title: DLPFC_Female_Schizophrenia_p_UCDavis_101057

value: Schiz Cohort 2


title: hiPS line 2, biological replicate 1

status: Public on Dec 20 2016

type: RNA

city: Ioannina

first: Carol

last: Murphy

address: Panepistimioupoli

department: Biomedical reseach

country: Greece

institute: FORTH-IMBB

description: gene expression data of human induced pluripotent line2

hyb_protocol: Following fragmentation and labeling (5.5ug of ssDNA was fragmented) (Affymetrix, #900671), 2.3 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G

data_processing: The data were analyzed using GeneSpring12.6 (Affymetrix Expression experiment type; Exon analysis type, RMA16 summarization algorithm)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: gene expression data in standard growth medium

label_protocol: Biotinylated cDNA was synthesized from 150ng of total RNA (was converted to cRNA then to ssDNA, using 10ug of cRNA for ssDNA synthesis) using Ambion WT Expression kit (#4491974)

growth_protocol: hiPS and HUES lines were grown on matrigel coating and mTeSR medium. HEFs fibroblasts growth medium was ATCC basal medium, suplemented with 10%FBS and 1%pen/step

extract_protocol: total RNA extraction was performed using Macherey-Nagel nucleospin RNA extraction kit (#740955.50) according to the manufacturer's instructions.

tag: tissue

value: fully reprogrammed cell line


title: DLPFC_Male_Schizophrenia_p_UCDavis_101421

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

country: USA

institute: University of Michigan

hyb_protocol: Sample labeling and hybridization followed the exact Affymetrix procedures.

scan_protocol: standard Affymetrix protocol

data_processing:
A fully-cited description of the preprocessing can be found in the supplementary section of Li 2013 PNAS 110: 9950-9955:    Microarray experiments were performed in separate experimental cohorts, ranging from five to eight cohorts depending on the brain region.  Each cohort contained a mixture of cases and controls, with most RNA samples analyzed in duplicate at two laboratories (some analyzed in three laboratories).  The generation of probe-level intensity data (i.e., the CEL files) relied on standard Affymetrix library files and further processed using a custom annotation file (see below).      While most cohorts were analyzed on Affymetrix U133A platform, several of the latest cohorts were analyzed on the newer, U133Plus-v2 platform, which contains all U133A probe sets as a subset.  We extracted the U133A subset of the data for these samples and combined them with data for those analyzed on the U133A platform.  We applied RMA (Robust Multi-array Analysis) to summarize probe set expression levels, using the web interface at http://arrayanalysis.mbni.med.umich.edu.  RMA output, in the form of logged (base 2) expression levels, was generated using the custom ENTREZ12.1 Chip Definition Files (CDF), which defined probe sets for 11,912 ENTREZ transcripts and 68 control probe sets (http://nmg-r.bioinformatics.nl/Packages_for_R2.12.html).  The reason for using our custom-defined CDF files rather than the probe annotation provided by Affymetrix was to re-map all probes to the latest human genome build available, and to annotate probes according to one of the most detailed gene models.  The RMA results in this study thus represented 11,912 transcripts defined by ENTREZ in 03/2010 and are covered by probes on the U133A microarrays.  All downstream analyses were performed in R, using contributed packages available in early 2010.      To gain an overview of sample heterogeneity, we calculated sample-sample similarities for each region using pairwise Pearson's correlation coefficients (r), and calculated the average r of each sample to all other samples of the same region.  We chose the threshold of average r = 0.85 to define and remove outlier microarrays.  The outliers could result from either technical or biological differences. We removed additional microarrays corresponding to data produced at one laboratory for one cohort due to low average r and poor match with the duplicate microarrays from the second laboratory (denoted “batch 15” in the GEO metadata).     Although the RMA method has normalized probe intensity distributions across microarrays, the resulting probe set summaries still showed between-cohort, between microarray type (U133A versus U133 Plus v2), and between-laboratory variations, thus requiring further normalization.  For each brain region, we quantile-normalized the probe set values, and used pairwise correlation coefficients to define recognizable batches, which usually coincides with naturally occurring sample groups (>15 samples) according to cohorts or chip types.  The 68 negative control probe sets on the microarray platform, representing spiked-in non-human transcripts, show nearly identical batch effects as using all probes (not shown), indicating that most of the batch variation is due to technical differences in reagents and instruments rather than due to biological differences between samples in different batches.   To adjust for batch effects, we median-centered the expression levels of each transcript within each batch, and confirmed, by using the correlation matrices, that the batch-effects were removed after the adjustment.     We compared the result of this simple correction with the alternative, Bayesian batch-correction approach implemented in combat, and did not see meaningful differences in performance in terms of duplicate-sample concordance (results not shown).  While this is contrary to the published comparison results showing that combat is a better algorithm for dealing with batch effects, its advantage is probably blunted in our dataset because (1) we have larger sample sizes per batch (typically >15) than what was tested in the published comparisons, and we used median centering rather than mean-centering.  The latter is susceptible to the influence of outlier values, yet was used in earlier comparisons with combat.  We note that combat has decreased the scale of variation for most transcripts (as a consequence of improving the group variance estimation) and resulted in under-reporting of fold-changes between sample groups.  We therefore opted to maintain the use of the median-centering approach in this study.  After per-batch median-centering, we quantile-normalized the resulting values, and averaged the replicate microarrays for the same samples, yielding a dataset for unique subjects for each region.
Microarray experiments were performed in separate experimental cohorts, ranging from five to eight cohorts depending on the brain region.  Each cohort contained a mixture of cases and controls, with most RNA samples analyzed in duplicate at two laboratories (some analyzed in three laboratories).  The generation of probe-level intensity data (i.e., the CEL files) relied on standard Affymetrix library files and further processed using a custom annotation file (see below).
While most cohorts were analyzed on Affymetrix U133A platform, several of the latest cohorts were analyzed on the newer, U133Plus-v2 platform, which contains all U133A probe sets as a subset.  We extracted the U133A subset of the data for these samples and combined them with data for those analyzed on the U133A platform.  We applied RMA (Robust Multi-array Analysis) to summarize probe set expression levels, using the web interface at http://arrayanalysis.mbni.med.umich.edu.  RMA output, in the form of logged (base 2) expression levels, was generated using the custom ENTREZ12.1 Chip Definition Files (CDF), which defined probe sets for 11,912 ENTREZ transcripts and 68 control probe sets (http://nmg-r.bioinformatics.nl/Packages_for_R2.12.html).  The reason for using our custom-defined CDF files rather than the probe annotation provided by Affymetrix was to re-map all probes to the latest human genome build available, and to annotate probes according to one of the most detailed gene models.  The RMA results in this study thus represented 11,912 transcripts defined by ENTREZ in 03/2010 and are covered by probes on the U133A microarrays.  All downstream analyses were performed in R, using contributed packages available in early 2010.
To gain an overview of sample heterogeneity, we calculated sample-sample similarities for each region using pairwise Pearson's correlation coefficients (r), and calculated the average r of each sample to all other samples of the same region.  We chose the threshold of average r = 0.85 to define and remove outlier microarrays.  The outliers could result from either technical or biological differences. We removed additional microarrays corresponding to data produced at one laboratory for one cohort due to low average r and poor match with the duplicate microarrays from the second laboratory (denoted “batch 15” in the GEO metadata).
Although the RMA method has normalized probe intensity distributions across microarrays, the resulting probe set summaries still showed between-cohort, between microarray type (U133A versus U133 Plus v2), and between-laboratory variations, thus requiring further normalization.  For each brain region, we quantile-normalized the probe set values, and used pairwise correlation coefficients to define recognizable batches, which usually coincides with naturally occurring sample groups (>15 samples) according to cohorts or chip types.  The 68 negative control probe sets on the microarray platform, representing spiked-in non-human transcripts, show nearly identical batch effects as using all probes (not shown), indicating that most of the batch variation is due to technical differences in reagents

extract_protocol: Coronal slices of the brain were rapidly frozen on pre-cooled (to −120°C) aluminum plates, and stored at −80°C. Dorsolateral prefrontal cortex samples (area 9 plus 46) were trimmed to include an approximately equal  ratio  of  gray  and  white  matter,  the  latter  being  restricted  to  a  region  approximately  the  same  thickness  as layer VI of the cortex. Samples were taken from the left side. Following tissue dissection, total RNA was isolated by using TRIzol reagents (Invitrogen, Carlsbad, CA, USA), and shipped to the three research groups that collaborate on this project (University of California, Irvine; University of California, Davis; University of Michigan). For details, see (Evans 2003 Neurobiol Dis 14:240-250, Vawter 2003 Neuropsychopharm 29: 373-384, Li 2004 Biol Psychiatry 55:346-352, Li 2013 PNAS 110: 9950-9955).

tag: cohort

tag: site of processing

tag: diagnosis

value: Schizophrenia

tag: subject id

tag: agonal factor

tag: tissue ph (cerebellum)

tag: gender

value: M

tag: race

value: Caucasian

tag: age

tag: post-mortem interval

tag: suicide (1=yes)

value: Dorsolateral Prefrontal Cortex


title: DLPFC_Male_Schizophrenia_r_p_UCDavis_101078

label_protocol: Sample labeling and hybridization followed the exact Affymetrix procedures.

value: Schiz Cohort 1


title: DLPFC_Male_Schizophrenia_p_UCDavis_101078


title: MSC line3 towards fibrous differentiation, biological rep3

description:
gene expression data of MSC1 in ligament induced part of the scaffold
MSCBR3 on scaffold fibrous

source_name: gene expression data of cells in the middle part of Leeds-Keio scaffold

growth_protocol: hiPS were committed towards mesenchymal differentiation through gradual replacement of pluripotency medium with medium of mesenchymal cells. Then,hiPS-MSC and MSC lines seeded on Leeds-Keio 3Dscaffold and treated for 21days with growth factors to enhance 3Ddifferentiation

value: MSC line3, in middle part of scaffold


title: MSC line2 towards fibrous differentiation, biological rep2

description:
gene expression data of MSC2 in ligament induced part of the scaffold
MSC20 on scaffold fibrous

treatment_protocol: hiPS were committed towards mesenchymal differentiation through gradual replacement of pluripotency medium with medium of mesenchymal cells. Then,hiPS-MSC and MSC lines seeded on Leeds-Keio 3Dscaffold and treated for 21days with growth factors to enhance 3Ddifferentiation

value: MSC line2, in middle part of scaffold


title: MSC line1 towards fibrous differentiation, biological rep1

description:
gene expression data of MSC1 in ligament induced part of the scaffold
MSC10 on scaffold fibrous

value: MSC line1, in middle part of scaffold


title: 173DK Trout_K20_PAH_B

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K20_PAH_B

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping.  Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents.  Each reaction was spiked with a range of concentrations (0.0049 â€“ 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene).  Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label.  cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates.  cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control.  Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation.  The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardtâ€™s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH).  Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation.  Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays.  Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier.

scan_protocol: Scanned images (5 um) were acquired with GenePix 4200A scanner (Molecular Devices) at an excitation of 532 nm for Cy3 and 635 nm for Cy5 and at 80% power.  The photomultiplier tube (PMT) settings for each fluor were set based on intensity of spiked internal alien controls to normalize among all slides in the experiment.  Image files were quantified in GenePix Pro 6.01 (Molecular Devices)

data_processing: Raw median signal and background values are included.  For experiment, data were background subtracted and normalized by LOWESS.  Stringent criteria were used to filter for genes that were regulated q<0.05 by ANOVA in GeneSpring v.11.

organism: Oncorhynchus mykiss

source_name: Rainbow trout fed PAH diet (400 ppm) for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 20 days post challenge.

label_protocol: Labeled using Genisphere Array 350 kit adapted from manufacturer protocol.

growth_protocol: Subyearling juvenile rainbow trout (7-10 g) were obtained from the Sinnhuber Aquatic Research Laboratory at Oregon State University (Corvallis, OR). A culture of A. salmonicida isolated from a natural furunculosis outbreak at Rock Creek Hatchery in Oregon was generously donated by Richard Holt (Oregon State University, Corvallis, OR, USA). The bacteria was grown in trypticase soy broth (TSB) (Sigma-Aldrich) at 208C under constant agi-tation on a digital oscillator (Thermoline Scientific) at a speed setting of 130 rpm until the early stationary phase, which corresponded to an optical density of 1 (OD¼1). The purity of the culture was confirmed by a Gram stain, positive reaction with rabbit anti-A. salmonicida in an agglutination test (BioNor mono-aqua test kit, BioNor), and by positive  growth on Comassie blue agar, which is a differential medium for A. salmonicida.

extract_protocol: Invitrogen TRIzol extraction according to vendor protocol.

treatment_protocol: Rainbow trout (Oncorhynchus mykiss) were fed a mixture of ten high molecular weight polycyclic aromatic hydrocarbons (PAH) at an environmentally relevant concentration (400ppm) for 50 days. After 50 days of PAH exposure, fish were challenged with Aeromonas salmonicida (A. Salmonicida), the causative agent of furunculosis, at a lethal concentration 30 (LC30) or growth media without the pathogen (mock challenge). There were a total of four treatment combinations: (1) mock-challenged, control-fed fish; (2) A. salmonicida-challenged, control-fed fish; (3) mock-challenged, PAH-fed fish; (4) A. salmonicida-challenged, PAH-fed fish. Head kidney was collected 2, 4, 10 and 20 days after challenge.

tag: day

value: Day 20

tag: chemical treatment

value: PAH treated

tag: bacteria challenge

value: A. salmonicida challenged

value: Kidney

source_name: Reference:  Rainbow trout fed control diet for 50 days and then challenged with mock (no bacteria).  RNA was pooled from head kidney  collected 2, 4, 10 and 20 days post challenge.

value: Control treated

value: Mock challenged


title: 177DK Trout_K20_PAH_B


title: hiPS line 3, biological replicate 2

description: gene expression data of human induced pluripotent line3

treatment_protocol: hiPS and HUES lines were grown on matrigel coating and mTeSR medium. HEFs fibroblasts growth medium was ATCC basal medium, suplemented with 10%FBS and 1%pen/step


title: hiPS-MSC line2 towards fibrous differentiation, biological rep2

description:
gene expression data of hiPS-MSC2 in ligament induced part of the scaffold
3.3 on scaffold fibrous

value: committed hiPS-MSC line2, in middle part of scaffold


title: 175DK Trout_K20_PAH_B


title: hiPS line 1, biological replicate1

description: gene expression data of human induced pluripotent line1


title: MSC line3 towards osseous differentiation, biological rep3

description:
gene expression data of MSC3 in osteo induced part of the scaffold
MSCBR3 on scaffold osteo

source_name: gene expression data of cells on edges of Leeds-Keio scaffold

value: MSC line3, in edges of scaffold


title: 164DK Trout_K20_PAH_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K20_PAH_A

source_name: Rainbow trout fed PAH diet (400ppm) for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 20 days post challenge.


title: 163DK Trout_K20_PAH_A


title: 174DK Trout_K20_PAH_B


title: DLPFC_Male_Control_p_UMichigan_101772

value: Dep Cohort 5

value: Control


title: hiPS-MSC line1 towards fibrous differentiation, biological rep1

description:
gene expression data of hiPS-MSC1 in ligament induced part of the scaffold
3.2 on scaffold fibrous

value: committed hiPS-MSC line1, in middle part of scaffold


title: 162DK Trout_K20_PAH_A


title: MSC line2 towards osseous differentiation, biological rep2

description:
gene expression data of MSC2 in osteo induced part of the scaffold
MSC20 on scaffold osteo

value: MSC line2, in edges of scaffold


title: 160DK Trout_K20_PAH_A


title: MSC line1 towards osseous differentiation, biological rep1

description:
gene expression data of MSC1 in osteo induced part of the scaffold
MSC10 on scaffold osteo

value: MSC line1, in edges of scaffold


title: hiPS-MSC line2 towards osseous differentiation, biological rep2

description:
gene expression data of hiPS-MSC2 in osteo induced part of the scaffold
3.3 on scaffold osteo

value: committed hiPS-MSC line2, in edges of scaffold


title: 176EK Trout_K20_CON_B

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K20_CON_B

source_name: Rainbow trout fed control diet for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 20 days post challenge.


title: hiPS-MSC line3 towards fibrous differentiation, biological rep3

description:
gene expression data of hiPS-MSC3 in ligament induced part of the scaffold
3.5 on scaffold fibrous

value: committed hiPS-MSC line3, in middle part of scaffold


title: 175EK Trout_K20_CON_B


title: hiPS-MSC line3 towards osseous differentiation, biological rep3

description:
gene expression data of hiPS-MSC3 in osteo induced part of the scaffold
3.5 on scaffold osteo

value: committed hiPS-MSC line3, in edges of scaffold


title: 172EK Trout_K20_CON_B


title: 174EK Trout_K20_CON_B


title: 163EK Trout_K20_CON_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K20_CON_A

source_name: Rainbow trout fed control diet for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 20 days post challenge.


title: hiPS-MSC line1 towards osseous differentiation, biological rep1

description:
gene expression data of hiPS-MSC1 in osteo induced part of the scaffold
3.2 on scaffold osteo

value: committed hiPS-MSC line1, in edges of scaffold


title: MSC line3, biological rep3

description:
gene expression data of mesenchymal stem cell line3
MSCBR3

value: undifferentiated mesenchymal stem cell line


title: 149DK Trout_K10_PAH_B

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K10_PAH_B

source_name: Rainbow trout fed PAH diet (400 ppm) for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 10 days post challenge.

value: Day 10

value: PAH treated


title: 150DK Trout_K10_PAH_B

value: A. salmonicida challenged

value: Kidney


title: MSC line1, biological rep1

description:
gene expression data of mesenchymal stem cell line1
MSC10


title: 151DK Trout_K10_PAH_B

value: Control treated

value: Mock challenged


title: 160EK Trout_K20_CON_A

value: Day 20


title: MSC line2, biological rep2

description:
gene expression data of mesenchymal stem cell line2
MSC20


title: hiPS-MSC line2, biological rep2

description:
gene expression data of committed hiPS-MSC line2
3.3 committed

value: committed hiPS-MSC line2


title: hiPS line2, biological rep2

description:
gene expression data of human induced pluripotent line2
3.3 pluri

value: induced pluripotent cell line2


title: hiPS line3, biological rep3

description:
gene expression data of human induced pluripotent line3
3.5 pluri

value: induced pluripotent cell line3


title: hiPS-MSC line1, biological rep1

description:
gene expression data of committed hiPS-MSC line1
3.2 committed

value: committed hiPS-MSC line1


title: 148DK Trout_K10_PAH_B


title: 162EK Trout_K20_CON_A


title: 161EK Trout_K20_CON_A


title: 143DK Trout_K10_PAH_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K10_PAH_A

source_name: Rainbow trout fed PAH diet (400ppm) for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 10 days post challenge.


title: 142DK Trout_K10_PAH_A


title: 141DK Trout_K10_PAH_A


title: lung_X179A infection_day 5 infected_rep2

city: Oxford

first: Suzanne

last: Cole

address: John Radcliffe Hospital, Headley Way

department: University of Oxford

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

hyb_protocol: Following fragmentation, ss-cDNA was hybridized for 16 hours at 45C on GeneChip Mouse Gene 1.0 ST Arrays in the Gene Chip Hybridization Oven 645. Gene Chips were washed and stained in GeneChip Fluidics Station 450

scan_protocol: Gene chips were scanned using the Affymetrix Gene Chip Scanner 3000 7G

data_processing: Data were analysed with Affymetrix Expression Console (RMA)

organism: Mus musculus

source_name: lung_X179A infection_day 5 infected

label_protocol: Amplified and biotinylated sense-strand DNA targets were prepared from 100ug total RNA using the WT PLUS Reagent Kit (Affymetrix)

extract_protocol: Lung pieces were homoginized in TRIzol reagent and cleaned up using Qiagen mini spin column (following manufacturer's instructions)

treatment_protocol: Lungs removed from euthanized mice, cut into small pieces and placed in RNA later

tag: strain

value: female

tag: infected with

value: mild H1N1 influenza virus (NYMC-X-179A)

tag: time point

value: day 5 post infection

value: lungs


title: hiPS line1, biological rep1

description:
gene expression data of human induced pluripotent line1
3.2 pluri

tag: tissue

value: induced pluripotent cell line1


title: lung_X179A infection_day 5 infected_rep3


title: lung_X179A infection_day 5 infected_rep1


title: lung_X179A infection_day 3 infected_rep3

source_name: lung_X179A infection_day 3 infected

value: day 3 post infection


title: 142EK Trout_K10_CON_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K10_CON_A

source_name: Rainbow trout fed control diet for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 10 days post challenge.

value: Day 10


title: hiPS-MSC line3, biological rep3

description:
gene expression data of committed hiPS-MSC line3
3.5 committed

value: committed hiPS-MSC line3


title: 140DK Trout_K10_PAH_A

value: PAH treated


title: 143EK Trout_K10_CON_A

value: Kidney


title: 141EK Trout_K10_CON_A

value: Control treated


title: lung_X179A infection_day 3 infected_rep2


title: 140EK Trout_K10_CON_A

value: Mock challenged


title: 151EK Trout_K10_CON_B

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K10_CON_B

source_name: Rainbow trout fed control diet for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 10 days post challenge.

value: A. salmonicida challenged


title: 150EK Trout_K10_CON_B


title: 149EK Trout_K10_CON_B


title: 137DK Trout_K4_PAH_B

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K4_PAH_B

source_name: Rainbow trout fed PAH diet (400 ppm) for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 4 days post challenge.

value: Day 4


title: surrounding control tissue specimen-3

city: Beijing

first: yanyang

last: zhao

address: No. 1 DAHUA Road

country: China

institute: The Key Laboratory of Geriatrics, National Institute of Geriatrics, Beijing Hospital, Ministry of Health

description: SAMPLE 5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings)
Normalization and probe summarization was carried out on the human specific probe sets only.

source_name: surrounding control tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: colon

tag: tissue subtype

value: surrounding control tissue


title: colon cancer tissue specimen-2

description: SAMPLE 4

source_name: colon cancer tissue

value: colon cancer tissue


title: surrounding control tissue specimen-2

description: SAMPLE 3


title: colon cancer tissue specimen-3

description: SAMPLE 6


title: lung_X179A infection_day 3 infected_rep1

value: female


title: 136DK Trout_K4_PAH_B


title: lung_X179A infection_uninfected_rep2

source_name: lung_X179A infection_uninfected

value: none (uninfected control)


title: colon cancer tissue specimen-1

description: SAMPLE 2


title: lung_H5N1 infection_day 5 infected

source_name: lung_H5N1 infection_day 5 infected

value: severe H5N1 influenza virus (VN/1203/04/H5N1)

value: day 5 post infection


title: 148EK Trout_K10_CON_B


title: lung_X179A infection_uninfected_rep1

value: lungs


title: lung_X179A infection_uninfected_rep3


title: lung_H5N1 infection_day 3 infected

source_name: lung_H5N1 infection_day 3 infected

value: day 3 post infection


title: lung_H5N1 infection_uninfected

source_name: lung_H5N1 infection_uninfected


title: surrounding control tissue specimen-1

description: SAMPLE 1


title: 133DK Trout_K4_PAH_B

source_name: Reference:  Rainbow trout fed control diet for 50 days and then challenged with mock (no bacteria).  RNA was pooled from head kidney  collected 2, 4, 10 and 20 days post challenge.


title: 123DK Trout_K4_PAH_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K4_PAH_A

source_name: Rainbow trout fed PAH diet (400ppm) for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 4 days post challenge.


title: 120DK Trout_K4_PAH_A


title: 122DK Trout_K4_PAH_A


title: 134DK Trout_K4_PAH_B


title: 133EK Trout_K4_CON_B

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K4_CON_B

source_name: Rainbow trout fed control diet for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 4 days post challenge.


title: 123EK Trout_K4_CON_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K4_CON_A

source_name: Rainbow trout fed control diet for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 4 days post challenge.


title: 135EK Trout_K4_CON_B


title: 132EK Trout_K4_CON_B


title: 137EK Trout_K4_CON_B


title: 121EK Trout_K4_CON_A


title: 120EK Trout_K4_CON_A


title: 122EK Trout_K4_CON_A


title: Fld_Xcv_rep1

city: Rosario

first: Juan

middle: José

last: Pierella Karlusich

state: Santa Fe

address: Esmeralda y Ocampo - Predio CONICET

country: Argentina

institute: Instituto de Biología Molecular y Celular de Rosario (IBR)

description:
Sample name: GF200_005
Gene expression after 19hr of infection with Xanthomonas campestris pv. vesicatoria in pfld4-2 tobacco leaves

hyb_protocol: Sample labeling, and hybridization were performed as described in the one-color microarray-based gene expression analysis protocol including the one-color RNA spike-in Kit according to the manufacturer's instructions (v5.0.1, Agilent Technologies).

scan_protocol: Slides were scanned on Agilent microarray scanner (G2505B) at high resolution.

data_processing: Data were extracted using feature extraction software (v9.5.3, Agilent Technologie) using a standard protocol. Data processing and statistical analysis were carried out with the Bioconductor library limma (Ritchie et al. 2015 Nucl Acids Res 43: e47). Background correction and normalization were performed using the normexp and quantile methods, respectively. Probes without intensities higher than 10% compared to intensities of the negative controls, in at least two samples, were omitted for subsequent analysis. Probe-to-unigene assignments were carried out using the corresponding file (microarray_nta_Agilent_4x44k_genes.txt) available at the GoMapMan website resource (www.gomapman.org; Ramšak et al., 2014 Nucleic Acids Res 42, D1167-1175).

organism: Nicotiana tabacum

source_name: pfld4-2 tobacco leaves infiltrated with a suspension of 10^8 CFU/mL Xanthomonas campestris pv. vesicatoria, 19hpi, replicate 1

growth_protocol: Plants were grown in soil at a light intensity of 250 μmol photons m−2 s−1, with a 16-h photoperiod and a relative humidity of 80% (greenhouse conditions). For the inoculation experiments, Xanthomonas campestris pv. vesicatoria cells were cultivated at 28°C in a modified yeast extract–peptone–dextrose (YPD) medium containing 1% (w/v) dextrose, 1% (w/v) bactopeptone, 1% (w/v) yeast extract, pH 7.3. An overnight culture was diluted (1:100) in fresh broth and grown for an additional 18 h. Bacterial cells were collected by centrifugation (15 min at 700 g), washed with 10 mM MgCl2 and finally resuspended in the same solution in a final concentration of 10^8 CFU mL−1.

extract_protocol: Leaf RNA was extracted as described by Logemann et al. (1987). RNA quantity and quality were determined with a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE) and by visual inspection after electrophoresis, respectively. One μg of RNA from each sample was treated with RQ1 DNase (Promega, Madison, WI) according to the manufacturer’s instructions, and used as template to generate cDNA with M-MLV Reverse Transcriptase (Promega, Madison, WI).

treatment_protocol: Xanthomonas campestris pv. vesicatoria suspensions (10^8 CFU mL−1) were inoculated on the abaxial side of one half of the main vein in the second youngest fully expanded leaves of 6-week-old wild-type and pfld4-2 plants using a plastic syringe, whereas the other half of the same leaf was infiltrated with 10 mM MgCl2 as a mock. After inoculation, plants were incubated at 250 μmol quanta m−2 s−1 for the times indicated in the text.

tag: cultivar

value: Petit Havana

value: leaves

tag: genotype

tag: treatment

value: infiltration with Xanthomonas campestris pv. Vesicatoria (suspension of 10^8 CFU/mL)


title: WT_Mock_rep1

description:
Sample name: GF200_003
Gene expression after 19hr of infiltration with mock solution in wild-type tobacco leaves

source_name: wild type tobacco leaves infiltrated with 10 mM MgCl2 mock solution, 19hpi, replicate 1

label_protocol: Sample labeling, and hybridization were performed as described in the one-color microarray-based gene expression analysis protocol including the one-color RNA spike-in Kit according to the manufacturer's instructions (v5.0.1, Agilent Technologies).

value: wild type

value: infiltration with mock solution (10 mM MgCl2)


title: RAD001, total, biological replicate 3

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

description: total RNA

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: RAD001, total

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse forelimbs dissected from day 11.5 mouse embryos

extract_protocol: Shh mutant phenotypes were manually identified as wild-type or mutants. All other samples were snap frozen in liquid N2 and genotyped. Either single or dual samples of equivalent genotyped samples (2-4 forelimbs) were used for all other samples. All samples contained 5Î¼g of carrier glycogen and were prepared using Trizol. Samples were then treated with the RiobMinusâ„¢ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: not applicable

tag: cell line


title: WT_Mock_rep2

description:
Sample name: GF200_004
Gene expression after 19hr of infiltration with mock solution in wild-type tobacco leaves

source_name: wild type tobacco leaves infiltrated with 10 mM MgCl2 mock solution, 19hpi, replicate 2


title: Fld_Mock_rep2

description:
Sample name: GF200_008
Gene expression after 19hr of infiltration with mock solution in pfld4-2 tobacco leaves

source_name: pfld4-2 tobacco leaves infiltrated with 10 mM MgCl2 mock solution, 19hpi, replicate 2


title: Fld_Mock_rep1

description:
Sample name: GF200_007
Gene expression after 19hr of infiltration with mock solution in pfld4-2 tobacco leaves

source_name: pfld4-2 tobacco leaves infiltrated with 10 mM MgCl2 mock solution, 19hpi, replicate 1


title: RAD001, total, biological replicate 1

description: total RNA


title: 115DK Trout_K2_PAH_B

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K2_PAH_B

source_name: Rainbow trout fed PAH diet (400 ppm) for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 2 days post challenge.

value: Day 2

value: PAH treated

value: Kidney

value: Control treated

value: Mock challenged


title: RAD001 + IR, total, biological replicate 2

description: total RNA

source_name: RAD001 + IR, total


title: 114DK Trout_K2_PAH_B

value: A. salmonicida challenged


title: Fld_Xcv_rep2

description:
Sample name: GF200_006
Gene expression after 19hr of infection with Xanthomonas campestris pv. vesicatoria in pfld4-2 tobacco leaves

source_name: pfld4-2 tobacco leaves infiltrated with a suspension of 10^8 CFU/mL Xanthomonas campestris pv. vesicatoria, 19hpi, replicate 2


title: RAD001 + IR, total, biological replicate 1

description: total RNA


title: RAD001 + IR, total, biological replicate 3

description: total RNA


title: RAD001, total, biological replicate 2

description: total RNA


title: 104DK Trout_K2_PAH_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K2_PAH_A

source_name: Rainbow trout fed PAH diet (400ppm) for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 2 days post challenge.


title: 113DK Trout_K2_PAH_B


title: 103DK Trout_K2_PAH_A


title: 101DK Trout_K2_PAH_A


title: RAD001, polysome, biological replicate 3

description: polysome RNA

source_name: RAD001, polysome


title: SNP array data for a Trp53-null mammary tumor developed in mouse E9

type: genomic

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Mouse diversity SNP array profiling data for a Trp53-null mammary tumor developed in female mouse E9 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

hyb_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facility by following the manufacturer's protocol.

data_processing: Normalization and data extraction from the scanned CEL files (together with >100 sample CEL files from inbred and F1 cross mice available from the Affymetrix website) were performed by using the Affymetrix Genotyping Console™ Software 4.2 with the BRLMM-P algorithm.

molecule: genomic DNA

source_name: SNP array data for a Trp53-null mammary tumor developed in female mouse E9 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

growth_protocol: Trp53-null mammary tumors were collected from Trp53L/L female mice after Ad-K8-Cre injection.

extract_protocol: Total genomic DNAs from Trp53-null mammary tumors and from mammary glands of a genetic background-matched wild-type female were prepared by the AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Trp53-null mammary tumors were obtained from Trp53L/L females 6-7 months after intraductal injection of Ad-K8-Cre adenovirus.

tag: gender

value: female

tag: cell type

value: Trp53-null mammary tumor


title: Human Oral cancer cells KB: Control vs. CD133 Overexpression

city: GWANGJU

first: Wonbong

last: Lim

address: 309 PILMUN-DAERO, DONG GU

department: Department of Premedical Science

country: South Korea

institute: School of Medicine, Chosun University

description: CD133 overexpression

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: KB

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: KB cells were purchased from the Korean Cell Line Bank (KCLB no. 10017, Seoul, Korea) and maintained in RPMI 1640 medium (Welgene, Daegu, Korea) supplemented with 10 % heat-inactivated fetal bovine serum (GIBCO/BRL Life Technologies, Rockville, MD, USA) and a 10 % antibiotic–antimycotic solution (Welgene) at 37 °C in a 5 % CO2 humidified chamber.

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

treatment_protocol: Stable cell lines overexpressing green fluorescent protein (GFP) or the CD133-GFP fusion protein were generated by transfecting confluent KB cells in 100-mm plates with 20 μg of pcDNA3.1/NT-GFPCD133 or pcDNA3.1/NT-GFP

value: KB

tag: transfection

value: control blank vector

value: Oral Cavity


title: WT_Xcv_rep2

description:
Sample name: GF200_002
Gene expression after 19hr of infection with Xanthomonas campestris pv. vesicatoria in wild-type tobacco leaves

source_name: wild type tobacco leaves infiltrated with a suspension of 10^8 CFU/mL Xanthomonas campestris pv. vesicatoria, 19hpi, replicate 2


title: RAD001 + IR, polysome, biological replicate 1

description: polysome RNA

source_name: RAD001 + IR, polysome


title: SNP array data for mammary glands from a background-matched wild-type control female

description: Mouse diversity SNP array profiling data for mammary glands from a strain background-matched wild-type control female

scan_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facility by following the manufacturer's protocol.

source_name: SNP array data for mammary glands from a strain background-matched wild-type control female

value: wild-type mammary glands


title: WT_Xcv_rep1

description:
Sample name: GF200_001
Gene expression after 19hr of infection with Xanthomonas campestris pv. vesicatoria in wild-type tobacco leaves

source_name: wild type tobacco leaves infiltrated with a suspension of 10^8 CFU/mL Xanthomonas campestris pv. vesicatoria, 19hpi, replicate 1

value: Petit Havana


title: RAD001 + IR, polysome, biological replicate 3

description: polysome RNA


title: 100DK Trout_K2_PAH_A

source_name: Reference:  Rainbow trout fed control diet for 50 days and then challenged with mock (no bacteria).  RNA was pooled from head kidney  collected 2, 4, 10 and 20 days post challenge.


title: SNP array data for a Trp53-null mammary tumor developed in mouse E8

description: Mouse diversity SNP array profiling data for a Trp53-null mammary tumor developed in female mouse E8 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

source_name: SNP array data for a Trp53-null mammary tumor developed in female mouse E8 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

label_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facility by following the manufacturer's protocol.


title: SNP array data for a Trp53-null mammary tumor developed in mouse E5

description: Mouse diversity SNP array profiling data for a Trp53-null mammary tumor developed in female mouse E5 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

source_name: SNP array data for a Trp53-null mammary tumor developed in female mouse E5 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus


title: 116EK Trout_K2_CON_B

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K2_CON_B

source_name: Rainbow trout fed control diet for 50 days and then challenged with A. salmonicida (bacteria).  Head kidney was collected 2 days post challenge.


title: 115EK Trout_K2_CON_B


title: RAD001, polysome, biological replicate 1

description: polysome RNA


title: RAD001, polysome, biological replicate 2

description: polysome RNA


title: SNP array data for a Trp53-null mammary tumor developed in mouse E2

description: Mouse diversity SNP array profiling data for a Trp53-null mammary tumor developed in female mouse E2 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

source_name: SNP array data for a Trp53-null mammary tumor developed in female mouse E2 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus


title: SNP array data for a Trp53-null mammary tumor developed in mouse E4

description: Mouse diversity SNP array profiling data for a Trp53-null mammary tumor developed in female mouse E4 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

source_name: SNP array data for a Trp53-null mammary tumor developed in female mouse E4 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus


title: 113EK Trout_K2_CON_B


title: 105EK Trout_K2_CON_A

description:
Rainbow trout were fed PAH or control diet for 50 days and were challenged with A. Salmonicida backteria or growth media without the pathogen (mock challenge). Head kidney was collected 2, 4, 10 and 20 days after challenge.
Trout_K2_CON_A

source_name: Rainbow trout fed control diet for 50 days and then challenged with mock (no bacteria).  Head kidney was collected 2 days post challenge.


title: 112EK Trout_K2_CON_B


title: 103EK Trout_K2_CON_A


title: 102EK Trout_K2_CON_A


title: 100EK Trout_K2_CON_A


title: PP242, total,  biological replicate 2

description: total RNA

source_name: PP242, total


title: PP242 + IR, total, biological replicate 1

description: total RNA

source_name: PP242 + IR, total


title: PP242 + IR, total, biological replicate 2

description: total RNA


title: PP242 + IR, polysome, biological replicate 3

description: polysome RNA

source_name: PP242 + IR, polysome


title: PP242, total,  biological replicate 1

description: total RNA


title: PP242, total,  biological replicate 3

description: total RNA


title: PP242, polysome, biological replicate 3

description: polysome RNA

source_name: PP242, polysome


title: PP242 + IR, polysome, biological replicate 2

description: polysome RNA


title: PP242 + IR, polysome, biological replicate 1

description: polysome RNA


title: RAD001 + IR, polysome, biological replicate 2

description: polysome RNA


title: PP242, polysome, biological replicate 2

description: polysome RNA


title: PP242, polysome, biological replicate 1

description: polysome RNA


title: DMSO, total, biological replicate 3

description: total RNA

source_name: DMSO, total


title: DMSO, total, biological replicate 2

description: total RNA


title: IR, total, biological replicate 3

description: total RNA

source_name: IR, total


title: IR, polysome, biological replicate 2

description: polysome RNA

source_name: IR, polysome


title: DMSO, total, biological replicate 1

description: total RNA


title: IR, polysome, biological replicate 3

description: polysome RNA


title: IR, total, biological replicate 2

description: total RNA


title: IR, polysome, biological replicate 1

description: polysome RNA


title: DMSO, polysome, biological replicate 2

description: polysome RNA

source_name: DMSO, polysome


title: IR, total, biological replicate 1

description: total RNA


title: PAO1 Fumarate + Glyoxylate 3

city: Cambridge

first: Jason

middle: H

last: Yang

address: 415 Main St, Rm 2017

department: Biological Engineering

institute: MIT / Broad Institute

description:
Fumarate + Glyoxylate 3
F_G3.CEL

hyb_protocol: 10 μg of cDNA were hybridized on Affymetrix P. aeruginosa Genome Arrays. The microarrays were then washed and stained.

scan_protocol: Arrays were washed and stained on Affymetrix Fluidics Station 450s using the appropriate Affymetrix protocol. The stained arrays were scanned at 532 nm using an Affymetrix GeneChip Scanner 3000.

data_processing: CEL files for the resulting expression profiles were background adjusted and RMA normalized using RMAExpress v1.1.0. Welch's t-test was used to compute statistical significance between different samples using MATLAB2016a.

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 Fumarate + Glyoxylate

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 10 μg total RNA

growth_protocol: Triplicate overnight P. aeruginosa PAO1 were prepared in M9 minimal media at 37C with shaking.

extract_protocol: RNA was extracted using the Qiagen Rneasy Protect Bacteria Mini Kit and Dnase treated using the Life Technologies Turbo DNA-free kit.

treatment_protocol: Stationary phase PAO1 cells were resuspended in M9 supplemented with 15 mM fumarate, 30 mM glyoxylate, or their combination. Cells were incubated for 1 hr at 37C with shaking and then harvested for RNA extraction.

tag: treated with

value: 15 mM fumarate and 30 mM glyoxylate


title: PAO1 Fumarate + Glyoxylate 2

description:
Fumarate + Glyoxylate 2
F_G2.CEL


title: DMSO, polysome, biological replicate 3

description: polysome RNA


title: PAO1 Fumarate + Glyoxylate 1

description:
Fumarate + Glyoxylate 1
F_G1.CEL


title: PAO1 Glyoxylate 3

description:
Glyoxylate 3
GLX3.CEL

source_name: PAO1 Glyoxylate

value: 30 mM glyoxylate


title: DMSO, polysome, biological replicate 1

description: polysome RNA


title: PAO1 Fumarate 3

description:
Fumarate 3
FMR3.CEL

source_name: PAO1 Fumarate

value: 15 mM fumarate


title: PAO1 Glyoxylate 2

description:
Glyoxylate 2
GLX2.CEL


title: PAO1 Fumarate 2

description:
Fumarate 2
FMR2.CEL


title: 20mGyB4/ reference male mouse1

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse1


title: 20mGyB5/ reference male mouse1

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: 20mGyB3/ reference male mouse1


title: PAO1 Glyoxylate 1

description:
Glyoxylate 1
GLX1.CEL


title: PAO1 Fumarate 1

description:
Fumarate 1
FMR1.CEL


title: 20mGyB2/ reference male mouse1


title: reference male mouse1/ 20mGyB4


title: reference male mouse1/ 20mGyB2


title: reference male mouse1/ 20mGyB5


title: PAO1 Control 3

description:
Control 3
CTL3.CEL

source_name: PAO1 Control

value: none (untreated)


title: PAO1 Control 2

description:
Control 2
CTL2.CEL


title: PAO1 Control 1

description:
Control 1
CTL1.CEL


title: 20mGyB1/ reference male mouse1


title: 20mGyBF/ reference male mouse1


title: reference male mouse1/ 20mGyB1


title: reference male mouse1/ 20mGyA5


title: reference male mouse1/ 20mGyBF


title: reference male mouse1/ 20mGyA6


title: reference male mouse1/ 20mGyA3


title: JKR 782-004 Keloids non-lesion

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

source_name: non-lesion

label_protocol: GeneChip Affymetrix protocol

extract_protocol: RNA was extracted from non-lesional, chronic keloid lesion and newly formed keloid biopsies using the RNeasy Mini KIT (Qiagen, Valencia, CA).

tag: patient

tag: condition

value: Keloids

value: human skin biopsy

tag: race

value: B


title: 20mGyA4/ reference male mouse1


title: 20mGyA5/ reference male mouse1


title: reference male mouse1/ 20mGyBM


title: reference male mouse1/ 20mGyA4


title: 20mGyA6/ reference male mouse1


title: JKR 782-003 Keloids new keloid formation

source_name: new keloid formation


title: 20mGyA2/ reference male mouse1


title: JKR 782-003 Keloids lesion

source_name: lesion


title: 20mGyA1/ reference male mouse1


title: 20mGyA3/ reference male mouse1


title: JKR 782-003 Keloids non-lesion


title: reference male mouse1/ 20mGyA1


title: JKR 782-004 Keloids lesion


title: 20mGyAF/ reference male mouse1


title: JKR 782-001 Keloids lesion


title: 22Rv1-M3-2 rep2

city: Taipei

first: Pei-Wen

last: Hsiao

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: ABRC

country: Taiwan

institute: Academia Sinica

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: PCa cell line

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

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

tag: tumor type

value: prostate tumor

tag: tumor stage

value: metastatic tumor


title: 22Rv1-M3-1 rep2

description: replicate 2


title: reference male mouse1/ 20mGyAF

tag: strain


title: 20mGyAM/ reference male mouse1


title: 22Rv1-M3-2 rep1

description: replicate 1


title: JKR 782-001 Keloids non-lesion


title: Tp80 treated Huh7/RepFeo cells rep2

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

description: Gene expression data from Tp80 treated Huh7/RepFeo cells

hyb_protocol: The RNA prepared was hybridized and stained onto the Human Genome U133 Plus 2.0 array (Affymetrix Inc.) using the GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc.).

scan_protocol: Signals were detected using the GeneChip® Scanner 3000G (Affymetrix Inc.).

data_processing: The data were calculated and normalized with a RMA method, Bioconductor package with a statistical package; R (http://www.r-project.org/).

source_name: Tp80 treated Huh7/RepFeo cells

label_protocol: RNA was prepared for microarray expression analysis by the GeneChip® 3’ IVT Expression Kit (Affymetrix Inc.) according to the manufacturer’s instructions.

growth_protocol: Huh7 cells or Huh7/RepFeo cells were plated in a 6-cm culture dish at a density of 1 × 105 cells per dish.

extract_protocol: Total RNA extraction using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.

treatment_protocol: Cells were incubated with a Tp80 or DMSO for 48 hours, respectively.

value: Huh7 cell

value: Huh7/RepFeo cells


title: Tp80 treated Huh7/RepFeo cells rep1


title: 22Rv1-M3-1 rep1

description: replicate 1


title: DMSO treated Huh7/RepFeo cells rep1

description: Gene expression data from DMSO treated Huh7/RepFeo cells

source_name: DMSO treated Huh7/RepFeo cells

value: DMSO


title: DMSO treated Huh7/RepFeo cells rep2


title: DMSO treated Huh7 cells rep2

description: Gene expression data from DMSO treated Huh7 cells

source_name: DMSO treated Huh7 cells

value: Huh7 cells


title: 22Rv1-PT rep2

description: replicate 2

value: primary tumor


title: 22Rv1-Luc2 rep2

description: replicate 2

value: parental cells


title: 22Rv1-PT rep1

description: replicate 1


title: DMSO treated Huh7 cells rep1


title: 22Rv1-Luc2 rep1

description: replicate 1


title: Lung pDC from donor 5 - replicate

status: Public on Dec 19 2016

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description: pDC isolated from the lung tissue of donor 5

hyb_protocol: Hybridization of cRNA was performed on Illumina Human-HT12 Version 4 chips for 16 hours at 58°C. The arrays were then washed and stained base on Illumina Wash Protocol

scan_protocol: The chips were scanned using BeadArray Scanner 500GX

data_processing: Probe level expression data were exported from Illlumina GenomeStudio software without background subtraction. These raw data were quantile normalized and log (base 2) transformed and in R (3.1.2) using Bioconductor lumi (version 2.18.0) package.

source_name: Lung

label_protocol: Biotinylated cRNA was prepared according to the protocol by Epicentre TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 using 500pg of total RNA

extract_protocol: Total RNA was isolated from FACS-sorted adult lung (APC  subsets following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy Micro clean-up procedure according to the manufacturer's protocol. Total RNA integrity was assessed using Agilent Bioanalyzer.

tag: celltype

value: pDC

tag: donorid

tag: comment

value: Technical replicate


title: Lung CD141+ DC from donor 5

description: CD141+.DC isolated from the lung tissue of donor 5


title: Lung CD1c+ DC from donor 5

description: CD1c+.DC isolated from the lung tissue of donor 5


title: Lung pDC from donor 2

description: pDC isolated from the lung tissue of donor 2


title: Lung CD141+ DC from donor 2

description: CD141+.DC isolated from the lung tissue of donor 2


title: reference male mouse6/ 0GyZ4

source_name: reference male mouse6

tag: tissue


title: reference male mouse6/ 0GyZ3


title: Lung CD14+ DC from donor 4

description: CD14+.DC isolated from the lung tissue of donor 4


title: Lung CD141+ DC from donor 4

description: CD141+.DC isolated from the lung tissue of donor 4


title: 0GyZ4/ reference male mouse6


title: Lung CD1c+ DC from donor 4

description: CD1c+.DC isolated from the lung tissue of donor 4


title: 0GyZ3/ reference male mouse6


title: Lung pDC from donor 4

description: pDC isolated from the lung tissue of donor 4


title: Lung CD14+ DC from donor 5

description: CD14+.DC isolated from the lung tissue of donor 5


title: 0GyZ1/ reference male mouse6


title: 0GyZF/ reference male mouse6


title: 0GyZ5/ reference male mouse6


title: Lung CD1c+ DC from donor 2 - replicate

description: CD1c+.DC isolated from the lung tissue of donor 2


title: Lung CD1c+ DC from donor 2


title: Lung CD14+ DC from donor 2

description: CD14+.DC isolated from the lung tissue of donor 2


title: reference male mouse6/ 0GyZ2


title: 0GyZ2/ reference male mouse6


title: reference male mouse1/ 20mGyB3


title: Lung CD141+ DC from donor 1

description: CD141+.DC isolated from the lung tissue of donor 1


title: reference male mouse6/ 0GyZ5


title: spleen CD14+ DC from donor 3

description:
CD14+ DC isolated from the spleen tissue of donor 3
none

source_name: spleen

label_protocol: Biotinylated cRNA was prepared according to the protocol by Epicentre TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 using 500pg of total RNA.

extract_protocol: Total RNA was isolated from FACS-sorted skin and spleen DC subsets following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy Micro clean-up procedure according to the manufacturer's protocol. Total RNA integrity was assessed using Agilent Bioanalyzer.


title: Lung CD14+ DC from donor 1 - replicate

description: CD14+.DC isolated from the lung tissue of donor 1


title: spleen CD1c+ DC from donor 1

description:
CD1c+ DC isolated from the spleen tissue of donor 1
none


title: 20mGyBM/ reference male mouse1


title: spleen CD1c+ DC from donor 4

description:
CD1c+ DC isolated from the spleen tissue of donor 4
none


title: Lung CD1c+ DC from donor 1

description: CD1c+.DC isolated from the lung tissue of donor 1


title: spleen CD14+ DC from donor 4

description:
CD14+ DC isolated from the spleen tissue of donor 4
none


title: Lung CD141+ DC from donor 4 - replicate


title: 0GyZM/ reference male mouse6


title: spleen CD1c+ DC from donor 3

description:
CD1c+ DC isolated from the spleen tissue of donor 3
none


title: spleen CD141+ DC from donor 3

description:
CD141+ DC isolated from the spleen tissue of donor 3
none


title: spleen CD141+ DC from donor 1

description:
CD141+ DC isolated from the spleen tissue of donor 1
none


title: skin CD1c+ DC from donor 6

description:
CD1c+ DC isolated from the skin tissue of donor 6
none

source_name: skin


title: spleen CD14+ DC from donor 1

description:
CD14+ DC isolated from the spleen tissue of donor 1
none


title: skin CD1c+ DC from donor 10

description:
CD1c+ DC isolated from the skin tissue of donor 10
none


title: skin CD14+ DC from donor 11

description:
CD14+ DC isolated from the skin tissue of donor 11
none


title: reference male mouse6/ 0GyZM


title: skin CD14+ DC from donor 10

description:
CD14+ DC isolated from the skin tissue of donor 10
none


title: spleen CD141+ DC from donor 4

description:
CD141+ DC isolated from the spleen tissue of donor 4
none


title: reference male mouse1/ 20mGyA2


title: skin CD1c+ DC from donor 11

description:
CD1c+ DC isolated from the skin tissue of donor 11
none


title: reference male mouse6/ 0GyZ1


title: A375 xenograft 12 day COMBO rep1

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

hyb_protocol: 750 ng of cRNA was hybridized on HumanHT-12_v.4 for 18 h. Array washes were performed using wash buffer

scan_protocol: Hybridized BeadChips were scanned using illumina Array reader

data_processing: Cubic Spline-normalized probe intensity data, togheter with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina)

source_name: A375 xenograft

label_protocol: Bioinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies)

growth_protocol: 6-week old CD1 female athymic mice were implanted subcutaneosly into the righ posterior flanks with A375 cell line and allowed to growth to 150-200 mm3 (over a period of approximately 20 days).

extract_protocol: Total RNA was extracted from frozen tumors with miRNeasy mini kit (Qiagen) after a preincubation with RNAlater (Life Technologies)

treatment_protocol: Mice were randomly assigned to different groups and treated with PLX4720 (60 mg/kg; daily gavage), bevacizumab (10 mg/kg; i.p. injection 3 times/week) and PLX4720+bevacizumab (COMBO)

value: with the combination of PLX4720 (60mg /kg) and bevacizumab (10 mg/kg)


title: reference male mouse6/ 0GyZF


title: Lung pDC from donor 5

description: pDC isolated from the lung tissue of donor 5


title: skin CD14+ DC from donor 6

description:
CD14+ DC isolated from the skin tissue of donor 6
none


title: A375 xenograft 12 day bevacizumab rep2

value: 3 times/week by i.p. administration of bevacizumab 10 mg/kg (saline 0.9%)


title: A375 xenograft 12 day PLX4720 rep2

value: daily by oral gavage with PLX4720 60 mg/kg (methylcellulose 1% w/v)


title: A375 xenograft 12 day bevacizumab rep3


title: Thymocytes from WT mouse, replicate 2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 5 micrograms of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1

source_name: CD4+CD8+ DP thymocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: CD4+CD8+ double-positive (DP) cells were isolated from thymuses of mice by fluorescence activated cell sorting (FACS)

extract_protocol: RNA was extracted using the Qiagen Rneasy kit

value: CD4+CD8+ DP thymocytes


title: reference male mouse1/ 20mGyAM

value: tail


title: Lung tissue_Virus_29d_rep3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Virus_29d_3
Gene expression data from lung tissue from mice infected with MHV-68 for 29 days, biological replicate 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol (HiScan).

data_processing: Data including background subtraction (GenomeStudio V2010.1 software, gene expression module version 1.6.0). Remaining negative values were removed by introducing an offset. Then, quantile normalisation.

label: Biotin

source_name: Lung tissue from mice infected with MHV-68 for 29 days

label_protocol: Illumina TotalPrep-96 RNA Amplification Kit (Ambion).

growth_protocol: Animals housed under spf conditions.

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment.

treatment_protocol: As described in the paper. Briefly, C57BL/6 mice were purchased from Charles River Laboratories (Sulzfeld, Germany) and housed in individually ventilated cages (IVC) during the MHV-68 infection period. Mice were anesthetized with ketamine and xylazine and infected i.n. with 5 x 10^4 PFU MHV-68. After 28 days, mice were either left untreated or instilled with 50 µg of spherical (CNP) or double-walled fibre-shaped carbon nanoparticles (DWCNT) per mouse. Lung tissue was harvested after 24 hours for transcriptome and metabolome analysis, as well as for determination of viral genomic load and for histology. All animal experiments were in compliance with protocols approved by the local Animal Care and Use Committee.

tag: strain/background

tag: age

value: 6-8 weeks

value: female

value: lung

value: MHV-68 for 29 days


title: A375 xenograft 12 day Vehicle rep3

tag: treatment

value: Vehicle (methylcellulose 1% w/v)

tag: cell line


title: skin CD14+ DC from donor 3

description:
CD14+ DC isolated from the skin tissue of donor 3
none


title: Lung tissue_Virus_29d_rep1

description:
Virus_29d_1
Gene expression data from lung tissue from mice infected with MHV-68 for 29 days, biological replicate 1.

tag: gender


title: A375 xenograft 12 day bevacizumab rep1


title: Thymocytes from hCD2-iCre x Gfi1fl/fl mouse, replicate 2


title: Tumor PyMT c609 pre-RFC vs c626 pre&post-R-Fc

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: MMTV-PyMT mammary tumor

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

growth_protocol: RNA was collected from tumor fragments

extract_protocol: Tripure (Roche)

treatment_protocol: RANK-Fc (10 mg/Kg) was injected intraperitoenally, 3 times per week into  WT FVB mice with an orthotopic PyMT tumor

value: FVB

value: MMTV-PyMT (FVB) orthotopic mammary tumor piece

value: Fc_CT c609:RANK-Fc neoadjuvant treatment, passage 2

value: Fc_FC c626:neoadjuvant & adjuvant treatment RANK-Fc, passage 2


title: A375 xenograft 12 day Vehicle rep2


title: A375 xenograft 12 day Vehicle rep1


title: A375 xenograft 12 day COMBO rep2


title: A375 xenograft 12 day PLX4720 rep1


title: A375 xenograft 12 day PLX4720 rep3


title: Thymocytes from WT mouse, replicate 1


title: Thymocytes from hCD2-iCre x Gfi1fl/fl mouse, replicate 1


title: Lung tissue_Virus_29d_rep2

description:
Virus_29d_2
Gene expression data from lung tissue from mice infected with MHV-68 for 29 days, biological replicate 2.


title: Lung tissue_Virus_6d_rep3

description:
Virus_06d_3
Gene expression data from lung tissue from mice infected with MHV-68 for 6 days, biological replicate 3.

source_name: Lung tissue from mice infected with MHV-68 for 6 days

value: MHV-68 for 6 days


title: Tumor PyMT  c566 CT vs c559 RFC

value: CT c566:control  passage 1

value: Fc c559: RANK-Fc adjuvant treatment, passage 1


title: Tumor PyMT c642 CT-CT vs  c603 pre-RFC

value: CT_CT c642:control  passage 2

value: Fc_CT c603:RANK-Fc neoadjuvant treatment, passage 2


title: Tumor PyMT preRFC c608 vs c567 FC

value: FC_CT c608:RANK-Fc neoadjuvant treatment, passage 2

value: FC c567:RANK-Fc adjuvant treatment, passage 1


title: Lung tissue_Virus_6d_rep2c

description:
Virus_06d_2c
Gene expression data from lung tissue from mice infected with MHV-68 for 6 days, biological replicate 2, technical replicate 3.


title: PCC6803_ΔpmgA_rep2

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays.

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture grown at standard conditions

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: A glucose tolerant strain of Synechocystis sp. PCC 6803 (a kind gift from Prof. Donald A. Bryant) was used as WT and to generate the ΔpmgA strain. WT and ΔpmgA were cultivated in BG-11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) buffered with 20 mM HEPES-NaOH to pH 8.0. The cultures were continuously bubbled with air supplemented with 3% (v/v) CO2 and grown at 30°C at a standard light intensity of 50 μmol photons m–2 s–1.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA) and treated with TURBO DNase (Invitrogen, CA, USA).

treatment_protocol: Synechocystis 6803 cells were collected by rapid filtration on hydrophilic polyethersulfone filters (Pall Supor 800 Filter, 0.8 µm).

tag: genotype/variation

value: deltapmgA


title: Lung CD14+ DC from donor 1

description: CD14+.DC isolated from the lung tissue of donor 1


title: Lung tissue_Virus_6d_rep1

description:
Virus_06d_1
Gene expression data from lung tissue from mice infected with MHV-68 for 6 days, biological replicate 1.

value: 6-8 weeks


title: Lung tissue_Virus_6d_rep2a

description:
Virus_06d_2a
Gene expression data from lung tissue from mice infected with MHV-68 for 6 days, biological replicate 2, technical replicate 1.

value: female


title: Lung tissue_Virus_28d_DWCNT_24h_rep3

description:
V_28d_DWCNT_24h_3
Gene expression data from lung tissue from mice infected with MHV-68 for 28 days and then treated with DWCNT for 24h, biological replicate 3.

source_name: Lung tissue from mice infected with MHV-68 for 28 days and then treated with DWCNT for 24h

value: lung

value: MHV-68 for 28 days and then DWCNT for 24h


title: Tumor PyMT  c607 pre&post-RFC vs c564 CT

value: FC_FC c607:RANK-Fc neoadjuvant & adjuvant treatment , passage 2

value: CT c564:control passage 1


title: Tumor PyMT c558 RFC vs c633 post-RFC

value: FVB

value: MMTV-PyMT (FVB) orthotopic mammary tumor piece

value: FC c558:RANK-Fc adjuvant treatment, passage 1

value: CT-FC c633:adjuvant treatment RANK-Fc, passage 2


title: Lung tissue_Virus_28d_DWCNT_24h_rep1

description:
V_28d_DWCNT_24h_1
Gene expression data from lung tissue from mice infected with MHV-68 for 28 days and then treated with DWCNT for 24h, biological replicate 1.


title: PCC6803_WT_rep2

value: WT


title: GNV019_hESCdNP_replicate 1

city: Bonn

first: Roman

last: Reinartz

address: Sigmund Freud Strasse 25

department: Institute of Reconstructive Neurobiology

institute: University of Bonn

description:
SAMPLE 24
replicate 1

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Embryonic Stem Cell Derived Neural Progenitor Cells

label_protocol: Biotinylated cRNA were prepared with the Epicentre TargetAmp Biotin labelling kit for Illumina arrays

growth_protocol: Conditions for cell expansion

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

treatment_protocol: No treatment

tag: cell type

value: hESCdNP

tag: passage


title: Tumor PyMT c635 post-RFC vs c641

value: CT_Fc c635:RANK-Fc adjuvant treatment, passage 2

value: CT_CT c641:control passage 2


title: GNV019_U87_replicate 1

description:
SAMPLE 22
replicate 1

source_name: Glioblastoma


title: PCC6803_ΔpmgA_rep3


title: PCC6803_WT_rep1


title: Lung tissue_Virus_28d_DWCNT_24h_rep2a

description:
V_28d_DWCNT_24h_2a
Gene expression data from lung tissue from mice infected with MHV-68 for 28 days and then treated with DWCNT for 24h, biological replicate 2, technical replicate 1.


title: Lung tissue_Virus_6d_rep2b

description:
Virus_06d_2b
Gene expression data from lung tissue from mice infected with MHV-68 for 6 days, biological replicate 2, technical replicate 2.

value: MHV-68 for 6 days


title: PCC6803_ΔpmgA_rep1


title: Lung tissue_Virus_28d_DWCNT_24h_rep2b

description:
V_28d_DWCNT_24h_2b
Gene expression data from lung tissue from mice infected with MHV-68 for 28 days and then treated with DWCNT for 24h, biological replicate 2, technical replicate 2.


title: Lung tissue_Virus_28d_CNP_24h_rep3

description:
V_28d_CNP_24h_3
Gene expression data from lung tissue from mice infected with MHV-68 for 28 days and then treated with CNP for 24h, biological replicate 3.

source_name: Lung tissue from mice infected with MHV-68 for 28 days and then treated with CNP for 24h

value: MHV-68 for 28 days and then CNP for 24h


title: GNV019_FIBRO_replicate 1

description:
SAMPLE 23
replicate 1

source_name: Dermal Fibroblasts

value: FIBRO


title: GNV019_PA+10_replicate 3

description:
SAMPLE 21
replicate 3

tag: cultured glioblastoma sample


title: Tumor PyMT c606 pre&post-RFc vs c646 post-RFC

value: Fc_Fc c606:RANK-Fc neoadjuvant & adjuvant treatment , passage 2

value: CT_FC c646:adjuvant treatment RANK-Fc, passage 2


title: MM18_2_blood

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

hyb_protocol: As described in the user guide, appendix A, of the The Encore™Biotin Module  (NuGEN)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G. CEL-files generated using AGCC

data_processing:
The CEL-files produced by the Affymetrix Expression Console were preprocessed and summarized to gene level using the RMA algorithm with the Bioconductor package affy using custom CDF-files [Dai M et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data http://dx.doi.org/10.1093/nar/gni179]
Probe set data extracted from custom CDF (HuEx-1_0-st-v2)
Probe set data extracted from custom CDF (HuEx-1_0-st-v29

label_protocol: The samples were prepared for hybridization to Affymetrix GeneChip Human Exon 1.0 ST Arrays using Affymetrix GeneChip WT Terminal Labeling and Controls Kit (P/N 901524)

growth_protocol: not applicable

extract_protocol: The frozen samples of the oral mucosa/nunonuclear cells were homogenized using TRIzolR Reagent (InvitrogenTM) and total RNA was isolated using the mirVanaTM miRNA Isolation Kit (AmbionR/InvitrogenTM) (Life Technologies Corporation). RNA amplification was performed using the “AmbionR WT Expression Kit” (Applied BiosystemsR) starting with 100 ng total RNA and a TP Basic Thermocycler real time PCR instrument (BiometraR). Amplificatio System (NuGEN Technologies, Inc., San Carlos, CA)

treatment_protocol: Consecutive homo sapiens buccal mucosa  and peripheral blood secured from 10 patients with multiple myeloma imediately before (day0), two days after (day2) and 21 days (day21) after high dose melphalan treatment (200mg/m2), and buccal mucosa and peripheral blood 10 healthy homo sapiens individuals. Mononuclear cells were isolated from the blood.

tag: mucositis grade

tag: person id

value: blood mononuclear cells


title: MM18_2_blood #2


title: Lung tissue_Virus_28d_CNP_24h_rep1

description:
V_28d_CNP_24h_1
Gene expression data from lung tissue from mice infected with MHV-68 for 28 days and then treated with CNP for 24h, biological replicate 1.

value: 6-8 weeks

value: female

value: lung


title: Lung tissue_Virus_28d_CNP_24h_rep2

description:
V_28d_CNP_24h_2
Gene expression data from lung tissue from mice infected with MHV-68 for 28 days and then treated with CNP for 24h, biological replicate 2.


title: GNV019_PA+10_replicate 2

description:
SAMPLE 20
replicate 2


title: GNV019_CL3

description: Genomic DNA extracted from primary glioblastoma cells GNV019 was genotyped using Infinium HumanHap610-Quadv1_B Genotyping BeadChips (Illumina).

hyb_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

data_processing:
Genomic DNA extracted from glioblastoma primary cells were genotyped using Infinium HumanHap550-2v3 and Human610-Quadv1_B Genotyping BeadChips (Illumina). Datasets from both arrays were merged according to Illuminas report Combining and Analyzing Data from Different BeadChips for integrated processing and analysis using GenomeStudio
Sample data table contains Genotype call, GC_SCORE, Theta, R, B_Allele_Freq, Log_R_Ratio exported from GenomeStudio

label: biotin/dinitrophenyl

label_protocol: C-Bio and A-DNP

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen)

value: cultured glioblastoma

tag: sample type

value: subclones derived from a parental culture


title: Lung tissue_DWCNT_24h_rep3

description:
DWCNT_24h_3
Gene expression data from lung tissue from mice treated with DWCNT for 24h, biological replicate 3.

source_name: Lung tissue from mice treated with DWCNT for 24h

value: DWCNT for 24h


title: Lung tissue_Ctrl_rep2

description:
Ctrl_3
Gene expression data from lung tissue from control mice, biological replicate 2.

source_name: Lung tissue from control mice

value: control


title: GNV019_CL7_replicate 3

description:
SAMPLE 18
replicate 3


title: GNV019_CL3_replicate 3

description:
SAMPLE 12
replicate 3


title: Lung tissue_DWCNT_24h_rep1

description:
DWCNT_24h_1
Gene expression data from lung tissue from mice treated with DWCNT for 24h, biological replicate 1.


title: Lung tissue_DWCNT_24h_rep2

description:
DWCNT_24h_2
Gene expression data from lung tissue from mice treated with DWCNT for 24h, biological replicate 2.


title: Lung tissue_CNP_24h_rep1

description:
CNP_24h_2
Gene expression data from lung tissue from mice treated with CNP for 24h, biological replicate 1.

source_name: Lung tissue from mice treated with CNP for 24h

value: CNP for 24h


title: GNV019_CL7_replicate 1

description:
SAMPLE 16
replicate 1


title: Lung tissue_CNP_24h_rep2

description:
CNP_24h_3
Gene expression data from lung tissue from mice treated with CNP for 24h, biological replicate 2.


title: GNV019_CL6_replicate 3

description:
SAMPLE 15
replicate 3


title: GNV019_CL2

scan_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: GNV019_PA+10_replicate 1

description:
SAMPLE 19
replicate 1


title: GNV019_CL6_replicate 1

description:
SAMPLE 13
replicate 1


title: GNV019_CL2_replicate 2

description:
SAMPLE 8
replicate 2


title: CON09_4_blood

data_processing:
The CEL-files produced by the Affymetrix Expression Console were preprocessed and summarized to gene level using the RMA algorithm with the Bioconductor package affy using custom CDF-files [Dai M et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data http://dx.doi.org/10.1093/nar/gni179]
Probe set data extracted from custom CDF (HuEx-1_0-st-v2)
Probe set data extracted from custom CDF (HuEx-1_0-st-v2)


title: GNV019_CL6_replicate 2

description:
SAMPLE 14
replicate 2


title: GNV019_CL3_replicate 2

description:
SAMPLE 11
replicate 2


title: GNV019_CL2_replicate 3

description:
SAMPLE 9
replicate 3


title: GNV019_CL3_replicate 1

description:
SAMPLE 10
replicate 1


title: Lung tissue_Ctrl_rep1

description:
Ctrl_2
Gene expression data from lung tissue from control mice, biological replicate 1.


title: GNV019_CL7_replicate 2

description:
SAMPLE 17
replicate 2


title: GNV019_CL1_replicate 3

description:
SAMPLE 6
replicate 3


title: GNV019_CL2_replicate 1

description:
SAMPLE 7
replicate 1


title: GNV019_CL1_replicate 1

description:
SAMPLE 4
replicate 1


title: GNV019_PA+5_replicate 3

description:
SAMPLE 3
replicate 3


title: GNV019_CL1_replicate 2

description:
SAMPLE 5
replicate 2


title: GNV019_PA+5_replicate 1

description:
SAMPLE 1
replicate 1


title: MM20_2_blood


title: MM20_1_blood


title: MM20_3_blood


title: MM18_1_blood


title: MM19_3_blood


title: MM15_3_blood


title: MM18_3_blood


title: MM07_3_blood


title: MM07_1_blood


title: MM05_3_blood


title: MM09_3_blood


title: MM05_1_blood


title: MM09_1_blood


title: MM04_1_blood


title: MM01_1_blood


title: MM20_3_mucosa

value: oral buccal mucosa


title: MM20_2_mucosa


title: MM20_1_mucosa


title: MM19_3_mucosa


title: MM02_3_blood


title: MM15_1_blood


title: MM05_2_blood


title: GNV019_PA+5_replicate 2

description:
SAMPLE 2
replicate 2


title: MM19_2_mucosa


title: MM18_3_mucosa


title: CON09_4_mucosa


title: MM18_2_mucosa


title: MM19_1_mucosa


title: MM15_3_mucosa


title: MM18_1_mucosa


title: MM15_2_mucosa


title: MM07_1_mucosa


title: MM09_3_mucosa


title: CB_-Glc_rep2

city: Zhuhai

first: Hong-Wei

last: Sun

address: 79 Kangning Road

department: The Affiliated Hospital of Beijing Institute of Technology (Zhuhai People's Hospital)

institute: Beijing Institute of Technology

description: Gene expression after 3days in GM-CSF and G-CSF treated cord blood CD34+ cells in glucose-deprived medium

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with GeneSpring Software GX 12.6.1 (Agilent technologies, Santa Clara, CA, US) using default parameters.

source_name: Expanded CD34+ cells, with GM-CSF and G-CSF, glucose-deprived DMEM, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was prepared using the TRIzol® Reagent (Cat#15596-026, Life Technologies) following the manufacturer's recommendations. Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Purified CD34+ cells from cord blood were cultured in HSC expansion media for 7-8 d. The expanded cells were then incubated with (GM+G) or without (Med) combined GM-CSF and G-CSF for 3 d. Cytokine-treated CB-MDSCs were cultured in DMEM medium or glucose-deprived DMEM medium (-Glc) supplemented with 10% fetal bovine serum.

tag: protocol

value: with GM-CSF and G-CSF

tag: medium

value: glucose-deprived DMEM


title: CB_GM+G_rep3

description: Gene expression after 3days in GM-CSF and G-CSF treated cord blood CD34+ cells

source_name: Expanded CD34+ cells, with GM-CSF and G-CSF, complete DMEM, replicate 3

value: complete DMEM


title: CB_-Glc_rep3

source_name: Expanded CD34+ cells, with GM-CSF and G-CSF, glucose-deprived DMEM, replicate 3


title: MM15_1_mucosa


title: CB_GM+G_rep1

source_name: Expanded CD34+ cells, with GM-CSF and G-CSF, complete DMEM, replicate 1


title: CB_Med_rep3

description: Gene expression after 3days in untreated cord blood CD34+ cells

source_name: Expanded CD34+ cells, without GM-CSF and G-CSF, complete DMEM, replicate 3

value: without GM-CSF and G-CSF


title: CB_Med_rep1

source_name: Expanded CD34+ cells, without GM-CSF and G-CSF, complete DMEM, replicate 1


title: MM07_2_mucosa


title: CB_GM+G_rep2

source_name: Expanded CD34+ cells, with GM-CSF and G-CSF, complete DMEM, replicate 2


title: naïve d5 3

city: London

first: Jean

last: Langhorne

address: The Ridgeway

institute: The Francis Crick institute

description:
replicate 3
SAMPLE 17

data_processing: Illumina GenomeStudio software was used to subtract background and scale average samples' signal intensity. Further normalization analyses were performed with GeneSpring 13.1.1 GX

source_name: microglia

label_protocol: Illumina protocol

extract_protocol: RNA was extracted using Ribopyre kit (Ambion) in accordance with the prescribed protocol provided with the kit. Quality control was performed by Agilent 2100 Bioanalyzer

tag: agent

tag: time point

value: 5 days

tag: strain

value: brain

value: 8 weeks


title: MM09_1_mucosa

tag: tissue


title: naïve d5 4

description:
replicate 4
SAMPLE 18

tag: age


title: naïve d5 5

description:
replicate 5
SAMPLE 19


title: MM09_2_mucosa


title: MM07_3_mucosa


title: naïve d5 2

description:
replicate 2
SAMPLE 16


title: naïve d5 1

description:
replicate 1
SAMPLE 15


title: CB_Med_rep2

source_name: Expanded CD34+ cells, without GM-CSF and G-CSF, complete DMEM, replicate 2


title: MM05_1_mucosa


title: MM05_2_mucosa


title: infected d5 4

description:
replicate 4
SAMPLE 13

value: Plasmodium berghei ANKA


title: MM05_3_mucosa


title: infected d5 3

description:
replicate 3
SAMPLE 12


title: MM04_2_mucosa


title: MM04_3_mucosa


title: infected d5 5

description:
replicate 5
SAMPLE 14


title: naïve d7 3

description:
replicate 3
SAMPLE 8

value: 7 days


title: infected d5 1

description:
replicate 1
SAMPLE 10

value: female


title: naïve d7 4

description:
replicate 4
SAMPLE 9


title: MM02_3_mucosa


title: MM02_2_mucosa


title: MM01_3_mucosa


title: naïve d7 2

description:
replicate 2
SAMPLE 7


title: infected d5 2

description:
replicate 2
SAMPLE 11


title: GW7647-treated hMADS cells, replicate 2

city: Toulouse cedex 4

first: Nathalie

last: Viguerie

address: 1 avenue Jean Poulhès BP 84225

department: Institute of Metabolic and Cardiovascular Diseases, UMR1048

country: France

institute: INSERM-Université Paul Sabatier

hyb_protocol: 825 ng of Cy5 labelled probe was cohybridized with the same amount of Cy3 labelled control probe. We used the Whole Human Genome Microarray Kit, 4x44K from Agilent with the gene expression hybridization kit according to the manufacturer’s protocol.

scan_protocol: Micro-arrays were scanned on a InnoScan 710A scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software version 5.1.1 (Innopsys).

data_processing: Labeling and hybridization qualities were verified with Agilent’s spike in kit. Features with a signal to background ratio strictly below 1.2 in both color as well as control spots were discarded. The data without background substraction were normalized with the Lowess procedure and quantiles method by use of R.

source_name: hMADS cells, D18, GW7647-treated

label_protocol: Total RNA quality was checked by capillary electrophoresis (Experion, BioRad) and quantified using Nanodrop ND-1000 Spectrophotometer (Labtech). Only good quality RNA extracts were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 500ng of RNA with the Quick Amp Labeling kit, two-color (Agilent).

extract_protocol: Total RNA was extracted using TRI-Reagent kit (Euromedex, Souffelweyersheim, France) according to the manufacturer’s instructions.

value: hMADS cells

tag: time of differentiation

value: Day 18

value: Adipocyte

source_name: Reference

value: Day 9


title: GW7647-treated hMADS cells, replicate 4

tag: cell line


title: MM04_1_mucosa


title: MM01_2_mucosa


title: GNV019_CL1

value: cultured glioblastoma

value: subclones derived from a parental culture


title: infected d7 5

description:
replicate 5
SAMPLE 5

tag: gender


title: MM02_1_mucosa

value: oral buccal mucosa


title: naïve d7 1

description:
replicate 1
SAMPLE 6


title: GW7647-treated hMADS cells, replicate 3


title: infected d7 3

description:
replicate 3
SAMPLE 3


title: GW7647-treated hMADS cells, replicate 1


title: Control hMADS cells, replicate 4

source_name: hMADS cells, D18, untreated


title: infected d7 2

description:
replicate 2
SAMPLE 2


title: MM01_1_mucosa


title: Rosiglitazone-treated hMADS cells, replicate 4

source_name: hMADS cells, D18, Rosiglitazone-treated


title: infected d7 4

description:
replicate 4
SAMPLE 4


title: A375 xenograft 12 day COMBO rep2

hyb_protocol: 1500 ng of cRNA was hybridized on MouseWG-6_v.2 for 18 h. Array washes were performed using wash buffer

source_name: A375 xenograft

tag: treatment

value: with the combination of PLX4720 (60mg /kg) and bevacizumab (10 mg/kg)


title: Control hMADS cells, replicate 3

tag: cell type


title: Rosiglitazone-treated hMADS cells, replicate 2


title: Rosiglitazone-treated hMADS cells, replicate 3


title: Rosiglitazone-treated hMADS cells, replicate 1


title: A375 xenograft 12 day COMBO rep1


title: Control hMADS cells, replicate 1


title: Control hMADS cells, replicate 2


title: A375 xenograft 12 day bevacizumab rep3

value: 3 times/week by i.p. administration of bevacizumab 10 mg/kg (saline 0.9%)


title: A375 xenograft 12 day bevacizumab rep1


title: infected d7 1

description:
replicate 1
SAMPLE 1


title: MEF_CycG2KO

city: Suita

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: The array was scanned with 5µm resolution using an Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction, LOWESS normalization, and dye-normalization.

source_name: Embryonic fibroblast cells derived from CycG2-/- C57BL/7J mice

label_protocol: 500 ng of total RNA was labeled using Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Mouse embryonic fibroblasts (MEFs) were cultured in DMEM + 10% inactivated fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.

extract_protocol: Cultured cells were lysed by QIAzol Lysis Reagent (Qiagen), then total RNA was extracted from aqueous phase of QIAzol homogenate with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

treatment_protocol: MEFs were grown at their logarithmic growth phase.

tag: strain/background

tag: genotype/variation

value: mouse embryonic fibroblasts (MEFs)

source_name: Embryonic fibroblast cells derived from CycG2+/+ C57BL/7J mice

value: CycG2+/+ (WT)


title: MEF_CycG1KO_dyeswap

source_name: Embryonic fibroblast cells derived from CycG1+/+ C57BL/6J mice

value: CycG1+/+ (WT)

source_name: Embryonic fibroblast cells derived from CycG1-/- C57BL/6J mice


title: A375 xenograft 12 day bevacizumab rep2


title: A375 xenograft 12 day PLX4720 rep3

value: daily by oral gavage with PLX4720 60 mg/kg (methylcellulose 1% w/v)


title: A375 xenograft 12 day Vehicle rep3

value: Vehicle (methylcellulose 1% w/v)


title: A375 xenograft 12 day Vehicle rep1


title: A375 xenograft 12 day PLX4720 rep1


title: MEF_CycG1KO


title: MEF_CycG2KO_dyeswap


title: A375 xenograft 12 day PLX4720 rep2


title: iNKT cells, Utx knock out, biological rep4, batch2

city: Boston

first: Jialiang

last: Huang

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description:
Gene expression data fromiNKT cells, Utx knock out
iNKT_UTX_KO4

hyb_protocol: Hybridized to Affymetrix mouse 430A 2.0 arrays based on standard protocol.

scan_protocol: All chips were scanned with the Affymetrix GeneChip(r) Scanner 3000 7G System using the standard protocol.

data_processing: Affymetrix CEL files were normalized using the Robust Multi array Average (RMA) method, and batch effects were removed using ComBat.

source_name: iNKT cells with Utx knock out

label_protocol: RNA was reverse transcribed and amplified using Ovation Pico RNA Amplification System V2(NuGEN), biotin-labeled (Encore Biotin Module, NuGEN)

growth_protocol: Sex- and age-matched animals between 8 and 12 weeks of age were used for experiments

extract_protocol: Cells were sorted into TRI Reagent (Life Technologies), and total RNA was isolated according to the manufacturer's instructions with following modification: the aqueous phase containing total RNA was purified using the RNeasy plus kit (Qiagen). RNA was converted to cDNA with cDNA synthesis kit (Bio-Rad).

value: 8-12 weeks

value: Utx knock out

value: thymic iNKT cells


title: A375 xenograft 12 day Vehicle rep2