NT2 macroH2A2 rep2 (chip B)

status: Public on Sep 06 2009

type: genomic

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description: comparison

hyb_protocol: Biological replicate experiments were performed for each hybridisation of IP sample versus input DNA as reference. Slides hybridized and washed as recommended by Agilent.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the Featrue Extraction software (Agilent Technology) version 9.5.3.1

data_processing: Microarray data were normalised using LIMMA software in Bioconductor. For each slide, background was corrected with the normexp method resulting in strictly positive values and reducing variability in the log ratios for genes with low levels of hybridization signal. Each slide was normalized with the global loess method and finally, slide values were adjusted for batch effect and scaled by their median absolute deviation to make arrays comparable.

molecule: genomic DNA

source_name: macroH2A2 ChIP DNA from NT2 cells

label_protocol: 2000ng of DNA were labelled using random primers and exo-Klenow fragments wiht the Agilent Genomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309), and hybridized following the manufacturer’s instructions (Agilent Mammalian ChIP-on-chip protocol, version 10.0, December 2007).

growth_protocol: DMEM medium supplemented with 10 % FBS at 37 ºC and 5% CO2

extract_protocol: Chromatin immunoprecipitations were performed as described by Frank et al., 2001. Immunoprecipitated material was amplified following the modified WGA Sigma protocol as described by O'Geen et al., 2006.

treatment_protocol: untreated

tag: genotype

value: wild-type

value: embryonal carcinoma clone (ATCC #CRL 1973)

tag: chip antibody

value: macroH2A2 homemade

source_name: Input DNA from NT2 cells

value: none, input


title: NT2 macroH2A2 rep1 (chip B)

description: comparison

tag: cell type


title: NT2 macroH2A1 rep4 (chip B)

description: comparison

source_name: macroH2A1 ChIP DNA from NT2 cells

value: macroH2A1 Upstate


title: NT2 macroH2A knock down, macroH2A1  rep1 (chip B)

description: comparison

source_name: macroH2A1 ChIP DNA from shmacroH2A1+2 treated NT2 cells

value: stable shmacroH2A1+2 expressing line

value: macroH2A1 homemade


title: NT2 macroH2A knock down, macroH2A1 rep2 (chip B)

description: comparison


title: NT2 macroH2A2 rep3 (chip B)

description: comparison


title: NT2 macroH2A knock down, macroH2A1 rep1 (chip B)

description: comparison


title: NT2 macroH2A1 rep2 (chip B)

description: comparison


title: NT2 macroH2A1 rep1 (chip B)

description: comparison


title: NT2 IgG rep3 (chip B)

description: comparison

source_name: IgG ChIP DNA from NT2 cells

value: IgG


title: NT2 macroH2A1 rep3 (chip B)

description: comparison


title: NT2 macroH2A1 rep2 (chip A)

description: comparison


title: NT2 macroH2A2 rep2 (chip A)

description: comparison


title: NT2 IgG rep2 (chip B)

description: comparison


title: G42 cells from S1, P40, biological replicate 3

status: Public on Sep 05 2009

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: Gene expression data from manually sorted G42 GFP labeled neurons from the somatosensory cortex (S1), age P40

hyb_protocol: Following fragmentation, 15 or 20 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Mouse Genome 430 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

data_processing: The data were processed with GCRMA algorithm in the Bioconductor with default settings.

organism: Mus musculus

source_name: brain,somatosensory cortex, fast spiking interneurons, P40

label_protocol: Biotinylated cRNA were prepared using two rounds of T7 in vitro transcription based aRNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.3 to 1 ng of total RNA.

growth_protocol: Mice were grown under normal animal facility condition.

extract_protocol: PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Acute 400 micron coronal brain slices were prepared from G42 mice(n =3 animals for each age) over a range of maturational time points: P7,  P10, P15, P25, and P40–P45. Brain slices were incubated in a protease  solution (1 mg/ml Pronase E; Sigma-Aldrich) for 1 h, after which  time the somatosensory cortex was microdissected under a dissecting  microscope. Microdissected tissue was then triturated in artificial CSF  (ACSF) using a series of three Pasteur pipettes of decreasing tip diameter.  The cell suspension was then poured into a small Petri dish, and, under  visual control on a fluorescence dissecting microscope, GFP-expressing  neurons were aspirated into a micropipette with a 30–50  m tip diameter  and transferred to a clean dish. After undergoing three such “washes,”  the sample was then lysed in 50  l of extraction buffer (PicoPure RNA  isolation kit; Arcturus), incubated at 42°C for 30 min, and then stored at   20°C.

tag: age

tag: number of cells

value: # cells:54

value: G42  labeled neurons from S1 cortex


title: NT2 IgG rep1 (chip B)

description: comparison


title: NT2 macroH2A knock down, macroH2A1 rep2 (chip A)

description: comparison


title: NT2 macroH2A knock down, macroH2A1  rep1 (chip A)

description: comparison


title: G42 cells from S1, P40, biological replicate 2

value: # cells:60


title: NT2 macroH2A knock down, macroH2A1 rep1 (chip A)

description: comparison


title: G42 cells from S1, P25, biological replicate 3

description: Gene expression data from manually sorted G42 GFP labeled neurons from the somatosensory cortex (S1), age P25

source_name: brain,somatosensory cortex, fast spiking interneurons, P25

value: # cells:55


title: NT2 macroH2A1 rep1 (chip A)

description: comparison


title: G42 cells from S1, P25, biological replicate 2

value: # cells:53


title: NT2 IgG rep3 (chip A)

description: comparison


title: NT2 macroH2A1 rep3 (chip A)

description: comparison


title: NT2 macroH2A1 rep4 (chip A)

description: comparison


title: NT2 IgG rep2 (chip A)

description: comparison


title: NT2 macroH2A2 rep3 (chip A)

description: comparison


title: NT2 macroH2A2 rep1 (chip A)

description: comparison


title: G42 cells from S1, P25, biological replicate 1

value: # cells:48


title: NT2 IgG rep1 (chip A)

description: comparison


title: G42 cells from S1, P15, biological replicate 3

description: Gene expression data from manually sorted G42 GFP labeled neurons from the somatosensory cortex (S1), age P15

source_name: brain,somatosensory cortex, fast spiking interneurons, P15

value: # cells:45


title: G42 cells from S1, P15, biological replicate 2

value: # cells:23


title: G42 cells from S1, P10, biological replicate 3

description: Gene expression data from manually sorted G42 GFP labeled neurons from the somatosensory cortex (S1), age P10

source_name: brain,somatosensory cortex, fast spiking interneurons, P10

value: # cells:47


title: G42 cells from S1, P10, biological replicate 1

value: # cells:71


title: G42 cells from S1, P15, biological replicate 1

value: # cells:34


title: G42 cells from S1, P7, biological replicate 1

description: Gene expression data from manually sorted G42 GFP labeled neurons from the somatosensory cortex (S1), age P7

source_name: brain,somatosensory cortex, fast spiking interneurons, P7

value: # cells:52


title: G42 cells from S1, P10, biological replicate 2

value: # cells:72


title: G42 cells from S1, P7, biological replicate 2

value: # cells:65


title: G42 cells from S1, P7, biological replicate 3

value: # cells:85


title: G42 cells from S1, P40, biological replicate 1

value: # cells:38


title: C.B6-(lmr1, lmr2) uninfected macrophages

status: Public on Sep 04 2009

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Samples were hybridised using Affymetrix protocols.

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

data_processing: The data were background corrected, normalized and summarized with the Bioconductor package gcrma. Full (fast=FALSE) parameter estimation was used.

source_name: bone marrow-derived macrophages

label_protocol: Samples were labelled using the Enzo BioArray HighYield RNA Transcript Labeling kit – Affymetrix, following the manufacturer's protocol.

growth_protocol: Bone marrow-derived macrophages from 6 mice each of C57BL/6, BALB/c, C.B6-(lmr1, lmr2) and B6.c-(lmr1, lmr2) were cultured for 3 days in the presence of FCS and L-cell conditioned media. After 2 days, adherent cells were discarded. This served to removed any fibroblasts present in the culture. The remaining cells were cultured for a further 4 days allowing non-adherent macrophage precursors to mature and adhere to the culture dish.

extract_protocol: RNA was prepared by using RNeasy (Qiagen, Valencia, CA).

treatment_protocol: After maturation of macrophage precursors, the cells were washed and incubated for 4 hours with or without L. major promoastigotes. The cells were then washed free of unbound parasites and incubated for 24hours before harvesting for RNA preparation.

value: BALB/c congenic

tag: l. major infection

value: uninfected

tag: gender

value: female

value: Bone marrow

value: macrophage

value: 6-8 weeks


title: B6.c-(lmr1, lmr2) infected macrophages

value: C57BL/6 congenic

value: infected

tag: tissue


title: BALB/c uninfected macrophages

description: Bc.U

tag: strain

value: BALB/c


title: B6.c-(lmr1, lmr2) uninfected macrophages


title: C57BL/6 infected macrophages


title: C57BL/6 uninfected macrophages


title: OriC-null genomic profile after overexpression of dnaN for 60 min

status: Public on Sep 01 2009

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

description: provides DNA profile of oriC-null cells under given conditions

hyb_protocol: see: Nutritional control of elongation of DNA replication by (p)ppGpp. Wang JD, Sanders GM, Grossman AD. Cell 2007 Mar 9;128(5):865-75 PMID: 17350574

data_processing: Arrays were normalized by setting the total signal of both channels to unity. Goranov et al. 2005.

organism: Bacillus subtilis

source_name: AIG278 gen DNA

growth_protocol: defined minimal medium with arabinose

treatment_protocol: Xylose added at time 0min. Tis sample is 60min after xylose addition

value: AIG278, OriC-null

tag: sample type

value: genomic DNA profile after dnaN overexpression

source_name: 1N reference DNA

treatment_protocol: arrest cells with dnaB-ts for 50min at 42C

value: 1N DNA reference


title: MMB26 genomic profile before dnaN expression 0 min

description: shows the genomic DNA profile of the population

hyb_protocol: See: Nutritional control of elongation of DNA replication by (p)ppGpp. Wang JD, Sanders GM, Grossman AD. Cell 2007 Mar 9;128(5):865-75. PMID: 17350574

source_name: MMB26 genomic DNA

treatment_protocol: exponentially growing in defined minimal media, w/o xylose

value: genomic DNA profile of cells growing asynchronously in defined minimal media

source_name: reference 1N bacillus DNA

extract_protocol:
synchronize dnaB cells to obtain a population with uniformly 1N DNA for 50min at 42C. DNA extraction as described in Nutritional control of elongation of DNA replication by (p)ppGpp.
Wang JD, Sanders GM, Grossman AD. Cell 2007 Mar 9;128(5):865-75.
PMID: 17350574

value: reference DNA, all loci equally represented, since DNA extracted from cells arrested for replication initiation


title: OriC-null asynchronous sample 0 min

scan_protocol: see: Nutritional control of elongation of DNA replication by (p)ppGpp. Wang JD, Sanders GM, Grossman AD. Cell 2007 Mar 9;128(5):865-75 PMID: 17350574

source_name: genomic DNA from AIG278

treatment_protocol: Xylose added at time 0min

value: genomic DNA form asynchronously growing population of OriC mutants which replicate from oriN 0min

source_name: reference 1N DNA

value: 1N reference DNA


title: MMB26 genomic profile 60 min  after DnaN overexpression

scan_protocol: See: Nutritional control of elongation of DNA replication by (p)ppGpp. Wang JD, Sanders GM, Grossman AD. Cell 2007 Mar 9;128(5):865-75. PMID: 17350574

treatment_protocol: exponentially growing in defined minimal media, with 1% xylose for 60min

value: genomic DNA profile of cells overexpressing dnaN for 60min

source_name: reference bacillus DNA


title: C.B6-(lmr1, lmr2) infected macrophages

value: BALB/c congenic


title: BALB/c infected macrophages

description: Bc.I


title: HCT116 p53KO cells treated with 4 uM nutlin (replicate 3)

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

country: Singapore

institute: Experimental Therapeutics Centre

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974020_H

hyb_protocol: Hybridization was performed according to Illumina 8-sample BeadChip IntelliHyb protocol

scan_protocol: Images were scanned using the Illumina BeadArray reader

data_processing: Data analysis performed with Illumina BeadStudio application. Data was normalized by cubic-spline method and background subtracted

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 4 uM nutlin (replicate 3)

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer's protocol

growth_protocol: Cells were grown in McCoy medium with 10% bovine serum supplemented with antibiotics and L-glutamine

extract_protocol: Total RNA extracted from cells using the Trizol method

treatment_protocol: Cells were first seeded overnight. Dosages for actinomycin D treatment was 1 nM, 10 nM, and 100 nM. Dosage for nutlin-3 was 4 uM. Dosages for leptomycin B was 2 nM and 20 nM. Cells were treated for 16 hours before RNA extraction.

tag: cell line

value: HCT116 p53KO


title: NHDF_MOCK_T0-1 (baseline, healthy FBs)

treatment_protocol:
0 hours of 24 hour timecourse of MOCK treatment.
Baseline measurement (1 of 3 triplicates in 24 hour TGFB/MOCK treatment timecourse)
Cells treated identically to those in timecourse with the exception of no addition of TGFB.

source_name: Universal Human Reference RNA

tag: pool of RNA from 10 different human cell lines, commercially available from Stratagene.


title: HCT116 p53KO cells untreated (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_D

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 3)


title: HCT116 wild type cells treated with 10 nM actinomycin D (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_A

source_name: HCT116 colon adenocarcinoma cell line, wild type, 10 nM actinomycin D (replicate 1)

value: HCT116 wild type


title: HCT116 p53KO cells untreated (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_C

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 2)


title: HCT116 wild type cells untreated (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_B

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 3)


title: HCT116 wild type cells treated with 1 nM actinomycin D (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_B

source_name: HCT116 colon adenocarcinoma cell line, wild type, 1 nM actinomycin D (replicate 2)


title: HCT116 p53KO cells treated with 10 nM actinomycin D (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_D

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 10 nM actinomycin D (replicate 2)


title: HCT116 wild type cells treated with 10 nM actinomycin D (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_E

source_name: HCT116 colon adenocarcinoma cell line, wild type, 10 nM actinomycin D (replicate 3)


title: HCT116 p53KO cells treated with 1 nM actinomycin D (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_F

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 1 nM actinomycin D (replicate 3)


title: HCT116 p53KO cells treated with 10 nM actinomycin D (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_C

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 10 nM actinomycin D (replicate 1)


title: HCT116 p53KO cells treated with 1 nM actinomycin D (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_D

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 1 nM actinomycin D (replicate 2)


title: HCT116 p53KO cells treated with 1 nM actinomycin D (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_C

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 1 nM actinomycin D (replicate 1)


title: HCT116 wild type cells treated with 100 nM actinomycin D (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_B

source_name: HCT116 colon adenocarcinoma cell line, wild type, 100 nM actinomycin D (replicate 2)


title: HCT116 wild type cells untreated (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190011_A

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 2)


title: HCT116 p53KO cells treated with 10 nM actinomycin D (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190026_F

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 10 nM actinomycin D (replicate 3)


title: HCT116 wild type cells treated with 1 nM actinomycin D (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_A

source_name: HCT116 colon adenocarcinoma cell line, wild type, 1 nM actinomycin D (replicate 1)


title: PfHP1-HA (ChIP on chip)

status: Public on Sep 03 2009

city: Nijmegen

first: Richard

last: Bartfai

address: Geert Grooteplein 26-28

country: Netherlands

institute: Nijmegen Center of Molecular Life Sciences

description: antiHA ChIP on chip experiment on 3D7/PfHP1-HA strain

hyb_protocol: manufacturer protocol (NimbleGen)

scan_protocol: manufacturer protocol (NimbleScan)

data_processing: Log2 ratios were computed for each sample pair and scaled using the Tukey bi-weight mean , using NimbleScan Version 2.1 software or newer versions(NimbleGen Systems Inc).  Log2 ratios  were plotted to generate a graphical representation of enrichment mapped to chromosome location.

organism: Plasmodium falciparum

source_name: input DNA from crosslinked 3D7/pfHP1-HA chromatin

label_protocol: Cy3 coupled random heptamers (at NimbleGen)

extract_protocol: ChIP followed by column purification (Qiagen)

value: synchronous late trophozoite/early schizont

source_name: antiHA chiped DNA from crosslinked 3D7/pfHP1-HA  chromatin

label_protocol: Cy5 coupled random heptamers (at NimbleGen)

value: anti HA (Abcam, ab9110)


title: HCT116 wild type cells treated with 4 uM nutlin (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4235974011_H

source_name: HCT116 colon adenocarcinoma cell line, wild type, 4 uM nutlin (replicate 3)


title: HCT116 p53KO cells treated with 4 uM nutlin (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_D

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 4 uM nutlin (replicate 2)


title: HCT116 p53KO cells treated with 4 uM nutlin (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_C

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 4 uM nutlin (replicate 1)


title: HCT116 wild type cells untreated (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_E

source_name: HCT116 colon adenocarcinoma cell line, wild type cells untreated (replicate 1)


title: HCT116 wild type cells treated with 1 nM actinomycin D (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190010_E

source_name: HCT116 colon adenocarcinoma cell line, wild type, 1 nM actinomycin D (replicate 3)


title: HCT116 p53KO cells untreated (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_G

source_name: HCT116 colon adenocarcinoma cell line, p53KO cells untreated (replicate 1)


title: HCT116 wild type cells treated with 4 uM nutlin (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_A

source_name: HCT116 colon adenocarcinoma cell line, wild type, 4 uM nutlin (replicate 1)


title: HCT116 wild type cells treated with 4 uM nutlin (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190002_B

source_name: HCT116 colon adenocarcinoma cell line, wild type, 4 uM nutlin (replicate 2)


title: HCT116 p53KO cells treated with 100 nM actinomycin D (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_F

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 100 nM actinomycin D (replicate 3)


title: HCT116 wild type cells treated with 100 nM actinomycin D (replicate 3)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_E

source_name: HCT116 colon adenocarcinoma cell line, wild type, 100 nM actinomycin D (replicate 3)


title: Echinostoma paraensei exposed 2

city: Albuquerque

first: Coen

middle: M

last: Adema

state: NM

address: 1 University of New Mexico

department: CETI Biology MSC03 2020

institute: University of New Mexico

description:
Test sample RNA consisted of RNA from five snails.
Reference sample RNA consisted of a mixture of RNA from snails.

hyb_protocol: Purified Cy3- and Cy5-labeled products were then pooled, ethanol precipitated, resuspended in 100 µL hybridization buffer (40 % formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for 3.0 h at 42°C in hybridization buffer prior to hybridization with labeled probes under lifterslips.  Labeled cDNA was hybridized overnight at 42°C.

scan_protocol: Microarray slides were scanned with a GenePix® 4000B scanner (Axon Instruments) with GenePix® Pro 6.0 (Axon Instruments) software using a modified protocol as described by Aragon et al.

data_processing: A preloaded grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians to Alien control spots. SAM was used to determine significiantly differentially regulated genes with a cut off of 2-fold and a false positive rate of less then 10%.

organism: Biomphalaria glabrata

source_name: 4-8 mm Biomphalaria glabrata, E. paraensei infected

label_protocol: Complementary DNA was synthesized, amplified, labeled and hybridized using the modified SMART (Clontech) cDNA labeling protocol described by Petalidis et al. Briefly, 300 ng total RNA were mixed with 3 µL of 10 μM 3′ SMART CDS primer IIA (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 µL 10 μM template switching primer (5′-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3′) and brought to a final volume of 15 µL with RNase-free dH2O. The template switching primer is a DNA:RNA hybrid where the last 3 bases are RNA. The reaction was then incubated at 72°C for 2 min and then placed on ice. Six microliters of 5x first-strand buffer (Clontech), 3 µL DTT (20 mM), 3 µL dNTPs (10 mM), and 3 µL and PowerScriptTM reverse transcriptase (Clontech) were then added to the reaction and the mixture incubated at 42°C for 1.0 h to generate first strand cDNA. Second-strand cDNA was then amplified by mixing 15 µL of the first-strand cDNA reaction with 57 µL dH2O, 10 µL 10x PCR buffer II (Applied Biosystems), 10 µL 25 mM MgCl2, 2 µL 10 mM dNTPs, 4 µL 10 μM 5’ PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 2 µl AmpliTaq® (40 U/µL). Amplification conditions were 95°C for 1 min for one cycle followed by 95°C for 5 s, 65°C for 5 s, and 68°C for 6 min for 15 cycles. Second-strand cDNA was then purified using a QIAquick® PCR Purification Kit (Qiagen), quantified using a NanoDrop® ND-1000 spectrophotometer and labeled with Cy3/Cy5 d-CTPs (GE Healthcare-Amersham) using BioPrime® DNA Labeling System (Invitrogen). For labeling, 200 ng of second-strand cDNA suspended in 21 µL dH2O was mixed with 20 μL of 2.5x random primer reaction buffer (Invitrogen) and incubated at 95°C for 5 min, then placed on ice. While on ice, 2 µL dH2O, 5 μL low-C dNTP mix (5 mM dATP, 5 mM dGTP, 5 mM dTTP, 2 mM dCTP), 1 µL Cy3 or Cy5 dCTP and 1 μL Klenow enzyme (40 U/µL; Invitrogen) were mixed and incubated at 37°C for 2.0 h. The labeling reaction was stopped by adding 5 μL stop buffer (Invitrogen). For all experiments, reference samples were labeled with Cy3 and experimental samples with Cy5. Cy3- and Cy5-labeled probes were purified separately using an AutoSeqTM G-50 Dye Terminator Removal Kit (GE Healthcare) and labeling efficiency quantified using a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: Snails, bacteria and trematodes used in this study were maintained at the University of New Mexico.

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

treatment_protocol: The five experimental groups and two control groups examined in this study were non-infected M line (control), stab-wounded but non-infected M-line, Escherichia coli infected, Micrococcus luteus infected M line B. glabrata (all four groups 10-12mm), and Echinostoma paraensei infected and Schistosoma mansoni infected B. glabrata and non-infected (control) M line (all three groups 4-8 mm) .  For each treatment, three pools of 5 snails were used as the biological replicates to reduce individual variability. Individual B. glabrata were exposed to 8-10 S. mansoni or E. paraensei miracidia in artificial spring water (ASW), (Loker and Hertel, 1987) for 12 hours and kept alive before the RNA extraction procedure (see below).  Control snails were placed into 24-well plates with ASW for 12 hours and preceded with RNA extraction at the same time point.  Snails in the bacteria-exposed groups were each injected in the headfoot with 50 μl of bacterial culture in LB medium (OD600 of 1.0 = 8 x 108 cells/ml) of E. coli or M. luteus using a G27 hypodermic needle, and kept on the bench for 5 minutes before being placed into 24-well plates with ASW for 12 hours (Adema et al., 1999) and proceeding with RNA extraction.

value: M line

tag: shell diameter

tag: infection

value: Echinostoma paraensei

tag: wounded

value: no

source_name: Reference

tag: sample

value: mixture of RNA from snails


title: Schistosoma mansoni exposed 2

source_name: 4-8 mm Biomphalaria glabrata, S. mansoni infected

value: Schistosoma mansoni


title: Schistosoma mansoni exposed 1


title: Echinostoma paraensei exposed 1


title: Schistosoma mansoni exposed 3


title: Control 6

source_name: 4-8 mm Biomphalaria glabrata, control

value: uninfected


title: Wounded 3

source_name: 10-12 mm Biomphalaria glabrata, wounded

value: yes


title: Control 4


title: Control 5


title: Wounded 1


title: HCT116 p53KO cells treated with 100 nM actinomycin D (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_D

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 100 nM actinomycin D (replicate 2)


title: Escherichia coli exposed 3

source_name: 10-12 mm Biomphalaria glabrata, E. coli infected

value: Escherichia coli


title: Wounded 2


title: Micrococcus luteus exposed 3

source_name: 10-12 mm Biomphalaria glabrata, M. luteus infected

value: Micrococcus luteus


title: Micrococcus luteus exposed 2


title: HCT116 wild type cells treated with 100 nM actinomycin D (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_A

source_name: HCT116 colon adenocarcinoma cell line, wild type, 100 nM actinomycin D (replicate 1)


title: HCT116 wild type cells treated with 10 nM actinomycin D (replicate 2)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_B

source_name: HCT116 colon adenocarcinoma cell line, wild type, 10 nM actinomycin D (replicate 2)


title: Echinostoma paraensei exposed 3


title: Escherichia coli exposed 2


title: Escherichia coli exposed 1


title: Control 1

source_name: 10-12 mm Biomphalaria glabrata, control


title: Micrococcus luteus exposed 1


title: Control 3


title: Control 2


title: HCT116 p53KO cells treated with 100 nM actinomycin D (replicate 1)

description:
The isogenic HCT116 cells were provided by B. Vogelstein from Johns Hopkins University
4067190001_C

source_name: HCT116 colon adenocarcinoma cell line, p53KO, 100 nM actinomycin D (replicate 1)


title: young murine 5 days post-fracture (replicate 1)

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: 5 days post fracture

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: All signals scaled to a target intensity of 150

source_name: young murine fracture tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol

value: 6 wk

tag: injury

value: 5 days post fracture

value: fracture callus

value: BALB/c


title: young murine 3 days post-fracture (replicate 1)

description: 3 days post fracture

value: 3 days post fracture


title: young murine 3 days post-fracture (replicate 3)

description: 3 days post fracture


title: old murine 3 days post-fracture (replicate 2)

description: 3 days post fracture

source_name: old murine fracture tissue

value: 8 mo


title: young murine 3 days post-fracture (replicate 2)

description: 3 days post fracture


title: young murine 1 day post-fracture (replicate 3)

description: 1 day post fracture

value: 1 day post fracture


title: old murine 3 days post-fracture (replicate 3)

description: 3 days post fracture


title: old murine 3 days post-fracture (replicate 1)

description: 3 days post fracture


title: young murine 1 day post-fracture (replicate 1)

description: 1 day post fracture


title: old murine 5 days post-fracture (replicate 2)

description: 5 days post fracture


title: young murine 5 days post-fracture (replicate 3)

description: 5 days post fracture


title: young murine 5 days post-fracture (replicate 2)

description: 5 days post fracture


title: young murine 1 day post-fracture (replicate 2)

description: 1 day post fracture


title: old murine 5 days post-fracture (replicate 3)

description: 5 days post fracture


title: Red+/Green- progenitor, experiment B

city: Boston

first: Ibrahim

middle: J

last: Domian

address: 185 Cambridge Street

department: Division of Cardiology

institute: Massachusetts General Hospital

description: Gene expression data from embryonic stem cell derived cardiac progenitors

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure.  The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1.  This resulted in the preprocessed data set.  Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage.  The clustered data was used to generate a heat map with the HeatMapImage module.

source_name: Color sorted embryonic stem cell progenitors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.

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

treatment_protocol: Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),

tag: developmental stage

value: dissociated day 6 embryoid bodies

tag: transgenic reporter

value: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP negative


title: Red+/Green+ progenitor, experiment C

value: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP positive


title: Red-/Green+ progenitor, experiment B

value: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP positive


title: Red-/Green- progenitor, experiment C

value: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP negative


title: Red-/Green- progenitor, experiment B


title: Red-/Green+ progenitor, experiment C


title: Red+/Green- progenitor, experiment C


title: old murine 1 day post-fracture (replicate 1)

description: fracture tissue collected 1 day post fracture

data_processing: All signals normalized to target intensity of 150


title: old murine 5 days post-fracture (replicate 1)

description: 5 days post fracture


title: old murine 1 day post-fracture (replicate 2)

description: 1 day post fracture


title: old murine 1 day post-fracture (replicate 3)

description: 1 day post fracture


title: tetO-Satb2 #3 +DOX

city: Freiburg

first: Rudolf

last: Engelke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology

description: Gene expression data from murine ES cells overexpressing Satb2

hyb_protocol: Performed by Genomics Core Facility, EMBL Heidelberg

data_processing: The data were analyzed using the RMA method of background correction, quantile normalization, and summarization of cell signal intensity

source_name: murine ES cells overexpressing Satb2

growth_protocol: Cells were passaged according to standard procedures with standard ES medium (Non essential AA, Pyruvate, PSG, LIF, 15% serum, beta-mercaptoethanol)

extract_protocol: After 2 days of culture, cells were trypsinized, resuspended in 15ml of medium, allowed to settle for 10 minutes to eliminate feeders. The top 50% of the suspension was used for RNA preparation/Trizol.

treatment_protocol: Cells were grown for 1 days on irradiated feeders after trypsinisation and either cultured for 1 more day under these conditions or induced for 24h by the addition of DOX.

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Satb2 overexpression


title: Red-/Green+ progenitor, experiment A


title: tetO-Satb1 #3 +DOX

description: Gene expression data from murine ES cells overexpressing Satb1

scan_protocol: Performed by Genomics Core Facility, EMBL Heidelberg

source_name: murine ES cells overexpressing Satb1

value: Satb1 overexpression


title: tetO-Satb2 #1

description: Gene expression data from murine ES cells

source_name: murine ES cells

label_protocol: Performed by Genomics Core Facility, EMBL Heidelberg

value: control


title: Red-/Green- progenitor, experiment A


title: tetO-Satb1 #1 +DOX


title: Red+/Green+ progenitor, experiment A


title: tetO-Satb1 #1


title: Satb1-/- clone 2-1

description: Gene expression data from murine Satb -/- ES cells

source_name: murine Satb1-/- ES cells

extract_protocol: After 3 days, cells were trypsinized, resuspended in 15ml of medium, allowed to settle for 10 minutes to eliminate feeders. The top 50% of the suspension was used for RNA preparation/Trizol.

treatment_protocol: Cells were grown for 3 days on irradiated feeders after trypsinisation and cultured in the presence of hygromycin

value: Satb1 knockout


title: Satb1-/- clone 1-1


title: Red+/Green+ progenitor, experiment B


title: tetO-Satb1 #2 +DOX


title: tetO-Satb2 #2


title: tetO-Satb2 #2 +DOX


title: WT #2


title: tetO-Satb2 #1 +DOX


title: WT #3


title: Red+/Green- progenitor, experiment A


title: tetO-Satb1 #2


title: Satb1-/- clone 1-2


title: OriC-null, yabA-null HPUra treated cells replicate 3

description: Investigating the effects of replication arrest on OriC-null, yabA-null cells

hyb_protocol: see: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. PMID: 16120674

source_name: AIG185 RNA

growth_protocol: defined minimal medium. Exponentially growing

treatment_protocol: 38ug/ml HPUra for 60min

value: AIG185, yabA-null, OriC-null

value: RNA from OriC-null, yabA-null cells arrested for replication.

source_name: reference RNA

value: pooled reference RNA


title: OriC-null, yabA-null HPUra treated cells replicate 2

scan_protocol: see: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. PMID: 16120674

value: RNA from cells arrested for replication


title: OriC-null, yabA-null HPUra treated cells replicate 1

label_protocol:
see: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.
PMID: 16120674

value: RNA from cells with arrested replication


title: WT #1


title: OriC-null, yabA-null untreated sample replicate 3

extract_protocol:
see: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.
PMID: 16120674

value: untreated RNA from cultures


title: OriC-null cells control untreated replicate 3

description: Investigating the effects of replication arrest on OriC-null cells

source_name: MMB170 RNA

value: MMB170, OriC-null

value: RNA from untreated control cultures

value: reference RNA


title: Oric-null cells control untreated replicate 2

description: Comparison of the transcriptional effects of arresting DNA replication in oriC-null strains

hyb_protocol: See: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. PMID: 16120674

molecule: cytoplasmic RNA

growth_protocol: defined minimal media 37C

value: untreated control culture. Replicate 2


title: OriC-null, yabA-null untreated sample replicate 1

value: total RNA from untreated yabA, OriC-null strain

value: pooled RNA reference


title: OriC-null cells control untreated replicate 1

scan_protocol: See: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. PMID: 16120674

source_name: MMB170 untreated RNA

value: control RNA from cells that are replicating

value: pooled RNA


title: OriC-null cells treated with HPUra replicate 1

label_protocol:
See: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.
PMID: 16120674

treatment_protocol: add 38ug/ml HPUra for 60min

value: RNA from OriC-null mutant treated with HPUra. Replicate 1

source_name: Reference RNA


title: OriC-null cells treated with HPUra replicate 2

extract_protocol:
See: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.
Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD.
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7.
PMID: 16120674

value: RNA from exponentially growing cells (Strain MMB170) treated with HPUra


title: OriC-null cells treated with HPUra replicate 3

source_name: MMB170 replicate 3 rna

value: RNA from cells with blocked replication HPUra treatment


title: gd T cells from calf 304 stimulated with Yamoa

status: Public on Aug 31 2009

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

description:
Gene expression data from stimulated bovine gamma delta T cells
304_yam

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

scan_protocol: GeneChips were scanned using Affymetrix scanner 7G.

data_processing: The data were imported into Genespring using RMA preprocessing for analysis.

organism: Bos taurus

source_name: Bovine gamma delta T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Peripheral blood was collected from  1 to 6 month old calves and gamma delta T cells were sorted to >97% purity.

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

treatment_protocol: Sorted cells were rested overnight then stimulated for 4 hours with either PBS, Yamoa (32.6ug/ml) or uLPS (10ug/ml).

tag: gamma delta T cells

tag: from bovine calves


title: M14_D13

city: Stanford

first: Elizabeth Ann

last: Joyce

email: ejoyce@stanford.edu, ea.joyce@gmail.com

state: CA

address: Mail Code: 5124

department: Microbiology and Immunology

institute: Stanford University School of Medicine

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66282.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 6760; Software: type: feature extraction; Performer: Elizabeth,,Joyce

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)

source_name: Amplified Universal mouse reference RNA (4ug)

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 4 ug; Parameter Type of label = Cy3; Performer: Elizabeth,,Joyce

extract_protocol:
Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = MELT Total nucleic Acid Isolation System; Parameter Channel 1 reference name = Amplified Universal mouse reference RNA; Parameter Extraction method reference = "Applied Biosystems/Ambion, USA"; Parameter Extracted molecule = RNA; Performer: Elizabeth,,Joyce
Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = RNA Polymerase; Parameter Amplification method reference = Ambion Amino Allyl Message Amp; Performer: Elizabeth,,Joyce

tag: reference

value: Amplified Universal mouse reference RNA

source_name: M14_D13_4ug aRNA

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 4 ug; Parameter Type of label = Cy5; Performer: Elizabeth,,Joyce

extract_protocol:
Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = MELT Total nucleic Acid Isolation System; Parameter Extraction method reference = "Applied Biosystems/Ambion, USA"; Parameter Extracted molecule = RNA; Performer: Elizabeth,,Joyce
Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = RNA Polymerase; Parameter Amplification method reference = Ambion Amino Allyl Message Amp; Performer: Elizabeth,,Joyce

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 13 Days; Parameter Infection = Intranasal infection with 2E8 Streptococcus pneumoniae; Performer: Elizabeth,,Joyce

tag: tissue type

value: Nasal Associated Lymphoid Tissue

tag: time


title: M21_D29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66290.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 5920; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M21_D29_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 29 Days; Parameter Infection = Intranasal infection with 2E8 Streptococcus pneumoniae; Performer: Elizabeth,,Joyce


title: C5_D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66274.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1360, 5400; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C5_D6_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 6 Days; Parameter Infection = Intranasal Mock Infection with PBS as control; Performer: Elizabeth,,Joyce

value: 6 d


title: C11_D29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66286.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1360, 6360; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C11_D29_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 29 Days; Parameter Infection = Intranasal Mock Infection with PBS as control; Performer: Elizabeth,,Joyce


title: M25_D42

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66296.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 6440; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M25_D42_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 42 Days; Parameter Infection = Intranasal infection with 2E8 Streptococcus pneumoniae; Performer: Elizabeth,,Joyce


title: M1_D1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66271.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 6240; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M1_D1_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 1 Day; Parameter Infection = Intranasal infection with 2E8 Streptococcus pneumoniae; Performer: Elizabeth,,Joyce

value: 1 d


title: C2_D1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66270.gif

source_name: C2_D1_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 1 Day; Parameter Infection = Intranasal Mock Infection with PBS as control; Performer: Elizabeth,,Joyce


title: M11_D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66277.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 6000; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M11_D6_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 6 Days; Parameter Infection = Intranasal infection with 2E8 Streptococcus pneumoniae; Performer: Elizabeth,,Joyce


title: M23_D42

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66294.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 5960; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M23_D42_4ug aRNA

value: Intranasal infection with 2E8 Streptococcus pneumoniae


title: C8_D13

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66280.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 7000; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C8_D13_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 13 Days; Parameter Infection = Intranasal Mock Infection with PBS as control; Performer: Elizabeth,,Joyce


title: M6_D1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66297.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 5480; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M6_D1_4ug aRNA


title: gd T cells from calf 304 stimulated with ultrapure LPS

description:
Gene expression data from stimulated bovine gamma delta T cells
304_uLPS


title: C6_D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66275.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 5760; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C6_D6_4ug aRNA

value: Intranasal Mock Infection with PBS as control


title: C10_D29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66285.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 6720; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C10_D29_4ug aRNA


title: C9_D13

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66281.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 6560; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C9_D13_4ug aRNA


title: M16_D13

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66283.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 6400; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M16_D13_4ug aRNA


title: C15_D42

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66293.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 6200; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C15_D42_4ug aRNA

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 42 Days; Parameter Infection = Intranasal Mock Infection with PBS as control; Performer: Elizabeth,,Joyce


title: gd T cells from calf 304 stimulated with vehicle only control

description:
Gene expression data from stimulated bovine gamma delta T cells
304_PBS

source_name: Bovine gamma delta T cells


title: C7_D13

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66279.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 7040; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: Amplified Universal mouse reference RNA (4ug)

source_name: C7_D13_4ug aRNA


title: C4_D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66273.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1320, 5800; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C4_D6_4ug aRNA


title: M10_D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66276.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 5440; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M10_D6_4ug aRNA


title: C13_D42

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66291.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 5920; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C13_D42_4ug aRNA


title: M20_D29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66289.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 6120; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M20_D29_4ug aRNA


title: C14_D42

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66292.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 5160; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: C14_D42_4ug aRNA


title: M19_D29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66288.gif

source_name: M19_D29_4ug aRNA


title: M13_D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66278.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 5840; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M13_D6_4ug aRNA


title: gd T cells from calf 303 stimulated with vehicle only control

description:
Gene expression data stimulated bovine gamma delta T cells
303_PBS

scan_protocol: GeneChips were scanned using Affymetrix scanner 7G.


title: acetic acid-adapted strain, no inhibitor, biological replicate 1

city: Tianjin

first: Bing-Zhi

last: Li

address: Weijin Road 92#

country: China

institute: Tianjin University

description: Gene expression at exponential phase.

hyb_protocol: The biotin-labeled cRNA was hybridized to the GeneChip® Yeast Genome 2.0 Array from Affymetrix (California, US) after dilution and fragmentation according to Affymetrix’s protocol.

scan_protocol: Microarrays were scanned with the Genechip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operation System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Saccharomyces cerevisiae

source_name: acetic acid-adapted strain, without inhibitor addition

label_protocol: Total RNA labeling was conducted according to the Affymetrix GeneChip Expression analysis technical manual (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Strains were incubated in 400 ml high-sugar YPD medium (10 g/L yeast extract, 20 g/L peptone, 100 g/L glucose) in a 2-liter conical flask with an initial OD600 of 0.35.

extract_protocol: Total RNA was isolated according to the hot phenol method.

treatment_protocol: Cultures for microarray analysis were collected 20 minutes after the addition of the inhibitor (furfural, phenol, or acedic acid) or medium, which was added at mid-exponential phase.

tag: strain

value: CGMCC 2756

tag: inhibitor


title: gd T cells from calf 303 stimulated with Yamoa

description:
Gene expression data from stimulated bovine gamma delta T cells
303_yam


title: acetic acid-adapted strain, acetic acid, biological replicate 1

description: Transcriptional response to acetic acid.

source_name: acetic acid-adapted strain, 20 minutes after acetic acid addition

value: acetic acid


title: acetic acid-adapted strain, no inhibitor, biological replicate 2

description: Gene expression at exponential phase.


title: gd T cells from calf 303 stimulated with ultrapure LPS

description:
Gene expression data from stimulated bovine gamma delta T cells
303_uLPS


title: gd T cells from calf 301 stimulated with ultrapure LPS

description:
Gene expression data stimulated bovine gamma delta T cells
301_uLPS


title: gd T cells from calf 301 stimulated with Yamoa

description:
Gene expression data stimulated bovine gamma delta T cells
301_yam


title: furfural-adapted strain, furfural, biological replicate 1

description: Transcriptional response to furfural.

source_name: furfural-adapted strain, 20 minutes after furfural addition

value: CGMCC 2755

value: furfural


title: Shg1 IP (1)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82472.gif
Antibody used in IP: TAP-tagged strain

hyb_protocol: cDNAs were fluorescently labeled and hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer.

scan_protocol: GenePix 4200A

source_name: total RNA extract Shg1-TAP (1)

label_protocol: not provided

extract_protocol: not provided

tag: organism

value: Saccharomyces cerevisiae

source_name: total RNA Shg1 IP (1)

label_protocol: RNAs were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture.

extract_protocol: Cells were grown to mid-log phase in rich media and harvested by centrifugation. TAP-tagged Shg1 was affinity-purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input) and from the purified protein sample with the RNAeasy Kit (Qiagen).


title: acetic acid-adapted strain, acetic acid, biological replicate 2


title: furfural-adapted strain, no inhibitor, biological replicate 2

description: Gene expression at exponential phase.

source_name: furfural-adapted strain, without inhibitor addition


title: Mock IP (3)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82468.gif
Antibody used in IP: not tagged strain

source_name: total RNA extract mock (3)

source_name: total RNA mock IP (3)


title: furfural-adapted strain, furfural, biological replicate 2

description: Transcriptional response to furfural.


title: M17_D13

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66284.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 6320; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: Amplified Universal mouse reference RNA (4ug)

source_name: M17_D13_4ug aRNA


title: Shg1 IP (3)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82474.gif
Antibody used in IP: TAP-tagged strain

source_name: total RNA extract Shg1-TAP (3)

source_name: total RNA Shg1 IP (3)


title: gd T cells from calf 301 stimulated with vehicle only control

description:
Gene expression data stimulated bovine gamma delta T cells
301_PBS

source_name: Bovine gamma delta T cells


title: Mock IP (1)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82469.gif
Antibody used in IP: not tagged strain

source_name: total RNA extract mock (1)

source_name: total RNA mock IP (1)


title: wild strain, acetic acid, biological replicate 2

source_name: industrial yeast, 20 minutes after acetic acid addition

value: angel yeast


title: Mock IP (4)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82470.gif
Antibody used in IP: not tagged strain

source_name: total RNA extract mock (4)

source_name: total RNA mock IP (4)


title: Shg1 IP (4)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82473.gif
Antibody used in IP: TAP-tagged strain

source_name: total RNA extract Shg1-TAP (4)

source_name: total RNA Shg1 IP (4)


title: M2_D1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66272.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1320, 5680; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M2_D1_4ug aRNA


title: wild strain, acetic acid, biological replicate 1


title: furfural-adapted strain, no inhibitor, biological replicate 1

description: Gene expression at exponential phase.


title: CE - 95-cell - Replicate C

city: Haifa

first: Itai

last: Yanai

address: Technion City

country: Israel

institute: Technion - Israel Institute of Technology

description: C. elegans (N2 strain) and C. briggsae (AF16 strain) embryos were isolated and staged as described previously (Baugh et al. 2003). The five embryonic stages assayed – the 4-, 28-, 55-, 95-, and 190-cell – were determined for each organism by DAPI staining and DIC microscopy. For C. elegans and C. briggsae the minutes following the 4-cell stage for the four later stages are 80’, 115’, 155’ and 200’ and 55’, 80’, 120’, 160’, respectively.

hyb_protocol: Agilent one-color hybridization protocol

scan_protocol: The arrays were scanned at 10% laser power to avoid signal saturation.

data_processing: Feature Extraction software was used to extract the data which was then mean-normalized.

organism: Caenorhabditis elegans

source_name: CE - 95-cell - Replicate C

label_protocol: 10 ug of aRNA was labeled with Cy3 using the Ambion MessageAmpII kit and 1.65µg labeled aRNA was used to hybridize onto each microarray.

extract_protocol: 50 embryos were isolated for each sample and the total RNA was extracted as described previously (Baugh et al. 2003). To obtain sufficient RNA for microarray analysis, RNA was amplified by two rounds of in vitro transcription (IVT) using the MessageAmpII kit (Ambion) with the following modifications designed to increase the average lengths of the aRNA populations (Baugh et al. 2001). First-round cDNA construction from total RNA was carried out at 1/5 of the recommended quantities and total volume, while IVT was carried out at 1/2 of the recommended volume. 100ng aRNA from the first round was used as input for the second round of amplification following the manufacturers protocol for amino-allyl modified nucleotides. Each embryonic stage was produced in biological triplicates, with the exception of C. elegans 55-cell and C. briggsae 4-cell and 95-cell, which were hybridized in duplicates due to poor amplification of one of the triplicates. The same procedure was also used to identify the C. elegans Hawaiian (CB4856) 4-cell stage transcriptome in triplicates.

value: 95-cell stage


title: Shg1 IP (2)

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82471.gif
Antibody used in IP: TAP-tagged strain

source_name: total RNA extract Shg1-TAP (2)

source_name: total RNA Shg1 IP (2)


title: M24_D42

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66295.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 6480; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: M24_D42_4ug aRNA


title: H9_2

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: Illumina HumanHT-12 V3.0

hyb_protocol: 750ng of labeled cRNA were hybridized on the Illumina HumanHT-12 V3.0 arrays according to Illumina's instructions.

scan_protocol: according to manufacturer

data_processing: Normalization and model-based expression measurements were performed with the Illumina analysis package (LUMI) available through the open-source Bioconductor project (http://www.bioconductor.org) within the statistical programming language R (http://cran.r-project.org/). A pair-wise comparison of neural crest cell from (H9 and C14-iPSC) versus FD-iPSC was performed using the Linear Models for Microarray Data package ( LIMMA) available through Bioconductor. Genes found to have an adjusted P-value < 0.05 and a fold change greater than two were considered significant.

source_name: hESC (undifferentiated)

label_protocol: 200ng of total RNA were labeled using the Illumina Total Prep RNA Amplification Kit (Ambion, cat#AMIL1791) according the manufacturer's instructions

extract_protocol: total RNA was extracted from cell pellet using Trizol (invitrogen)

value: hESC (undifferentiated)


title: C12_D29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66287.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1360, 6360; Software: type: feature extraction; Performer: Elizabeth,,Joyce

source_name: Amplified Universal mouse reference RNA (4ug)

source_name: C12_D29_4ug aRNA


title: C14_4

description: Illumina HumanHT-12 V3.0

source_name: control-hiPSC (undifferentiated)

value: control-hiPSC (undifferentiated)


title: wild strain, phenol, biological replicate 2

description: Transcriptional response to phenol.

source_name: industrial yeast, 20 minutes after phenol addition

value: phenol


title: C14_1

description: Illumina HumanHT-12 V3.0


title: H9_1

description: Illumina HumanHT-12 V3.0


title: wild strain, phenol, biological replicate 1

description: Transcriptional response to phenol.


title: CE - 4-cell - Hawaiian - Replicate C

source_name: CE - Hawaiian - 4-cell - Replicate C

value: 4-cell stage

value: Hawaiian


title: wild strain, furfural, biological replicate 2

description: Transcriptional response to furfural.

source_name: industrial yeast, 20 minutes after furfural addition


title: wild strain, furfural, biological replicate 1

description: Transcriptional response to furfural.


title: CE - 4-cell - Replicate C

source_name: CE - 4-cell - Replicate C


title: FDiPS102_1

description: Illumina HumanHT-12 V3.0

source_name: FD#102-iPSC (undifferentiated)

value: FD#102-iPSC (undifferentiated)