title: EOM strabismic D8

city: Reno

first: Amy

middle: L.

last: Altick

state: NV

address: No. Virginia St., MS 352

department: Physiology and Cell Biology

institute: University of Nevada, Reno

hyb_protocol: Hybridization was done as per Affymetrix protocols using GeneChip Hybridization Oven 640. Staining was done as per Affymetrix protocols in GeneChip Fluidics Station 450.

scan_protocol: Gene chips were scanned using GeneChip Scanner 3000 7G.

data_processing: Data were first assessed for quality and presence (P) or absence (A) of each probe set using Expression Console by Affymetrix at default settings; data then went through strict quality control steps and RMA-normalization (see associated publication for details); matrix table is the set of probe sets that were present (P) on at least 6 of 8 arrays.

source_name: corrective surgery

label_protocol: Samples were processed by Nevada Genomics Center following Affymetrix protocols. RNA was amplified to 15ug, 1ul RNA spike was added to 4ul RNA solution, in vitro transciption incubaioin time was 3 hours. 20ug RNA was procesed in the fragmentation reaction.

extract_protocol: Samples were homogenized in TRIzol; centrifuged; and supernatant was mixed with chloroform, transferred to Phase Lock Gel tubes and centrifuged.  Supernatant was mixed with EtOH, and loaded onto RNAeasy columns from Qiagen.  Kit protocol was followed including on-column DNAse digestion. RNA was eluted in approximately 15-25ul of H2O, quantified on nanodrop spectrometer, gel-verified, and stored at -80C.

treatment_protocol: Samples were collected directly into 1ml RNAlater in the case of surgery or between 1-2.5 hours after death in the case of organ donors. Samples were frozen at -80C until used for RNA extraction.

value: Extraocular muscle, Medial Rectus, right

tag: age (yrs)

value: F

tag: sample wt (mg)

tag: phenotype

value: strabismus


title: Dis XVI 15 Min heatshock

status: Public on Aug 14 2012

type: RNA

city: Cambridge

first: Ana

middle: B

last: Oromendia

state: MA

address: 500 Main St

country: USA

institute: MIT- Koch Institute

hyb_protocol: Equal masses of both sample and reference RNA were hybridized for 16-20 hours

scan_protocol: Scanned on a Agilent Technologies Scanner model G2505B

data_processing: Extraction Software: Agilent Feature Extraction, version 10.5.1.1. Opened on puma.db

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Dis XVI RNA 15 min 37C

label_protocol: RNA was labeled with Agilent QuickAmp labeling kit.

extract_protocol: Total RNA was extracted via acid-phenol extraction

tag: genotype

value: disomic chr. XVI

tag: time

tag: treatment

tag: genetic background

source_name: WT 25 C

value: reference

value: wild type


title: EOM donor 5RMRb

label: biotin

organism: Homo sapiens

source_name: organ donor

tag: tissue

tag: gender

value: normal


title: R20

status: Public on Aug 15 2012

city: Cleveland

first: Matthew

last: Ginsberg

state: OH

address: 9500 Euclid Ave

department: Lerner College of Medicine

institute: Cleveland Clinic Foundation

description: Additional subject data may be obtained from the Autism Tissue Program

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized, variance-stabilized, and filtered for probes with detection p-values less than or equal to 0.01 in R using the lumi Bioconductor package.

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Qiagen AllPrep Kit was used to co-extract DNA and RNA from frozen brain tissue samples of about 40mg each.

tag: brain region

value: cerebellum

tag: age (years)

tag: postmortem interval (hours)

tag: Cause of death

value: Other


title: Dis X 30 Min heatshock

source_name: Dis X RNA 30 min 37C

value: disomic chr. X


title: huBM_CD38_fresh_rep3

city: los angeles

first: Lisa

last: Kohn

state: ca

address: 650 charles e young drive south

institute: UCLA

description: gene expression from human bone marrow CD38-

hyb_protocol: Hybridized to GeneChip expression arrays, stained with a streptavidin phycoerythrin conjugate

scan_protocol: GeneChip Scanner 3000DX V.2.

data_processing: CEL files were normalised using RMA method using affy package from Bioconductor version 2.8

source_name: CD34 enriched Bone Marrow, Sorted CD34+ CD38-

label_protocol: Affymetrix protocol

growth_protocol: None, freshly isolated human bone marrow

extract_protocol: RNA from BM from 3 different individuals was extracted using Microkit (Qiagen, Valencia California)

treatment_protocol: Freshly isolated human bone marrow was ficoll purified, CD34 enriched with an immunomagnetic column, and then sorted on a FACS Aria

tag: cell type

value: human bone marrow CD38-


title: huBM_CD38_fresh_rep2


title: Dis XIV 15 Min heatshock

source_name: Dis XIV RNA 15 min 37C

value: disomic chr. XIV


title: Dis XIV 0 Min heatshock

source_name: Dis XIV RNA 0 min 37C


title: Dis XIV 5 Min heatshock

source_name: Dis XIV RNA 5 min 37C


title: Dis XVI 0 Min heatshock

source_name: Dis XVI RNA 0 min 37C


title: EOM donor ALMR

value: Extraocular muscle, Medial Rectus, left


title: EOM donor DRMR

value: M


title: Dis X 15 Min heatshock

source_name: Dis X RNA 15 min 37C


title: EOM strabismic A8


title: EOM strabismic E3


title: EOM strabismic F1-R

value: Extraocular muscle, Lateral Rectus, right


title: EOM donor 5RMRa


title: Dis X 5 Min heatshock

source_name: Dis X RNA 5 min 37C


title: Dis X 0 Min heatshock

source_name: Dis X RNA 0 min 37C


title: Dis V 30 Min heatshock

source_name: Dis V RNA 30 min 37C

value: disomic chr. V


title: Dis V 5 Min heatshock

source_name: Dis V RNA 5 min 37C


title: Dis V 15 Min heatshock

source_name: Dis V RNA 15 min 37C


title: WT 30 Min heatshock

source_name: WT RNA 30 min 37C


title: WT 0 Min heatshock

source_name: WT RNA 0 min 37C


title: WT 15 Min heatshock

source_name: WT RNA 15 min 37C


title: WT 5 Min heatshock

source_name: WT RNA 5 min 37C

source_name: WT 25 C


title: Dis V 0 Min heatshock

source_name: Dis V RNA 0 min 37C


title: 4312 WT MEP, 21216

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: Labeled targets were hybridized to Mouse Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using Affymetrix GeneArray scanner GS 3000.

data_processing:
Raw data were processed with the RMA algorithm in Partek Genomics Suite (version 6.6).
Extended exons were included in the analysis.

Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.extended.mps

organism: Mus musculus

source_name: Bone marrow, megakaryocyte erythrocyte progenitor, Bl/6 Taconic, 7 wks

label_protocol: Amplified cDNA was biotin labeled using the EncoreTM Biotin Module (NuGen Technologies, San Carlos, CA) according to the manufacturer's instructions.

extract_protocol: Total cellular RNA was purified using Trizol reagent, quantified using UV spectroscopy (Nanodrop Technologies, Wilmington, DE) and qualitatively assessed using an Experian Bioanalyzer (Hercules, CA). Amplified cDNA was prepared from 20ng of total RNA using the whole transcript WT-Ovation TM RNA Amplification System.

tag: strain/background

value: Bl/6 Taconic

tag: genotype/variation

value: WT

value: bone marrow

value: megakaryocyte erythrocyte progenitor

tag: time of progression

value: 7 wks


title: 4313 WT MEP, 21217


title: 4311 WT MEP, 21215


title: 4212 WT GMP, 21212

source_name: Bone marrow, granulocyte monocyte progenitor, Bl/6 Taconic, 7 wks

value: granulocyte monocyte progenitor


title: 4213 WT GMP, 21213


title: 4310 WT MEP, 21214


title: 4113 WT CMP, 21209

source_name: Bone marrow, common myeloid progenitors, Bl/6 Taconic, 7 wks

value: common myeloid progenitors


title: 4211 WT GMP, 21211


title: 4111 WT CMP, 21207


title: 5316 mCG-PR MEP, 21205

source_name: Bone marrow, megakaryocyte erythrocyte progenitor, mCG-PR N24 Bl/6 Taconic, 9 wks

value: mCG-PR N24

value: 9 wks


title: 4112 WT CMP, 21208


title: 5213 mCG-PR GMP, 21198

source_name: Bone marrow, granulocyte monocyte progenitor, mCG-PR N24 Bl/6 Taconic, 9 wks


title: 5116 mCG-PR CMP, 21197

source_name: Bone marrow, common myeloid progenitors, mCG-PR N24 Bl/6 Taconic, 9 wks


title: 5313 mCG-PR MEP, 21202


title: 5215 mCG-PR GMP, 21200


title: mCG-PR Neutrophils_rep3, 19271

source_name: Bone marrow, neutrophils, mCG-PR N22 Bl/6 Taconic, 6 wks

value: mCG-PR N22

value: neutrophils

value: 6 wks


title: 5216 mCG-PR GMP, 21201


title: 5315 mCG-PR MEP, 21204


title: mCG-PR Neutrophils_rep1, 19269


title: 5214 mCG-PR GMP, 21199


title: WT Neutrophils_rep4, 17471

source_name: Bone marrow, neutrophils, Bl/6 Taconic, 6 wks


title: 5113 mCG-PR CMP, 21194


title: WT Promyelocytes_rep5, 17468

source_name: Bone marrow, promyelocytes, Bl/6 Taconic, 6 wks

value: promyelocytes


title: 5314 mCG-PR MEP, 21203


title: 4210 WT GMP, 21210


title: mCG-PR Promyelocytes_rep2, 19267

source_name: Bone marrow, promyelocytes, mCG-PR N22 Bl/6 Taconic, 6 wks


title: 5115 mCG-PR CMP, 21196


title: mCG-PR Promyelocytes_rep1, 19266


title: mCG-PR Promyelocytes_rep3, 19268


title: mCG-PR Neutrophils_rep2, 19270


title: WT Neutrophils_rep3, 17470


title: 5114 mCG-PR CMP, 21195


title: Ctsg KO KLS_rep2, 17042

source_name: Bone marrow, KLS, Ctsg KO N10 Bl/6, 10 wks

value: Ctsg KO N10

value: KLS

value: 10 wks


title: WT Promyelocytes_rep4, 17256


title: WT Promyelocytes_rep6, 17469


title: Ctsg KO KLS_rep1, 17041


title: WT Promyelocytes_rep3, 16853


title: tumour#7 gene expression

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

description: Gene expression data from murine B cell lymphoma

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

label: Biotin

source_name: tumour

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).

treatment_protocol: Diagnostic sorted B cell lymphoma samples derived from Cgamma1-cre; R26StopFLMYC;R26StopFLP110* transplanted animals

value: B cell lymphoma

tag: tumor number


title: tumour#8 gene expression


title: tumour#11 gene expression


title: WT Promyelocytes_rep2, 16852

value: Bl/6 Taconic


title: tumour#6 gene expression


title: Mouse APL 9500, 16848

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 335 days

value: mCG-PR N10

value: spleen

value: murine acute promyelocytic leukemia

value: 335 days


title: Mouse APL 9523, 16847

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 334 days

value: 334 days


title: Mouse APL 9495, 16846

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 338 days

value: 338 days


title: Mouse APL 9529, 16843

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 294 days

value: 294 days


title: Mouse APL 9514, 16841

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 553 days

value: 553 days


title: Mouse APL 33, 16844

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 295 days

value: 295 days


title: hypoxia, biological rep 1 [IterPlier-exon level]

city: Marburg

first: Julia

middle: E.

last: Weigand

address: Marbacher Weg 6

department: Pharmacy

institute: University of Marburg

description:
CEL file: H1.CEL (on the Series record)
H1-Iter-exon level
48 h incubation under hypoxic conditions

hyb_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.

data_processing:
Data were processed using the EAA (exon array analyzer, version 2.2, http://eaa.mpi-bn.mpg.de/exon/index.php);
RMA or Iter-PLIER normalized; gene and exon expression levels from Affymetrix Power Tools
Exon Array Analyzer: a web interface for Affymetrix exon array analysis, Bioinformatics (2009) 25 (24): 3323-3324, PMID: 19808879
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

growth_protocol: HUVECs (Lonza) were grown in EBM medium (Lonza) suppelement with EGM single quots (Lonza) and 10% FCS (Gibco). After the third passage, 1 Mio cells were seeded into 6 cm dishes.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol. The optional on-column DNA digestion was performed, using the RNase-free DNase Set (Qiagen).

treatment_protocol: After 18 h attchement, cells were supplied with fresh medium and incubated for 48 h under normoxic (21%) or hypoxic (1%) conditions.

tag: cell line

value: HUVEC

value: human umbilical vein endothelial cells

tag: oxygen

value: 1% (hypoxia)


title: Mouse APL 36, 16845

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 309 days

value: 309 days


title: hypoxia, biological rep 3 [IterPlier-exon level]

description:
CEL file: H3.CEL (on the Series record)
H3-Iter-exon level
48 h incubation under hypoxic conditions

scan_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.


title: Mouse APL 31, 16849

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 344 days

value: 344 days


title: WT Promyelocytes_rep1, 16838

value: WT

value: bone marrow

value: promyelocytes

value: 6 wks


title: Mouse APL 9504, 16836

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 393 days

value: Bl/6 Taconic

value: mCG-PR N10

value: spleen

value: 393 days


title: Mouse APL 9508, 16850

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 367 days

value: murine acute promyelocytic leukemia

value: 367 days


title: hypoxia, biological rep 2 [IterPlier-exon level]

description:
CEL file: H2.CEL (on the Series record)
H2-Iter-exon level
48 h incubation under hypoxic conditions

label_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.


title: WT Neutrophils_rep1, 16837

value: neutrophils


title: normoxia, biological rep 1 [IterPlier-exon level]

description:
CEL file: N1.CEL (on the Series record)
N1-Iter-exon level
48 h incubation under normoxic conditions

value: 21% (normoxia)


title: hypoxia, biological rep 3 [RMA-exon level]

description:
CEL file: H3.CEL (on the Series record)
H3-RMA-exon level
48 h incubation under hypoxic conditions

value: HUVEC


title: hypoxia, biological rep 2 [RMA-exon level]

description:
CEL file: H2.CEL (on the Series record)
H2-RMA-exon level
48 h incubation under hypoxic conditions

value: human umbilical vein endothelial cells


title: tumour#10 gene expression

value: B cell lymphoma


title: Mouse APL 9509, 16839

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 313 days

value: 313 days


title: normoxia, biological rep 3 [IterPlier-exon level]

description:
CEL file: N3.CEL (on the Series record)
N3-Iter-exon level
48 h incubation under normoxic conditions


title: EXP-NHM 7-TERT-PMA

city: Chapel Hill

first: Craig

last: Carson

state: North Carolina

address: 413 Mary Ellen Jones Bldg

department: DERMATOLOGY

institute: UNC-CH

description: Reference RNA

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human Melanoma Cell lIne 80% confluent, 24 hr old media

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in the indicated media, the media was removed and new media was added 24 hours prior to harvesting the cells

extract_protocol: RNA was extracted using Qiagen RNAeasy Kit

treatment_protocol: Cells were not treated unless stated above

value: NHM 7

value: TERT + PMA

tag: media

value: Telomerase added

source_name: Invitrogen Reference RNA

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: sample type

value: Invitrogen Reference RNA


title: normoxia, biological rep 3 [RMA-exon level]

description:
CEL file: N3.CEL (on the Series record)
N3-RMA-exon level
48 h incubation under normoxic conditions


title: EXP-WM 35

description: Reference RNA

value: WM 35

value: Tu 2%

tag: d0 rank (amount of radiation that allows 37% of the cells to survive)

tag: genotype

value: raf


title: normoxia, biological rep 2 [RMA-exon level]

description:
CEL file: N2.CEL (on the Series record)
N2-RMA-exon level
48 h incubation under normoxic conditions


title: normoxia, biological rep 2 [IterPlier-exon level]

description:
CEL file: N2.CEL (on the Series record)
N2-Iter-exon level
48 h incubation under normoxic conditions


title: WT Neutrophils_rep2, 16840

source_name: Bone marrow, neutrophils, Bl/6 Taconic, 6 wks

value: Bl/6 Taconic

value: WT

tag: tissue

value: bone marrow

value: 6 wks


title: normoxia, biological rep 1 [RMA-exon level]

description:
CEL file: N1.CEL (on the Series record)
N1-RMA-exon level
48 h incubation under normoxic conditions


title: Mouse APL 9520, 16835

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 277 days

value: mCG-PR N10

value: spleen

value: murine acute promyelocytic leukemia

value: 277 days


title: WT_SLAM_6wks_rep2, 17269

source_name: Bone marrow, SLAM, Bl/6 Taconic, 6 wks

value: SLAM


title: Mouse APL 29, 16834

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 238 days

value: 238 days


title: hypoxia, biological rep 1 [RMA-exon level]

description:
CEL file: H1.CEL (on the Series record)
H1-RMA-exon level
48 h incubation under hypoxic conditions

value: HUVEC

value: human umbilical vein endothelial cells

value: 1% (hypoxia)


title: EXP-WM 2664

description: Reference RNA

value: DMEM 10% FBS

value: Invitrogen Reference RNA


title: EXP-WM 1361a

description: Reference RNA

value: Tu 2%

tag: g1 checkpoint  (percentage of the cells that arrest in g1 after irradiation)


title: Mouse APL 9492, 16832

source_name: Spleen, acute promyelocytic leukemia, mCG-PR N10 Bl/6 Taconic, 252 days

value: 252 days


title: EXP-WM 1232

description: Reference RNA


title: tumour#19 gene expression

source_name: tumour

value: B cell lymphoma


title: EXP-WM 1158

description: Reference RNA

value: TU 2%

value: raf

tag: g2 checkpoint (the percentage of cells that arrest in g2 after irradiation)


title: WT_KLS_13wks_rep3, 17265

source_name: Bone marrow, KLS, Bl/6 Taconic, 12 wks

value: Bl/6 Taconic

value: WT

value: bone marrow

value: KLS

value: 12 wks


title: EXP-UACC 257

description: Reference RNA

value: UACC 257

value: RPMI, 10% FBS

tag: sf2 (the amount of radiation that allows for 50% of the cells to survive)


title: EXP-VMM 39

description: Reference RNA

value: VMM 39

value: ras


title: mCG-PR_KLS_6wks_rep3, 17264

source_name: Bone marrow, KLS, mCG-PR N17 Bl/6 Taconic, 6 wks

value: mCG-PR N17

value: 6 wks


title: EXP-SKMEL 78

description: Reference RNA

value: SKMEL 78

tag: additional information about cells

value: Same Cell Line as SKMEL 88

value: wt

value: Invitrogen Reference RNA


title: mCG-PR_KLS_13wks_rep2, 17261

source_name: Bone marrow, KLS, mCG-PR N17 Bl/6 Taconic, 13 wks

value: 13 wks


title: Malignant Mesothelioma Amo SM 4

type: genomic

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: According to the manufacturer's protocol (Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis, Protocol Version 4.0, June 2006).

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Normal kidney, Fischer 344 / Brown Norway F1 hybrid

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

tag: disease state

value: Normal

value: kidney

tag: strain

value: Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Amo 3-5-4

value: Malignant Mesothelioma

tag: treatment


title: mCG-PR_KLS_13wks_rep1, 17260

tag: strain/background

value: Bl/6 Taconic

tag: genotype/variation

value: bone marrow

tag: cell type

value: KLS


title: Malignant Mesothelioma Amo EM 3

scan_protocol: According to the manufacturer's protocol (Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis, Protocol Version 4.0, June 2006).

source_name: Malignant Mesothelioma, Amo 4-5-4


title: WT_KLS_13wks_rep4, 17266

value: WT

tag: time of progression

value: 12 wks


title: EXP-SKMEL 88

description: Reference RNA

tag: cell line

value: SKMEL 88

value: RPMI, 10% FBS

value: Same Cell Line as SKMEL 78


title: mCG-PR_KLS_6wks_rep1, 17262

value: mCG-PR N17

value: 6 wks


title: Mouse APL 26, 16833

value: mCG-PR N10

value: spleen

value: murine acute promyelocytic leukemia

value: 238 days


title: Malignant Mesothelioma Amo SM 1

label_protocol: According to the manufacturer's protocol (Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis, Protocol Version 4.0, June 2006).

value: Normal

value: kidney

source_name: Malignant Mesothelioma, Amo 3-5-1


title: Malignant Mesothelioma Amo SM 3

value: Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Amo 4-6-1

value: Malignant Mesothelioma


title: mCG-PR_SLAM_7wks_rep2, 17259

source_name: Bone marrow, SLAM, mCG-PR N17 Bl/6 Taconic, 7 wks

value: Bl/6 Taconic

value: bone marrow

value: SLAM

value: 7 wks


title: Malignant Mesothelioma Amo BM 1

source_name: Malignant Mesothelioma, Amo 3-6-6


title: Malignant Mesothelioma Cro SM 3

source_name: Malignant Mesothelioma, Cro 4-3-2-4


title: Malignant Mesothelioma Amo EM 2

source_name: Malignant Mesothelioma, Amo 3-5-7


title: Malignant Mesothelioma Amo EM 1

source_name: Malignant Mesothelioma, Amo 3-6-7


title: Malignant Mesothelioma Amo SM 2

source_name: Malignant Mesothelioma, Amo 3-6-5


title: WT_KLS_13wks_rep2, 16981

source_name: Bone marrow, KLS, Bl/6 Taconic, 13 wks

value: WT

value: KLS

value: 13 wks


title: Malignant Mesothelioma Cro SM 2

source_name: Malignant Mesothelioma, Cro 3-3-8


title: EXP-SKMEL 27

description: Reference RNA

source_name: Human Melanoma Cell lIne 80% confluent, 24 hr old media

value: SKMEL 27

tag: media

value: RPMI, 10% FBS

value: raf

source_name: Invitrogen Reference RNA

value: Invitrogen Reference RNA


title: mCG-PR_SLAM_7wks_rep1, 17258

value: mCG-PR N17


title: mCG-PR_KLS_6wks_rep2, 17263

source_name: Bone marrow, KLS, mCG-PR N17 Bl/6 Taconic, 6 wks

value: 6 wks


title: EXP-SKMEL 24

description: Reference RNA

value: SKMEL 24

value: MEM, 0.5XAA, 10% FBS

tag: sample type


title: hypoxia, biological rep 3 [IterPlier-gene level]

description:
CEL file: H3.CEL (on the Series record)
H3-Iter-gene level
48 h incubation under hypoxic conditions

value: HUVEC

value: human umbilical vein endothelial cells

tag: oxygen

value: 1% (hypoxia)


title: hypoxia, biological rep 2 [IterPlier-gene level]

description:
CEL file: H2.CEL (on the Series record)
H2-Iter-gene level
48 h incubation under hypoxic conditions


title: EXP-SKMEL 239

description: Reference RNA

value: SKMEL 239

tag: d0 rank (amount of radiation that allows 37% of the cells to survive)

tag: genotype


title: Malignant Mesothelioma Cro BM 3

value: Normal

tag: tissue

value: kidney

value: Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Cro 4-3-1-1

value: Malignant Mesothelioma


title: hypoxia, biological rep 1 [IterPlier-gene level]

description:
CEL file: H1.CEL (on the Series record)
H1-Iter-gene level
48 h incubation under hypoxic conditions


title: Malignant Mesothelioma Cro BM 2

source_name: Normal kidney, Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Cro 3-4-6


title: Malignant Mesothelioma Amo BM 2

source_name: Malignant Mesothelioma, Amo 3-6-4


title: Malignant Mesothelioma Cro BM 1

source_name: Malignant Mesothelioma, Cro 3-4-4


title: normoxia, biological rep 3 [IterPlier-gene level]

description:
CEL file: N3.CEL (on the Series record)
N3-Iter-gene level
48 h incubation under normoxic conditions

value: 21% (normoxia)


title: EXP-SKMEL 235

description: Reference RNA

value: SKMEL 235

tag: g1 checkpoint  (percentage of the cells that arrest in g1 after irradiation)

tag: g2 checkpoint (the percentage of cells that arrest in g2 after irradiation)


title: WT_SLAM_6wks_rep1, 17267

source_name: Bone marrow, SLAM, Bl/6 Taconic, 6 wks

value: Bl/6 Taconic

value: WT

value: bone marrow

value: SLAM


title: EXP-SKMEL 28

description: Reference RNA

value: SKMEL 28

value: raf

tag: sf2 (the amount of radiation that allows for 50% of the cells to survive)

value: Invitrogen Reference RNA


title: EXP-SKMEL 23

description: Reference RNA

value: SKMEL 23

value: DMEM 10% FBS

value: wt


title: Malignant Mesothelioma Cro EM 2

tag: disease state

source_name: Malignant Mesothelioma, Cro 4-3-1-5


title: low CcpA induction replicate 3

city: Groningen

first: Bogumila

last: Marciniak

address: Nijenborgh 7

department: Department of Genetics

country: Netherlands

institute: Rijksuniversiteit Groningen

description:
replicate 3
slide 95

hyb_protocol: The labelled cDNA was hybridized to oligo DNA microarray in Ambion Slidehyb #1 buffer (Ambion Eurpe Ltd) at 48°C for 18 hours. Next, microarray slides were washed in 2 × SSC with 0.5% SDS, 1 × SSC with 0.25% SDS and 1 × SSC with 0.1% SDS and dried by centrifugation.

scan_protocol: Images were acquired with GeneTac LS IV confocal laser scanner (Genomics Solutions).

data_processing:
Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP (van Hijum et. al. (2003) Appl. Bioinformatics 2, 241-244). Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of overexpression mutant strain over the wild-type strain were calculated and are represented in Matrix1. Further analysis was performed with a Cyber-T Student t test for paired data and resulting ratios are represented in Matrix2 (provided as a supplementary file on the Series record).
Matrix2 value definition: log2 normalized across samples mean ratio representing test/control

organism: Bacillus subtilis

source_name: Net intensity (tr.mean) {A}

label_protocol: 20 μg of total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a CyScribe GFX purification kit (Amersham Biosciences).

growth_protocol: B. subtilis strain MP902 [strain MP901 (Ptet-ccpA, KmR) carrying pWH119 (Pxyl-tetR, EmR)] was grown at 37°C (with shaking) in 50 ml of reach TY medium supplemented with 15 mg/ml kanamycine, 2.5 mg/ml arythromycine, 1% glucose, 0.2% xylose and different concentrations of anhydrotetracyclin (aTc): 0, 0.02, 0.002 or 0.0001 μM.

extract_protocol: 16 ml of culture at OD600=0.8 was harvested for total RNA isolation. RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) according to the manufacturer's instruction. Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures and from one culture of each strain an additional sample was collected for technical replicate.

treatment_protocol: TY medium was supplemented with 0.2% xylose for induction of tetR expression and different concentrations of aTc for ccpA expression induction.

tag: strain

tag: reference

value: test

source_name: Net intensity (tr.mean) {B}

value: 0 μM aTc

value: control


title: normoxia, biological rep 2 [IterPlier-gene level]

description:
CEL file: N2.CEL (on the Series record)
N2-Iter-gene level
48 h incubation under normoxic conditions

value: HUVEC

value: human umbilical vein endothelial cells


title: low CcpA induction replicate 2

description:
replicate 2
slide 91

tag: treatment


title: WT_KLS_13wks_rep1, 16980

tag: strain/background

tag: genotype/variation

value: KLS

value: 13 wks


title: Malignant Mesothelioma Chry SM 2

value: Normal

value: kidney

value: Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Chry 3-1-5

value: Malignant Mesothelioma


title: EXP-SKMEL 187

description: Reference RNA

value: SKMEL 187


title: hypoxia, biological rep 3 [RMA-gene level]

description:
CEL file: H3.CEL (on the Series record)
H3-RMA-gene level
48 h incubation under hypoxic conditions

tag: cell type

value: 1% (hypoxia)


title: EXP-SKMEL 190

description: Reference RNA

tag: cell line

value: SKMEL 190

value: RPMI, 10% FBS

value: raf

value: Invitrogen Reference RNA


title: normoxia, biological rep 1 [IterPlier-gene level]

description:
CEL file: N1.CEL (on the Series record)
N1-Iter-gene level
48 h incubation under normoxic conditions

value: 21% (normoxia)


title: EXP-SKMEL 224

description: Reference RNA

value: SKMEL 224

tag: media

value: ras


title: Malignant Mesothelioma Cro EM 3

source_name: Malignant Mesothelioma, Cro 4-3-2-2


title: Malignant Mesothelioma Chry BM 3

source_name: Malignant Mesothelioma, Chry 3-2-3


title: low CcpA induction replicate 1

description:
replicate 1
slide 88

value: test

value: 0 μM aTc

value: control


title: medium CcpA induction replicate 3

description:
replicate 3
slide 28

value: 0.002 μM aTc


title: hypoxia, biological rep 2 [RMA-gene level]

description:
CEL file: H2.CEL (on the Series record)
H2-RMA-gene level
48 h incubation under hypoxic conditions

value: HUVEC

value: human umbilical vein endothelial cells


title: Malignant Mesothelioma Chry BM 2

value: Normal

value: kidney

value: Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Chry 3-2-11


title: Malignant Mesothelioma Chry BM 1

source_name: Malignant Mesothelioma, Chry 3-1-4

value: Malignant Mesothelioma


title: Malignant Mesothelioma Cro EM 1

source_name: Malignant Mesothelioma, Cro 4-4-1-2


title: Malignant Mesothelioma Chry SM 1

source_name: Malignant Mesothelioma, Chry 3-1-2


title: Malignant Mesothelioma Cro SM 1

source_name: Malignant Mesothelioma, Cro 4-4-1-1


title: medium CcpA induction replicate 2

description:
replicate 2
slide 24


title: Malignant Mesothelioma Chry SM 3

source_name: Malignant Mesothelioma, Chry 4-2-1


title: EXP-SKMEL 186

description: Reference RNA

source_name: Human Melanoma Cell lIne 80% confluent, 24 hr old media

value: SKMEL 186

source_name: Invitrogen Reference RNA

tag: sample type


title: normoxia, biological rep 3 [RMA-gene level]

description:
CEL file: N3.CEL (on the Series record)
N3-RMA-gene level
48 h incubation under normoxic conditions

tag: oxygen


title: hypoxia, biological rep 1 [RMA-gene level]

description:
CEL file: H1.CEL (on the Series record)
H1-RMA-gene level
48 h incubation under hypoxic conditions

value: 1% (hypoxia)


title: normoxia, biological rep 2 [RMA-gene level]

description:
CEL file: N2.CEL (on the Series record)
N2-RMA-gene level
48 h incubation under normoxic conditions


title: Malignant Mesothelioma Chry EM 3

source_name: Normal kidney, Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Chry 4-1-3


title: high CcpA induction replicate 4

description:
replicate 4
slide 92

value: 0.02 μM aTc


title: medium CcpA induction replicate 1

description:
replicate 1
slide 05


title: EXP-SKMEL 173

description: Reference RNA

value: SKMEL 173

value: DMEM 10% FBS

tag: d0 rank (amount of radiation that allows 37% of the cells to survive)

value: Invitrogen Reference RNA


title: EXP-SKMEL 181

description: Reference RNA

value: SKMEL 181

value: RPMI, 10% FBS

tag: genotype

value: raf


title: high CcpA induction replicate 3

description:
replicate 3
slide 79

value: 0 μM aTc

value: control

value: test


title: EXP-SKMEL 178

description: Reference RNA

value: SKMEL 178

tag: additional information about cells

value: Same Cell Line as SKMEL 130


title: IM003_Mu_mock_d5_1

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to Mouse Whole Genome Gene Expression Microarray (G4122F) slides.

scan_protocol: Dry slides were scanned on an Agilent Technologies Scanner (Model G2505C) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using the Agi4x44PreProcess package.

source_name: Lung, mock infection, day 5

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol: Lung tissue was homogenized in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol). RNA was isolated from lung lysates by precipitation using phenol-choloroform-isoamyl alcohol, then washed with isopropanol and resuspended in RNase-free water. The RNA concentration was measured using a Thermo Scientific Nanodrop 2000TM and the integrity of each RNA sample was determined using an Agilent 2100 Bioanalyzer.

treatment_protocol:
Six-to-eight-week-old female BALB/c mice were anesthetized and inoculated with either 50 μl of phosphate-buffered saline (PBS; Mock) or with 10^6 pfu of pandemic H1N1 influenza A/California/04/2009 virus in a 50 μl volume. Nine animals for the infection group were used for array analysis, three animals per time point. Eight animals for the mock group were used for array analysis, three animals for the day 1 and 3 time points and 2 animals for the day 5 time point.
Lung samples were stored in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol) at -80°C until processing.

value: BALB/c

tag: gender

value: female

tag: age

value: 6-8 weeks

tag: tissue

value: lung

value: mock infection

tag: time of sample collection

value: day 5 post-inoculation


title: high CcpA induction replicate 2

description:
replicate 2
slide 75

tag: strain

value: 0.02 μM aTc


title: Malignant Mesothelioma Chry EM 1

tag: disease state

value: Normal

value: kidney

value: Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Chry 3-2-1

value: Malignant Mesothelioma


title: IM003_Mu_mock_d3_1

source_name: Lung, mock infection, day 3

tag: treatment

value: day 3 post-inoculation


title: EXP-SKMEL 153

description: Reference RNA

value: SKMEL 153

value: RPMI, 10% FBS

value: raf

tag: g1 checkpoint  (percentage of the cells that arrest in g1 after irradiation)

tag: g2 checkpoint (the percentage of cells that arrest in g2 after irradiation)

value: Invitrogen Reference RNA


title: high CcpA induction replicate 1

description:
replicate 1
slide 71

source_name: Net intensity (tr.mean) {A}

value: 0 μM aTc

tag: reference

value: control

source_name: Net intensity (tr.mean) {B}

value: test


title: EXP-SKMEL 15

description: Reference RNA

tag: cell line

value: SKMEL 15


title: IM003_Mu_mock_d3_2

value: BALB/c

value: female

value: 6-8 weeks

value: lung


title: EXP-SKMEL 147

description: Reference RNA

value: SKMEL 147

tag: media

value: DMEM 10% FBS

value: ras

tag: sf2 (the amount of radiation that allows for 50% of the cells to survive)


title: IM003_Mu_mock_d3_3

value: mock infection


title: Malignant Mesothelioma Chry EM 2

value: Normal

value: kidney

value: Fischer 344 / Brown Norway F1 hybrid

source_name: Malignant Mesothelioma, Chry 3-2-8

value: Malignant Mesothelioma


title: OK03C_OK09C

city: Toronto

first: George

middle: M

last: Yousef

state: ON

address: 30 Bond Street

country: Canada

institute: St.Michael's Hospital

hyb_protocol: RNA hybridization was performed overnight on a µParafloTM microfluidic chip.

scan_protocol: Hybridization images were collected using a GenePix 4000B laser scanner (Molecular Device, Sunnyvale, CA) and digitized using Array-Pro image analysis software (Media Cybernetics, Bethesda, MD).

data_processing: Data were analyzed by completing background subtraction, followed by normalizing the signals using a LOWESS filter (Locally-weighted Regression). Additional statistical analyses were conducted to identify significantly dysregulated miRNAs.

source_name: Oncocytoma tumor

label_protocol: Using 4µg of total RNA, an oligonucleotide tag was ligated to the poly(A) tail for fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two tissue types in each matched pair.

extract_protocol: Total RNA was extracted using the miRNeasy Extraction Kit (Qiagen, Mississauga, Canada), following the manufacturer's recommended protocol.

tag: study no.

tag: subtype

value: Oncocytoma

value: F

tag: tumor stage

source_name: Oncocytoma

tag: tissue type

value: M

value: TX

tag: tumor size (cm)


title: OK02C_OK07C

tag: gender

tag: age


title: IM003_Mu_mock_d5_2

tag: tissue

tag: time of sample collection

value: day 5 post-inoculation


title: IM003_Mu_mock_d1_2

source_name: Lung, mock infection, day 1

tag: strain

value: BALB/c

value: day 1 post-inoculation


title: OK01C_OK06C


title: IM003_Mu_mock_d1_3

value: female

value: 6-8 weeks

tag: treatment


title: EXP-SKMEL 119

description: Reference RNA

value: SKMEL 119

tag: d0 rank (amount of radiation that allows 37% of the cells to survive)

tag: genotype

tag: sample type

value: Invitrogen Reference RNA


title: normoxia, biological rep 1 [RMA-gene level]

description:
CEL file: N1.CEL (on the Series record)
N1-RMA-gene level
48 h incubation under normoxic conditions

tag: cell line

value: HUVEC

tag: cell type

value: human umbilical vein endothelial cells

tag: oxygen

value: 21% (normoxia)


title: SK43C_OK05C

tag: study no.


title: EXP-SKMEL 130

description: Reference RNA

value: SKMEL 130

tag: media

value: RPMI, 10% FBS

tag: additional information about cells

value: Same Cell Line as SKMEL 178

value: raf

tag: g1 checkpoint  (percentage of the cells that arrest in g1 after irradiation)

tag: g2 checkpoint (the percentage of cells that arrest in g2 after irradiation)


title: SK39C_OK04C

tag: subtype

value: Oncocytoma

tag: gender

value: F

tag: tumor size (cm)

tag: tissue type

tag: tumor stage


title: IM003_Mu_mock_d1_1

tag: strain

tag: age

tag: tissue

value: lung

tag: treatment

value: mock infection

tag: time of sample collection


title: IM003_Mu_CA0409_10^6pfu_d5_3

source_name: Lung, CA04 virus infection, day 5

value: BALB/c

value: CA04 virus infection

value: day 5 post-inoculation


title: EXP-SKMEL 103

description: Reference RNA

tag: cell line

value: SKMEL 103

value: DMEM 10% FBS

tag: d0 rank (amount of radiation that allows 37% of the cells to survive)

tag: genotype

value: ras

tag: sf2 (the amount of radiation that allows for 50% of the cells to survive)

tag: sample type


title: EXP-SBC 12

description: Reference RNA

value: SBC 12

tag: media

value: DMEM 10% FCS

value: wt

tag: g1 checkpoint  (percentage of the cells that arrest in g1 after irradiation)

value: Invitrogen Reference RNA


title: IM003_Mu_CA0409_10^6pfu_d5_1

value: female

value: 6-8 weeks


title: SK31C_OK23C

source_name: chRCC tumor

tag: study no.

tag: subtype

value: chRCC tumor

tag: tumor grade

value: chRCC


title: IM003_Mu_CA0409_10^6pfu_d5_2

tag: gender


title: EXP-RPMI 7951

description: Reference RNA

value: RPMI 7951

value: MEM, 0.5XAA, 10% FBS

value: raf

tag: g2 checkpoint (the percentage of cells that arrest in g2 after irradiation)


title: SK37C_OK24C

value: M

tag: tumor stage

tag: tumor size (cm)

tag: tissue type


title: SK28C_OK22C

value: F

tag: age

value: data unavailable


title: H1N1_Exp1_Ca_D1_RL_L_613

description:
16099
251542110215_1_1

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to Rhesus Macaque Gene Expression Microarray (G2519F) slides.

organism: Macaca fascicularis

source_name: lung, CA04 virus infection, day 1

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Cynomolgus macaques (Macaca fascicularis), 4-15 y/o, weighing 3.0-8.7 kg, were infected with CA04 under anesthesia through a combination of intratracheal (4 ml), intranasal (0.5 ml per nostril), conjunctival (0.5 ml per eyelid) and oral (1 ml) routes with a suspension containing 1x10^6 TCID50/ml (total infectious dose was 7x10^6 TCID50).

tag: tissue

value: lung

tag: treatment

value: CA04 virus infection

tag: time of sample collection

value: day 1 post-inoculation


title: H1N1_Exp1_Ca_D6_RL_L_224

description:
16093
251542110219_1_3

source_name: lung, CA04 virus infection, day 6

value: day 6 post-inoculation


title: H1N1_Exp1_Battelle_rep2

description:
CR
251542110487_1_2

source_name: lung, uninfected


title: IM003_Mu_CA0409_10^6pfu_d3_1

source_name: Lung, CA04 virus infection, day 3

tag: strain

value: BALB/c

value: day 3 post-inoculation


title: EXP-SKMEL 100

description: Reference RNA

source_name: Human Melanoma Cell lIne 80% confluent, 24 hr old media

tag: cell line

value: SKMEL 100

value: RPMI, 10% FBS

tag: d0 rank (amount of radiation that allows 37% of the cells to survive)

tag: genotype

source_name: Invitrogen Reference RNA

value: Invitrogen Reference RNA


title: IM003_Mu_CA0409_10^6pfu_d3_3

value: female

value: 6-8 weeks


title: EXP-PMWK

description: Reference RNA

value: PMWK

tag: media

value: wt

tag: sf2 (the amount of radiation that allows for 50% of the cells to survive)

tag: sample type


title: EXP-RPMI 8322

description: Reference RNA

value: RPMI 8322


title: SK19C_OK21C

tag: study no.

tag: subtype

value: chRCC tumor

value: M

tag: tumor grade

value: chRCC


title: IM003_Mu_CA0409_10^6pfu_d3_2

tag: gender

value: lung


title: H1N1_Exp1_Battelle_rep1

description:
CR
251542110488_1_2


title: IM003_Mu_CA0409_10^6pfu_d1_3

source_name: Lung, CA04 virus infection, day 1

value: CA04 virus infection


title: IM003_Mu_CA0409_10^6pfu_d1_2

value: day 1 post-inoculation


title: SK14C_SK61C

tag: tumor stage

tag: tumor size (cm)

value: F


title: SK80C_OK15C

source_name: pRCC tumor

value: pRCC tumor

tag: age

tag: tissue type

value: pRCC


title: H1N1_Exp1_141M_a_CA_LL_Day6

description:
16104
251542110216_1_1

tag: tissue

tag: treatment

value: day 6 post-inoculation


title: SK74C_OK14C

value: 3 to 4


title: H1N1_Exp1_143M_b_CA_LL_Day1

description:
16095
251542110216_1_4

tag: time of sample collection


title: EXP-NHM 7 PMA

description: Reference RNA

source_name: Human Melanocyte 80% confluent, 24 hr old media

tag: cell line

value: NHM 7

value: PMA

value: Medium 254 + HMGS-1

value: Invitrogen Reference RNA


title: EXP-NHM 7 TERT ET1

description: Reference RNA

value: TERT + ET1

value: Medium 254 + HMGS-2

tag: additional information about cells

value: Telomerase added


title: Contents of anterior hindgut beetle 4

city: Berkeley

first: Nhu

last: Nguyen

state: CA

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

hyb_protocol: Method for hybridization were according to Brodie et al. (2006)

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

data_processing: The data were analyzed with GeneChip Microarray Analysis Suite version 5.1

organism: beetle metagenome

source_name: anterior hindgut section

label_protocol: Method for biotin label were according to Brodie et al. (2006)

extract_protocol: Each gut section was macerated and extracted using standard phenol-chloroform phase extraction, then followed by a cleanup with the AllPrep DNA/RNA kit (Qaigen).

treatment_protocol: Each beetle was surface washed with 95% EtOH and then washed with sterile PBS buffer. The beetles were dissected and each gut section was separated from the others, and placed in RNA later.

value: content of anterior hindgut


title: SK71C_OK13C

value: M


title: EXP-NHM 7 ET1

description: Reference RNA


title: 1 mg/kg MPH trl003

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Institute

description: Gene expression data from mRNA of substantia nigra from 1mg/kg methylphenidate-treated mouse

hyb_protocol: Following fragmentation, 5 microgram of cRNA were hybridized for 16 hr at 45C on HT MG-430 PM array plate.  Arrays were washed and stained in the Affymetrix GeneTitan.

scan_protocol: Arrays were scanned using the Affymetrix GeneTian

data_processing: The data were normalized using RMA method with arrays on the plate.  Batch correction was done using ComBat.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix expression protocol from 100 nanograms total RNA (GeneChip 3' IVT Expression Kit, P/N 702646 Rev. 5).

extract_protocol: mRNA was isolated from SN in accordance with the protocol outlined in RNAqueous-Micro kit (Ambion, Austin, TX) according to manufacturer's recommendations.

tag: strain

value: Swiss Webster

value: 1mg/kg MPH

value: substantia nigra


title: IM003_Mu_CA0409_10^6pfu_d1_1

value: BALB/c

value: female

value: 6-8 weeks

value: lung

value: CA04 virus infection

value: day 1 post-inoculation


title: Contents of posterior hindgut beetle 4

source_name: posterior hindgut section

value: content of posterior hindgut


title: Contents of midgut beetle 4

source_name: midgut section

value: content of midgut


title: SK47C_OK12C

value: pRCC tumor

value: F

value: pRCC


title: EXP-NHM 20 PMA

description: Reference RNA

value: NHM 20

value: PMA

tag: media

value: Medium 254 + HMGS-1

value: Invitrogen Reference RNA


title: 1 mg/kg MPH trl002

source_name: mRNA of substantia nigra from 1mg/kg methylphenidate-treated mouse

value: Swiss Webster

value: 1mg/kg MPH


title: 1 mg/kg MPH trl001

value: substantia nigra


title: EXP-NHM 21-TERT-PMA

description: Reference RNA

value: NHM 21

value: TERT + PMA

value: Telomerase added


title: SK20C_OK11C

value: M


title: 10 mg/kg MPH tr1003

description: Gene expression data from mRNA of substantia nigra from 10mg/kg methylphenidate-treated mouse

value: 10mg/kg MPH


title: EXP-NHM 24 ET1

description: Reference RNA

value: NHM 24

value: Medium 254 + HMGS-2


title: Contents of posterior hindgut beetle 3

value: content of posterior hindgut


title: (OK39_A1C1)

data_processing: Data were analyzed by completing background subtraction. Additional statistical analyses were conducted to identify significantly dysregulated miRNAs in metastatic compared to primary clear cell renal cell carcinoma (Series GSE23085).

source_name: metastatic RCC

tag: tumor type

value: Metastatic RCC

value: F

tag: Stage

tag: tumor size

tag: metastatic site

value: femur

value: metastatic RCC

value: adrenal


title: Contents of foregut beetle 4

source_name: foregut section

tag: sample type

value: content of foregut


title: (OK37_OK38)

tag: study no.

tag: gender

tag: tumor grade

value: lung


title: Contents of anterior hindgut beetle 3

value: content of anterior hindgut


title: 10 mg/kg MPH tr1002

source_name: mRNA of substantia nigra from 10mg/kg methylphenidate-treated mouse

value: Swiss Webster

value: substantia nigra


title: Contents of midgut beetle 3

value: content of midgut


title: (OK35_OK36)

tag: age

value: chest wall


title: saline ctr003

description: Gene expression data from mRNA of substantia nigra from saline-treated mouse

value: Saline


title: EXP-NHM 24 PMA

description: Reference RNA

value: PMA

value: Medium 254 + HMGS-1

value: Invitrogen Reference RNA


title: Contents of foregut beetle 3


title: 10 mg/kg MPH tr1001

value: 10mg/kg MPH


title: Contents of posterior hindgut beetle 2

value: content of posterior hindgut


title: EXP-NHM 16 PMA

description: Reference RNA

value: NHM 16


title: (OK33_OK34)

value: Metastatic RCC

value: M

tag: tissue type

value: F


title: EXP-NHM 17 PMA

description: Reference RNA

value: NHM 17


title: EXP-NHM 16 ET1

description: Reference RNA

value: Medium 254 + HMGS-2


title: Contents of anterior hindgut beetle 2

value: content of anterior hindgut


title: (OK31_OK32)

value: pancreas

value: metastatic RCC


title: EXP-NHM 16-TERT-ET-1

description: Reference RNA

value: TERT + ET1

value: Telomerase added


title: saline ctr002

source_name: mRNA of substantia nigra from saline-treated mouse

value: Swiss Webster

value: Saline

tag: tissue

value: substantia nigra


title: EXP-NHM 13 PMA

description: Reference RNA

value: NHM 13

tag: treatment

value: PMA

value: Medium 254 + HMGS-1

value: Invitrogen Reference RNA


title: saline ctr001


title: Contents of foregut beetle 2

value: content of foregut


title: Contents of midgut beetle 2

value: content of midgut


title: tumour#19 SNP array

description: Hybridized to Mouse Diversity Genotyping Arrays

data_processing:
CEL files were generated the Command_Console Software (Affymetrix) and processed by aroma.affymetrix.
Normalization and detecition of genomic aberrations was carried out using the R packages aroma.affymetrix and DNAcopy (H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics 2008, 24, pp759-767).

source_name: tumour

label_protocol: Affymetrix Mouse Diversity Genotyping Arrays were labeled using the Genome Wide Human SNP Nsp/Sty 5.0/6.0 Assay Kit according to the manufacturer’s recommendations (Affymetrix).

extract_protocol: DNA from diagnostic sorted B cell lymphoma samples derived from Cgamma1-cre; R26StopFLMYC;R26StopFLP110* transplanted animals and germline DNA (tail) was isolated with Dneasy according manufacturer’s recommendations (Qiagen).

tag: cell type

value: B cell lymphoma

tag: tumor number


title: EXP-NHM 16-TERT-PMA

description: Reference RNA

tag: cell line

value: NHM 16

value: TERT + PMA

tag: additional information about cells


title: Pax5sz2 vs. clone4 huPax5 (-Dox)

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed on reporter and sequence level with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

label_protocol: Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Pax5-/- (CD45.2) a kind gift of Dr. M. Busslinger, Research Institute of Molecular Pathology, Vienna) and Rag-2-/- (CD45.1) mice were bred in the laboratory animal facility of the Max Planck Institute for Infection Biology, Berlin under SPF conditions. All of the experimental procedures complied with National Regulations for the Care and Use of Laboratory Animals (protocol G0099/08 approved by the Landesamt für Gesundheit und Soziales, Berlin).   Bone marrow-derived Pax5-/- pro/preB cells were grown on a layer of gamma-irradiated (3000 cGy) OP9 stromal cells in IMDM-based medium (Gibco, Auckland) supplemented with 2% FCS (Sigma-Aldrich, Seelze), 0.03% Primatone-RL (Quest, Naarden) and 1% mouse IL-7 which was added as a culture supernatant as described previously20,25. The adherent stromal cell line OP9 and OP9-Δl-1 (a kind gift of Dr. Zuniga-Pfluecker, University of Toronto) were cultured in αMEM medium supplemented with 2% FCS and 0.03% Primatone-RL. The PhoenixTM-eco virus producer cell line (Orbigen Inc., San Diego) was cultured in RPMI (L-Glutamine) (Gibco, Auckland) supplemented with 10% FCS. Cytokine supernatants were produced by using the appropriate hybridoma cell lines: IL-3 (X63/IL-3), IL-6 (X63/IL-6), IL-7(J558L/IL-7), SCF (CHO-SCF, a kind gift of Dr. Thorsten Feyerabend, University of Ulm), Flt3l (Sp2.0-Flt3l, a kind gift of Dr. Paulo Vieira, Institute Pasteur, Paris), GM-CSF (X63-GM-CSF, kindly provided by Antonius Rolink, University of Basel).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 10e8 cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.

treatment_protocol: Vector particles were produced by transient transfection of the PhoenixTM-eco virus producer cell line. 5x105 cells were seeded per well of a 6-well-plate (Costar® CellBIND® , Corning Life Sciences, NY) in 2ml RPMI (L-Glutamine) supplemented with 10% FCS. After 24h the cells were transfected with 2μg retroviral vector plasmid mixed with 10μl LipofectamineTM (Invitrogen, Karlsruhe) for 5h. The cell culture supernatants were changed after 24h and harvested after further 24h. For transduction of Pax5-/- pro/preB cells 2x105 cells were spininfected with 700μl virus supernatant at 1150g for 3h 30min at 30°C. Cells were resuspended and cultures were continued on γ-irradiated semi-confluent OP9 layers in the presence of 1% IL- 7. One day after transfection, cells were selected by addition of histidinol (Sigma-Aldrich, Seelze) (pSR-rtTA-IRES-HISRes) or puromycin (Calbiochem, Beeston) (pSR-TRE-huPax5).

tag: transgene

value: rtTA

value: doxycycline

tag: concentration

value: transduced with rtTA only

source_name: clone4 huPax5 (-Dox)

value: naive


title: Contents of anterior hindgut beetle 1

value: content of anterior hindgut


title: Contents of posterior hindgut beetle 1

value: content of posterior hindgut


title: clone4 +Dox (10ng/ml) vs. clone4 huPax5 (-Dox)

source_name: clone4 +Dox (10ng/ml)

value: Bone marrow-derived Pax5-/- pro/preB cells


title: EXP-NHM 11 PMA

description: Reference RNA

value: NHM 11

tag: media


title: tumour#11 SNP array


title: EXP-NHM 11 ET1

description: Reference RNA

value: Medium 254 + HMGS-2


title: clone4 huPax5 (-Dox) vs. Pax5sz2


title: Contents of midgut beetle 1


title: ∆VNG0258 mutant, 1440 minutes after the addition of paraquat, replicate B, dye flip

status: Public on Aug 13 2012

city: Durham

first: Nicholas

middle: A

last: Gillum

institute: Duke University

hyb_protocol: Samples were hybridized to a custom 60-mer oligonucleotide microarray (Agilent technologies, Santa Clara, CA, 8 x 15,000 feature array, AMADID ID #30108). Probes for each ORF were spotted on each array six-fold and dye-swapping was conducted (to rule out bias in dye incorporation) for all samples, yielding 12 technical replicates per gene per time point. Slide hybridization and washing protocols were performed according to the manufacturer’s instructions except that hybridization was conducted in the presence of 37.5% formamide at 68˚C to ensure proper stringency due to the high G+C content of the H. salinarum genome.

scan_protocol: Slide scanning and spotfinding were conducted using Feature Extraction software (Agilent).

data_processing: Using the R/Bioconductor m-array and limma packages, resultant raw data were background-subtracted using normexp (Silver JD, Ritchie ME, and Smyth GK, 2007) Loess normalized within each array, and quantile normalized between all arrays. Any of the 12 gene-specific probes for each gene lying outside the 99th% confidence interval were removed using Dixon’s test (Dixon, 1951). Finally, remaining probe intensities for each gene were averaged and log2 ratios were calculated, yielding one expression ratio per gene. Note that the values here are the averages for the forward array and dye flip array individually after the outliers have been removed. As such, their average needs to be weighted by the number of probes from which the average was calculated (either 5 or 6 dependent on whether an outlier was removed).

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium standard reference sample

label_protocol: 600 ng of each quality-checked RNA sample directly labeled with Cy3 and Cy5 dyes (Kreatech) as described previously (Schmid et. al, 2007)  and combined in equimolar amounts with oppositely labeled H. salinarum NRC-1 reference RNA (from batch cultures grown in CM at 37C to mid-logarithmic phase). This common reference RNA was used across all ~950 microarray experiments listed in the H. salinarum NRC-1 microarray data repository.

extract_protocol: For each biological duplicate time course, all samples were removed from the same culture to ensure coherence of gene expression between unstressed and stressed cultures. From each sample, cells were immediately pelleted by centrifugation (12,000g, 30 sec, 25°C) and snap-frozen in liquid nitrogen. Sample pellets were stored overnight at -80C, followed by RNA preparation using the Absolutely-RNA kit (Stratagene, La Jolla, CA) according to the manufacturer's instructions. RNA quality was assessed using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Freedom from DNA contamination was ensured by PCR amplification of 200 ng of each RNA sample.

tag: strain

value: NRC-1 wild type

value: 0 mM

tag: [paraquat]

source_name: ∆VNG0258 mutant_1440 min after the addition of paraquat

value: ∆VNG0258 mutant


title: EXP-MEL 505

description: Reference RNA

source_name: Human Melanoma Cell lIne 80% confluent, 24 hr old media

value: MEL 505

value: RPMI, 10% FBS

tag: d0 rank (amount of radiation that allows 37% of the cells to survive)

tag: genotype

value: wt

tag: sf2 (the amount of radiation that allows for 50% of the cells to survive)

tag: g1 checkpoint  (percentage of the cells that arrest in g1 after irradiation)

tag: g2 checkpoint (the percentage of cells that arrest in g2 after irradiation)

source_name: Invitrogen Reference RNA

tag: sample type

value: Invitrogen Reference RNA


title: EXP-MALME-3

description: Reference RNA

value: RPMI1640 10%FCS


title: EXP-MEL 537

description: Reference RNA

value: MEL 537


title: Contents of foregut beetle 1

value: content of foregut


title: EXP-A375

description: Reference RNA

value: DMEM 10% FBS

value: raf


title: EXP-A2058

description: Reference RNA


title: clone4 +Dox (300ng/ml) vs. clone4 huPax5 (-Dox)

source_name: clone4 +Dox (300ng/ml)

value: doxycycline

value: naive


title: ∆VNG0258 mutant, 1440 minutes after the addition of paraquat, replicate B


title: ∆VNG0258 mutant, 1440 minutes after the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 480 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆VNG0258 mutant_480 min after the addition of paraquat


title: clone4 huPax5 (-Dox) vs. clone4 +Dox (300ng/ml)

value: Bone marrow-derived Pax5-/- pro/preB cells


title: tumour#8 SNP array

value: B cell lymphoma


title: ∆VNG0258 mutant, 1440 minutes after the addition of paraquat, replicate A


title: clone4 +Dox (1000ng/ml) vs. clone4 huPax5 (-Dox)

source_name: clone4 +Dox (1000ng/ml)


title: ∆VNG0258 mutant, 480 minutes after the addition of paraquat, replicate A


title: ∆VNG0258 mutant, 480 minutes after the addition of paraquat, replicate B


title: ∆VNG0258 mutant, 480 minutes after the addition of paraquat, replicate A, dye flip


title: clone4 huPax5 (-Dox) vs. clone4 +Dox (10ng/ml)


title: germline SNP array

source_name: tail

value: connective tissue


title: Knockin.2.1.1 [expression]

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description: IDH1 R132H/wild-type heterozygous knockin clone 2

hyb_protocol: Fragmented cRNA and hybridization controls were hybridized to U133A GeneChips (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)

scan_protocol: The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000 according to the manufacturer's protocol

data_processing: Data were RMA normalized using Expression Console (Affymetrix) Version 1.1. Detection was determined using MAS5.0 analysis, also conducted in Expression Console.

source_name: HCT116 cultured cells knockin 2 heterozygotes for IDH1 R132H

label_protocol: T7-based RNA amplication was performed on total RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).

growth_protocol: Cell lines were cultured in McCoy’s 5A Medium supplemented with 10% FBS. All cells were maintained in 5% CO2 at 37°C

extract_protocol: RNA isolation was performed using the RNeasy Kit (Qiagen) following the manufacturer's protocol

treatment_protocol: 2,000,000 cells were plated to a 25cm2 flask and harvested after 48 hours for RNA isolation

tag: genotype/variation

value: IDH1 R132H


title: clone4 huPax5 (-Dox) vs. clone4 +Dox (1000ng/ml)

tag: treatment


title: Knockin.2.1.2 [expression]


title: ∆VNG0258 mutant, 120 minutes after the addition of paraquat, replicate B

source_name: ∆VNG0258 mutant_120 min after the addition of paraquat

value: 0 mM

value: NRC-1 wild type


title: ∆VNG0258 mutant, 120 minutes after the addition of paraquat, replicate B, dye flip

value: ∆VNG0258 mutant


title: ∆VNG0258 mutant, 80 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆VNG0258 mutant_80 min after the addition of paraquat


title: ∆VNG0258 mutant, 120 minutes after the addition of paraquat, replicate A


title: ∆VNG0258 mutant, 80 minutes after the addition of paraquat, replicate B


title: ∆VNG0258 mutant, 120 minutes after the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 80 minutes after the addition of paraquat, replicate A


title: ∆VNG0258 mutant, 60 minutes after the addition of paraquat, replicate A

source_name: ∆VNG0258 mutant_60 min after the addition of paraquat


title: ∆VNG0258 mutant, 60 minutes after the addition of paraquat, replicate B, dye flip


title: tumour#7 SNP array

tag: cell type


title: ∆VNG0258 mutant, 60 minutes after the addition of paraquat, replicate B


title: ∆VNG0258 mutant, 80 minutes after the addition of paraquat, replicate A, dye flip


title: tumour#6 SNP array

tag: tumor number


title: Knockin.1.1.2 [expression]

description: IDH1 R132H/wild-type heterozygous knockin clone 1

source_name: HCT116 cultured cells knockin 1 heterozygotes for IDH1 R132H


title: ∆VNG0258 mutant, 40 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆VNG0258 mutant_40 min after the addition of paraquat


title: ∆VNG0258 mutant, 60 minutes after the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 40 minutes after the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 40 minutes after the addition of paraquat, replicate B


title: tumour#10 SNP array

source_name: tumour


title: HCT116.Parent.2 [expression]

description: HCT116 wild-type parent cells

source_name: HCT116 cultured cells wild-type for IDH1

value: wild-type


title: HCT116.Parent.1 [expression]

description: HCT116 wild-type parent cells


title: ∆VNG0258 mutant, 40 minutes after the addition of paraquat, replicate A


title: Knockin.1.1.1 [expression]


title: ∆VNG0258 mutant, 20 minutes after the addition of paraquat, replicate A

source_name: ∆VNG0258 mutant_20 min after the addition of paraquat


title: ∆VNG0258 mutant, 20 minutes after the addition of paraquat, replicate B

source_name: Halobacterium standard reference sample


title: ∆VNG0258 mutant, 20 minutes after the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 20 minutes after the addition of paraquat, replicate B, dye flip


title: ∆VNG0258 mutant, 10 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆VNG0258 mutant_10 min after the addition of paraquat


title: ∆VNG0258 mutant, 10 minutes after the addition of paraquat, replicate A


title: ∆VNG0258 mutant, 10 minutes after the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 10 minutes after the addition of paraquat, replicate B


title: WAT_Nonobese [4873_miRNA]

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: The labelled samples were placed in a hybridization cocktail mix containing 4% formamide and hybridised overnight to Affymetrix microRNA Arrays (Affymetrix Inc.) following the indicated Genisphere protocol.

scan_protocol: The arrays were washed, stained and scanned in an Affymetrix GCS 3000 scanner.

data_processing: Signal intensities and present calls were generated by using the microRNA QC tool by Affymetrix. The normalization algorithm used was the default settings in miRNA QCTool (from Affymetrix), that is background adjustment, BC-CG Adjust; normalization, Quantile; summarization, median polish.

source_name: Abdominal subcutaneous adipose tissue

label_protocol: 1 μg of total adipose RNA was labelled using the FlashTag biotin HSR labeling kit (Genisphere Inc., Hatfield, PA) according to the supplier’s protocol.

growth_protocol: Subcutaneous adipose tissue biopsies (at least 1.5 g) was obtained from 56 subjects (30 obese and 26 non-obese) by needel aspiration and subsequently snap frozen in liquid nitrogen.

extract_protocol: Total RNA was extracted from snap frozen intact tissue and RNA concentration as well as purity was measured spectrophotometrically using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific) and high quality (total and small) RNA was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: One part (400 mg) of the biopsy was kept at -70 °C for subsequent measures of miRNAs.

tag: tissue

value: White adipose tissue

tag: gender

value: female

tag: age


title: WAT_Obese [3731_miRNA]


title: WAT_Obese [4264_miRNA]


title: WAT_Obese [3725_miRNA]


title: WAT_Obese [4595_miRNA]


title: WAT_Obese [4872_miRNA]


title: WAT_Nonobese [4635_miRNA]


title: ∆VNG0258 mutant, immediately before the addition of paraquat, replicate B

source_name: ∆VNG0258 mutant_immediately before the addition of paraquat


title: WAT_Obese [4642_miRNA]


title: WAT_Obese [2636_miRNA]


title: WAT_Obese [3825_miRNA]


title: ∆VNG0258 mutant, immediately before the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, immediately before the addition of paraquat, replicate B, dye flip


title: ∆VNG0258 mutant, 20 minutes prior to the addition of paraquat, replicate B, dye flip

source_name: ∆VNG0258 mutant_20 min prior to the addition of paraquat


title: WAT_Obese [3708_miRNA]


title: WAT_Obese [1529_miRNA]


title: WAT_Obese [1914_miRNA]


title: WAT_Nonobese [1892_miRNA]


title: ∆VNG0258 mutant, immediately before the addition of paraquat, replicate A


title: WAT_Nonobese [3664_miRNA]


title: ∆VNG0258 mutant, 20 minutes prior to the addition of paraquat, replicate A


title: ∆VNG0258 mutant, 20 minutes prior to the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 20 minutes prior to the addition of paraquat, replicate B


title: WAT_Obese [2343_miRNA]


title: WAT_Obese [3698_miRNA]


title: ∆VNG0258 mutant, 40 minutes prior to the addition of paraquat, replicate B, dye flip

source_name: ∆VNG0258 mutant_40 min prior to the addition of paraquat


title: ∆VNG0258 mutant, 40 minutes prior to the addition of paraquat, replicate A, dye flip


title: ∆VNG0258 mutant, 40 minutes prior to the addition of paraquat, replicate A


title: ∆VNG0258 mutant, 40 minutes prior to the addition of paraquat, replicate B


title: WAT_Nonobese [199_miRNA]


title: WAT_Nonobese [828_miRNA]


title: WAT_Nonobese [136_miRNA]


title: WAT_Nonobese [202_miRNA]


title: ∆ura3 strain, 1440 minutes after the addition of paraquat, replicate A, dye flip

source_name: ∆ura3 strain_1440 min after the addition of paraquat

value: ∆ura3 isogenic parent control


title: WAT_Nonobese [404_miRNA]


title: ∆ura3 strain, 1440 minutes after the addition of paraquat, replicate B


title: ∆ura3 strain, 1440 minutes after the addition of paraquat, replicate A


title: ∆ura3 strain, 1440 minutes after the addition of paraquat, replicate B, dye flip


title: ∆ura3 strain, 480 minutes after the addition of paraquat, replicate B

source_name: ∆ura3 strain_480 min after the addition of paraquat


title: WAT_Nonobese [469_miRNA]


title: WAT_Nonobese [13_miRNA]


title: WAT_Nonobese [467_miRNA]


title: WAT_Nonobese [3604_miRNA]


title: ∆ura3 strain, 480 minutes after the addition of paraquat, replicate A, dye flip


title: ∆ura3 strain, 480 minutes after the addition of paraquat, replicate A


title: ∆ura3 strain, 120 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆ura3 strain_120 min after the addition of paraquat


title: ∆ura3 strain, 480 minutes after the addition of paraquat, replicate B, dye flip


title: ∆ura3 strain, 60 minutes after the addition of paraquat, replicate B

source_name: ∆ura3 strain_60 min after the addition of paraquat


title: WAT_Nonobese [83_miRNA]


title: ∆ura3 strain, 120 minutes after the addition of paraquat, replicate B


title: WAT_Obese [4649_miRNA]


title: ∆ura3 strain, 120 minutes after the addition of paraquat, replicate A, dye flip


title: ∆ura3 strain, 120 minutes after the addition of paraquat, replicate A


title: ∆ura3 strain, 80 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆ura3 strain_80 min after the addition of paraquat


title: ∆ura3 strain, 60 minutes after the addition of paraquat, replicate B, dye flip


title: ∆ura3 strain, 80 minutes after the addition of paraquat, replicate B


title: WAT_Obese [48_miRNA]


title: ∆ura3 strain, 80 minutes after the addition of paraquat, replicate A


title: ∆ura3 strain, 80 minutes after the addition of paraquat, replicate A, dye flip


title: WAT_Obese [4659_miRNA]


title: WAT_Obese [4615_miRNA]


title: WAT_Obese [4625_miRNA]


title: WAT_Nonobese [3712_miRNA]


title: WAT_Obese [4639_miRNA]


title: WAT_Obese [4648_miRNA]


title: WAT_Obese [3655_miRNA]


title: WAT_Obese [4275_miRNA]


title: WAT_Nonobese [3988_miRNA]


title: ∆ura3 strain, 40 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆ura3 strain_40 min after the addition of paraquat


title: ∆ura3 strain, 40 minutes after the addition of paraquat, replicate B


title: ∆ura3 strain, 40 minutes after the addition of paraquat, replicate A, dye flip


title: ∆ura3 strain, 60 minutes after the addition of paraquat, replicate A, dye flip


title: ∆ura3 strain, 60 minutes after the addition of paraquat, replicate A


title: ∆ura3 strain, 40 minutes after the addition of paraquat, replicate A


title: WAT_Nonobese [4613_miRNA]


title: WAT_Nonobese [4082_miRNA]


title: ∆ura3 strain, 20 minutes after the addition of paraquat, replicate B, dye flip

source_name: ∆ura3 strain_20 min after the addition of paraquat


title: ∆ura3 strain, 10 minutes after the addition of paraquat, replicate B

source_name: ∆ura3 strain_10 min after the addition of paraquat


title: WAT_Obese [4281_miRNA]


title: WAT_Obese [4645_miRNA]


title: ∆ura3 strain, 20 minutes after the addition of paraquat, replicate B


title: ∆ura3 strain, 10 minutes after the addition of paraquat, replicate A, dye flip


title: ∆ura3 strain, 20 minutes after the addition of paraquat, replicate A, dye flip


title: ∆ura3 strain, 20 minutes after the addition of paraquat, replicate A


title: WAT_Obese [4640_miRNA]


title: WAT_Nonobese [4203_miRNA]


title: ∆ura3 strain, 10 minutes after the addition of paraquat, replicate B, dye flip


title: ∆ura3 strain, 10 minutes after the addition of paraquat, replicate A


title: ∆ura3 strain, immediately before the addition of paraquat, replicate B, dye flip

source_name: ∆ura3 strain_immediately before the addition of paraquat


title: WAT_Nonobese [101_miRNA]


title: ∆ura3 strain, immediately before the addition of paraquat, replicate B


title: ∆ura3 strain, immediately before the addition of paraquat, replicate A, dye flip


title: WAT_Obese [4810_miRNA]


title: WAT_Nonobese [24_miRNA]


title: WAT_Obese [795_miRNA]


title: WAT_Obese [1116_miRNA]


title: WAT_Nonobese [134_miRNA]


title: WAT_Obese [3651_miRNA]


title: ∆ura3 strain, immediately before the addition of paraquat, replicate A


title: ∆ura3 strain, 20 minutes prior to the addition of paraquat, replicate A, dye flip

source_name: ∆ura3 strain_20 min prior to the addition of paraquat


title: ∆ura3 strain, 20 minutes prior to the addition of paraquat, replicate B, dye flip


title: WAT_Nonobese [398_miRNA]


title: In vitro differentiated adipocytes_subject 70_day 12

hyb_protocol: From non-degraded high-quality total RNA, we prepared and hybridized biotinylated complementary RNA to Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: Pre-processing was performed using the Affymetrix Expression Console version 1.1 and the following settings: Summarization: PLIER; Background Correction: PM-GCBG; Normalization: Global Median.

source_name: Isolated preadipocytes from subcutaneous adipose tissue, late differentiation

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: Subcutaneous adipose tissue was obtained from healthy subjects undergoing cosmetic liposuction (n=12). There was no selection for age, sex or BMI. From the tissue, we isolated and in vitro differentiated preadipocytes to adipocytes.

extract_protocol: Total RNA was extracted from the cells at day 4/5 (early), 8 (middle) and 12 (late) of differentiation using the Nucleospin RNA11 kit (Macherey-Nagel, Duren, Germany). RNA concentration and purity were measured spectrophotometrically using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific), and high quality RNA was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Isolation, culture and differentiation of cells were performed exactly as described in PMID: 15492368.

value: subcutaneous adipose tissue

value: preadipocytes during in vitro differentiation to adipocytes

tag: time of differentiation

value: day 12

tag: subject


title: ∆ura3 strain, 20 minutes prior to the addition of paraquat, replicate A

tag: strain

source_name: Halobacterium standard reference sample


title: In vitro differentiated adipocytes_subject 68_day 8

source_name: Isolated preadipocytes from subcutaneous adipose tissue, middle differentiation

value: day 8


title: In vitro differentiated adipocytes_subject 70_day 8


title: WAT_Obese [126_miRNA]

source_name: Abdominal subcutaneous adipose tissue


title: ∆ura3 strain, 20 minutes prior to the addition of paraquat, replicate B

tag: [paraquat]


title: ∆ura3 strain, 40 minutes prior to the addition of paraquat, replicate B, dye flip

source_name: ∆ura3 strain_40 min prior to the addition of paraquat


title: ∆ura3 strain, 40 minutes prior to the addition of paraquat, replicate B


title: WAT_Nonobese [43_miRNA]


title: In vitro differentiated adipocytes_subject 73_day 8


title: WAT_Nonobese [1732_miRNA]


title: In vitro differentiated adipocytes_subject 73_day 4/5

source_name: Isolated preadipocytes from subcutaneous adipose tissue, early differentiation

value: day 4/5


title: ∆ura3 strain, 40 minutes prior to the addition of paraquat, replicate A, dye flip


title: In vitro differentiated adipocytes_subject 73_day 12


title: In vitro differentiated adipocytes_subject 68_day 12


title: WAT_Nonobese [399_miRNA]


title: In vitro differentiated adipocytes_subject 67_day 8


title: In vitro differentiated adipocytes_subject 68_day 4/5


title: In vitro differentiated adipocytes_subject 70_day 4/5


title: In vitro differentiated adipocytes_subject 67_day 12


title: ∆VNG0258 mutant, 80 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆VNG0258 mutant_80 min after the addition of H2O2

value: 25 mM


title: ∆ura3 strain, 40 minutes prior to the addition of paraquat, replicate A


title: ∆VNG0258 mutant, 80 minutes after the addition of H2O2, replicate A, dye flip


title: ∆VNG0258 mutant, 80 minutes after the addition of H2O2, replicate B


title: ∆VNG0258 mutant, 80 minutes after the addition of H2O2, replicate A


title: In vitro differentiated adipocytes_subject 67_day 4/5


title: In vitro differentiated adipocytes_subject 96_day 4/5


title: In vitro differentiated adipocytes_subject 96_day 8


title: In vitro differentiated adipocytes_subject 96_day 12


title: In vitro differentiated adipocytes_subject 91_day 8


title: ∆VNG0258 mutant, 60 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆VNG0258 mutant_60 min after the addition of H2O2


title: ∆VNG0258 mutant, 60 minutes after the addition of H2O2, replicate B


title: ∆VNG0258 mutant, 40 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆VNG0258 mutant_40 min after the addition of H2O2


title: ∆VNG0258 mutant, 40 minutes after the addition of H2O2, replicate B


title: In vitro differentiated adipocytes_subject 91_day 12


title: ∆VNG0258 mutant, 60 minutes after the addition of H2O2, replicate A, dye flip


title: In vitro differentiated adipocytes_subject 85_day 12


title: In vitro differentiated adipocytes_subject 85_day 8


title: In vitro differentiated adipocytes_subject 84_day 4/5


title: ∆VNG0258 mutant, 40 minutes after the addition of H2O2, replicate A, dye flip


title: ∆VNG0258 mutant, 40 minutes after the addition of H2O2, replicate A


title: ∆VNG0258 mutant, 20 minutes after the addition of H2O2, replicate A, dye flip

source_name: ∆VNG0258 mutant_20 min after the addition of H2O2


title: ∆VNG0258 mutant, 60 minutes after the addition of H2O2, replicate A


title: ∆VNG0258 mutant, 20 minutes after the addition of H2O2, replicate A


title: In vitro differentiated adipocytes_subject 91_day 4/5


title: ∆VNG0258 mutant, 10 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆VNG0258 mutant_10 min after the addition of H2O2


title: In vitro differentiated adipocytes_subject 85_day 4/5


title: In vitro differentiated adipocytes_subject 84_day 8


title: ∆VNG0258 mutant, 10 minutes after the addition of H2O2, replicate B


title: ∆VNG0258 mutant, 10 minutes after the addition of H2O2, replicate A, dye flip


title: In vitro differentiated adipocytes_subject 84_day 12


title: In vitro differentiated adipocytes_subject 83_day 4/5


title: In vitro differentiated adipocytes_subject 81_day 12


title: In vitro differentiated adipocytes_subject 81_day 8


title: ∆VNG0258 mutant, 10 minutes after the addition of H2O2, replicate A


title: ∆VNG0258 mutant, immediately before the addition of H2O2, replicate B

source_name: ∆VNG0258 mutant immediately before the addition of H2O2


title: In vitro differentiated adipocytes_subject 83_day 12


title: ∆VNG0258 mutant, immediately before the addition of H2O2, replicate A, dye flip


title: ∆VNG0258 mutant, immediately before the addition of H2O2, replicate A


title: ∆VNG0258 mutant, 20 minutes prior to the addition of H2O2, replicate B, dye flip

source_name: ∆VNG0258 mutant_20 min prior to the addition of H2O2


title: ∆VNG0258 mutant, 20 minutes prior to the addition of H2O2, replicate B


title: ∆VNG0258 mutant, immediately before the addition of H2O2, replicate B, dye flip


title: In vitro differentiated adipocytes_subject 81_day 4/5


title: ∆VNG0258 mutant, 20 minutes prior to the addition of H2O2, replicate A, dye flip


title: ∆VNG0258 mutant, 20 minutes prior to the addition of H2O2, replicate A


title: In vitro differentiated adipocytes_subject 77_day 12


title: In vitro differentiated adipocytes_subject 83_day 8


title: In vitro differentiated adipocytes_subject 77_day 4/5


title: In vitro differentiated adipocytes_subject 74_day 12


title: In vitro differentiated adipocytes_subject 77_day 8


title: In vitro differentiated adipocytes_subject 74_day 8


title: ∆VNG0258 mutant, 40 minutes prior to the addition of H2O2, replicate A, dye flip

source_name: ∆VNG0258 mutant_40 min prior to the addition of H2O2


title: ∆VNG0258 mutant, 40 minutes prior to the addition of H2O2, replicate B


title: In vitro differentiated adipocytes_subject 74_day 4/5


title: ∆VNG0258 mutant, 40 minutes prior to the addition of H2O2, replicate A


title: ∆VNG0258 mutant, 40 minutes prior to the addition of H2O2, replicate B, dye flip


title: ∆ura3 strain, 80 minutes after the addition of H2O2, replicate B

source_name: ∆ura3 strain_80 min after the addition of H2O2


title: ∆ura3 strain, 80 minutes after the addition of H2O2, replicate A


title: ∆ura3 strain, 80 minutes after the addition of H2O2, replicate A, dye flip


title: ∆ura3 strain, 80 minutes after the addition of H2O2, replicate B, dye flip


title: ∆ura3 strain, 60 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆ura3 strain_60 min after the addition of H2O2


title: ∆ura3 strain, 60 minutes after the addition of H2O2, replicate B


title: WAT_Obese [4659]

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probe set scaling to target signal 100. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: RNA was extracted using the Nucleospin RNA11 kit (Macherey-Nagel, Duren, Germany). RNA samples were treated with RNase-free DNase (Macherey-Nagel).


title: WAT_Obese [4872]


title: WAT_Obese [4649]


title: WAT_Obese [4810]


title: WAT_Nonobese [4873]


title: WAT_Obese [4639]


title: WAT_Obese [4640]


title: WAT_Obese [4645]


title: ∆ura3 strain, 60 minutes after the addition of H2O2, replicate A, dye flip


title: WAT_Nonobese [4635]


title: WAT_Obese [4648]


title: WAT_Obese [4595]


title: ∆ura3 strain, 40 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆ura3 strain_40 min after the addition of H2O2


title: ∆ura3 strain, 60 minutes after the addition of H2O2, replicate A


title: WAT_Obese [4281]


title: ∆ura3 strain, 40 minutes after the addition of H2O2, replicate A, dye flip


title: ∆ura3 strain, 40 minutes after the addition of H2O2, replicate B


title: WAT_Nonobese [4613]


title: WAT_Obese [4642]


title: WAT_Obese [4615]


title: WAT_Obese [4625]


title: ∆ura3 strain, 40 minutes after the addition of H2O2, replicate A


title: ∆ura3 strain, 20 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆ura3 strain_20 min after the addition of H2O2


title: ∆ura3 strain, 20 minutes after the addition of H2O2, replicate B

source_name: Halobacterium standard reference sample


title: ∆ura3 strain, 20 minutes after the addition of H2O2, replicate A, dye flip


title: ∆ura3 strain, 20 minutes after the addition of H2O2, replicate A


title: WAT_Obese [4264]


title: ∆ura3 strain, 10 minutes after the addition of H2O2, replicate B, dye flip

source_name: ∆ura3 strain_10 min after the addition of H2O2


title: WAT_Nonobese [4082]

source_name: Abdominal subcutaneous adipose tissue


title: WAT_Obese [4275]


title: ∆ura3 strain, 10 minutes after the addition of H2O2, replicate B


title: ∆ura3 strain, 10 minutes after the addition of H2O2, replicate A, dye flip


title: ∆ura3 strain, 10 minutes after the addition of H2O2, replicate A


title: WAT_Obese [3825]


title: WAT_Nonobese [4203]


title: WAT_Nonobese [3988]


title: ∆ura3 strain, immediately before the addition of H2O2, replicate B, dye flip

source_name: ∆ura3 strain immediately before the addition of H2O2


title: WAT_Obese [3731]


title: WAT_Nonobese [3712]


title: WAT_Nonobese [3664]


title: WAT_Obese [3651]


title: WAT_Obese [3655]


title: WAT_Obese [3725]


title: WAT_Nonobese [3604]


title: WAT_Obese [3698]


title: ∆ura3 strain, 20 minutes prior to the addition of H2O2, replicate A

source_name: ∆ura3 strain_20 min prior to the addition of H2O2


title: ∆ura3 strain, 40 minutes prior to the addition of H2O2, replicate B, dye flip

source_name: ∆ura3 strain_40 min prior to the addition of H2O2


title: WAT_Obese [3708]


title: WAT_Obese [2636]


title: WAT_Obese [2343]


title: Lgr5-GFP_high normal si vs Lgr5-GFP_high adenoma array_3 dyeswap

city: Dresden

first: Daniel

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using featuere extraction (V.9.5.3, Agilent Technologies).

source_name: FACS sorted intestinal adenoma cells from induced Apc_fl/fl-Lgr5-EGFP-ires-CreERT2 mice

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: FACS sorted GFP-high cells from induced intestinal adenomas of Apc_fl/fl-Lgr5_EGFP_ires_CreERT2 mice were compared to GFP-high cells from normal small intestine of Lgr5_EGFP_ires_CreERT2 mice.

extract_protocol: RNA was isolated using Trizol (Invitrogen).

tag: origin

value: adenoma

source_name: FACS sorted intestinal cells from Lgr5-EGFP-ires-CreERT2 mice

value: normal small intestine


title: Lgr5-GFP_high normal si vs Lgr5-GFP_high adenoma array_1


title: ∆ura3 strain, 40 minutes prior to the addition of H2O2, replicate B


title: Lgr5-GFP_high normal si vs Lgr5-GFP_high adenoma array_1 dyeswap


title: WAT_Obese [1914]

tag: genotype


title: ∆ura3 strain, 20 minutes prior to the addition of H2O2, replicate A, dye flip


title: ∆ura3 strain, immediately before the addition of H2O2, replicate B

source_name: ∆ura3 strain_immediately before the addition of H2O2


title: Lgr5-GFP_high normal si vs Lgr5-GFP_high adenoma array_2 dyeswap


title: Lgr5-GFP_high normal si vs Lgr5-GFP_high adenoma array_3


title: ∆ura3 strain, 20 minutes prior to the addition of H2O2, replicate B


title: ∆ura3 strain, 20 minutes prior to the addition of H2O2, replicate B, dye flip


title: ∆ura3 strain, 40 minutes prior to the addition of H2O2, replicate A, dye flip


title: ∆ura3 strain, immediately before the addition of H2O2, replicate A, dye flip


title: ∆ura3 strain, immediately before the addition of H2O2, replicate A


title: WAT_Nonobese [1732]


title: WAT_Nonobese [1892]


title: WAT_Obese [1529]


title: ∆ura3 strain, 40 minutes prior to the addition of H2O2, replicate A


title: Lgr5-GFP_high adenoma vs Lgr5-GFP_low adenoma array_3

growth_protocol: RNA was isolated from two FACS sorted cell populations of intestinal adenomas from induced Apc_fl/fl-Lgr5_EGFP_ires_CreERT2 mice : adenoma GFP-high cells and adenoma GFP-low cells.

tag: gfp level

value: high

value: low


title: Lgr5-GFP_high normal si vs Lgr5-GFP_high adenoma array_2


title: Lgr5-GFP_high adenoma vs Lgr5-GFP_low adenoma array_3 dyeswap


title: WAT_Obese [1116]


title: WAT_Nonobese [828]


title: Knockin.2.2.2 [methylation]

description: HCT116 IDH1 R132H heterzygous knockin

scan_protocol: Followed the manufacturer's (Illumina) specifications on an iScan

data_processing: Data were interpreted in GenomeStudio v2010.3 Methylation Module 1.8.5 and exported for analysis

label: biotin nucleotide or dinitrophenyl labeled

source_name: cell culture

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen)

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: cell line

value: IDH1 R132H


title: Knockin.2.2.1 [methylation]

description: HCT116 IDH1 R132H heterzygous knockin

hyb_protocol: Followed the manufacturer's (Illumina) specifications


title: P21-9 (5 μM Senexin A)

city: Columbia

first: Igor

last: Roninson

state: SC

address: 715 Sumter St

department: Pharmaceutical and Biomedical Sciences

institute: SC College of Pharmacy

description: Gene expression data from P21-9 cells with Senexin A treatment only

hyb_protocol: Samples were hybridized using Affymetrix hybridization equipment, kits and instructions.

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing:
Raw signal intensities of each probeset in four samples were generated from Affymetrix Software Expression Console using RMA-core-Sketch-Quantile algorithm.
List of Relative fold change (presented in log2 value) between treated sample and the untreated control sample [S1_Ctrl_(HuEx-1_0-st-v2)] generated by the software Genespring GX 9 (Agilent).

source_name: HT1080 p21-9 cells

label_protocol: Enzymatic fragmentation and labeling with the WT Terminal Labeling Kit (Affymetrix), per manufacturer's instructions.

growth_protocol: Human HT1080 p21-9 fibrosarcoma cells that express p21 from an IPTG-inducible promoter were cultured in DMEM(HG) media supplemented with 10% FCII serum.

extract_protocol: RNA was extracted from cells using Trizol (Invitrogen) and further purified with RNeasy Plus Micro kit (Qiagen) per manufacturer’s instructions. Quality of RNA samples was analyzed by Bioanalyzer Chips (Agilent); only RNAs with a RIN of 9.0 or higher were used.  Single-standed cDNA was generated with the WT cDNA Synthesis Kit (Affymetrix).

treatment_protocol: HT1080 p21-9 cells were plated in the media containing carrier (DMSO) alone, or 5 μM Senexin A or 50 μM IPTG, alone or in combination,  for 72 h before RNA extraction.

value: Fibrosarcoma

tag: protocol

value: with Senexin A treatment only


title: Day 6 post-carbon depletion, biological replicate 2/2

city: Leiden

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

institute: Leiden University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: The RMA Bioconductor package was used for data processing

organism: Aspergillus niger

source_name: Mycelial biomass

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol:
Conidial suspensions for inoculation of bioreactor cultures were prepared by growing the A. niger laboratory strain N402 (cspA1 derivative of ATCC9029) (Bos et al., 1988) on solidified (1.5% agar) complete medium (CM) for three days at 30◦C in the dark. Spores were harvested with sterile physiological salt solution (0.9% NaCl) and filtered through Myracloth (Calbiochem, San Diego, CA, USA) to retain mycelial debris and solidified medium. CM contained per liter: 10 g glucose, 6 g NaNO3 , 1.5 g KH2PO4 , 0.5 g KCl, 0.5 g MgSO4 · 7H2O, 1 g casamino acids, 5 g yeast extract and 1 ml trace metal solution. e pH was adjusted to 5.8 with NaOH. e trace metal solution, modi ed from Vishniac et al. (1957), contained per liter: 10 g EDTA, 4.4 g ZnSO4 · 7H2O, 1.01 g MnCl2 · 4H2O, 0.32 g CoCl2 · 6H2O, 0.315 g CuSO4 · 5H2O, 0.22 g (NH4) · 6Mo7O24 · 4H2O, 1.47 g CaCl2 · 2H2O and 1 g FeSO4 · 7H2O. Minimal medium (MM) for bioreactor cultivations contained per liter: 4.5 g NH4Cl, 1.5 g KH2PO4 , 0.5 g KCl, 0.5 g MgSO4 · 7H2O and 1 ml trace metal solution. e pH was set to 3 with HCl. Aer autoclavation, 16 ml of heat-sterilized 50% (w/v) maltose monohydrate solution were added per kg of MM.
Batch cultures were performed in 6.6 L BioFlo3000 bioreactors (New Brunswick Scientific) as previously described by Jørgensen et al. (2010). Briefly, autoclaved bioreactor vessels were filled with 5 L (kg) sterile MM. During cultivation at 30◦C, the controller was set to maintain pH 3 by addition of titrants (2 M NaOH and 1 M HCl). Sterile air was supplied at a rate of 1 L per min. Prior to inoculation, 1.5 ml of 10% (w/v) filter-sterilized yeast extract was added to enhance conidial germination. Cultures were inoculated with freshly harvested spore suspensions to give 10 to the power of 9 conidia per liter. To reduce the loss of hydrophobic conidia during germination, the stirrer speed was set to 250 rpm and the culture was aerated via the headspace during the first six hours aer inoculation. Subsequently, the stirrer speed was increased to 750 rpm, 0.5 ml of polypropyleneglycol P2000 was added as antifoam agent and air was supplied via the sparger.

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen).

treatment_protocol: Day 1 post-carbon starvation during maltose-limited submerged batch cultivation

value: N402 wild-type (ATCC 64974)

tag: culture age

value: day 6 post-carbon depletion


title: P21-9 (50 μM IPTG)

description: Gene expression data from P21-9 cells with p21 induction (by IPTG) without Senexin A


title: P21-9 (50 μM IPTG + 5 μM Senexin A)

description: Gene expression data from P21-9 cells with p21 induction (by IPTG) and Senexin A treatment


title: P21-9 (Untreated Control)

description: Gene expression data from P21-9 cells without p21 induction (by IPTG) and Senexin A treatment


title: WAT_Nonobese [467]

value: White adipose tissue

value: female


title: WAT_Nonobese [399]


title: WAT_Obese [795]


title: Lgr5-GFP_high adenoma vs Lgr5-GFP_low adenoma array_2 dyeswap