title: Huvecs, Untreated, 72h, Biological Rep 3

description: gene expression data from Huvecs under normal growth conditions after 72h


title: A_TBS45_29

status: Public on Nov 30 2015

type: RNA

city: Bochum

first: Robert

last: Kumsta

address: Universitätsstraße 150

department: Department of Genetic Psychology

country: Germany

institute: Ruhr-University Bochum

description: Gene expression 45 minutes before psychosocial stress exposure in isolated monocytes

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

molecule: total RNA

organism: Homo sapiens

source_name: Isolated monocytes, 45min pre-stress, control group

label_protocol: In order to produce Cy3- labeled cRNA 100 ng of 176 out of the 180 RNA samples and 50 ng of the RNA samples 100, 166, 168 and 167  was used as template. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. The samples were processed in a high throughput approach using 96-well microtiter plates and the RNeasy® 96 kit (Qiagen) for the purification of the labeled / amplified cRNA.

extract_protocol: RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel) following manufacturer's instructions

treatment_protocol: CD14+ monocyted were isolated (MACS, Miltenyi) from freshly drawn peripheral blood from healthy volunteers. Isolated monocytes were snap-frozen and stored at -80 degrees Celsius until RNA isolation

tag: tissue

value: CD14+ monocytes

tag: gender

value: female

tag: age


title: A_TBS45_1


title: Huvecs, Cold Control, 72h, Biological Rep1

city: Liverpool

first: Rui

middle: Augusto

last: Martins Cordeiro

state: Merseyside

address: Crown Street

department: Integrative Biology

country: United Kingdom

institute: University of Liverpool

hyb_protocol: Following amplification 15ug of RNA was fragmented and 12.5ug of fragmented labelled RNA was hybridised onto Affymetrix GeneChip C. elegans Genome Arrays as per the manufacturer’s instructions. These were hybridised for 16 hours at 45°C and 60rpm in an Affymetrix hybridisation oven 640. Hybridised arrays were washed using Affymetrix Hybridisation wash and stain kit on a GeneChip Fluidics station 450

scan_protocol: scanned using an Affymetrix GeneChip scanner 3000 7G

data_processing: Affymetrix GeneChip Command Console Software and Affymetric Expression Console were used to generate .CEL files and QC metrics. Analysis of gene expression data was done with the Affymetrix® Transcriptome Analysis Console (TAC) Software. Affymetrix Transcriptome Analysis Console (TAC) Software was used to analyze gene expression data. Normalization was performed using the Robust Multi-chip Average (RMA) method. The data in the matrix table contains the log2 transformed RMA normalized signal from all 15 samples.

label: biotin

source_name: Huvecs exposed to 4°C for 2hours while perfused with LM5 and then left to incubate under normal growth conditions for 72h

label_protocol: labelled using the Affymetric GeneChip 3@ IVT Express labelling kit as per the manufacturer’s instructions using 200ng of total RNA was input into the labelling reaction

extract_protocol: qiagen's Rneasy according to manufacture's instructions

value: Human Umbilical Vein

tag: treatment


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 3 DNEV-3

type: other

city: México

first: Maria

middle: L

last: Muñoz

address: Av. Instituto Politécnico Nacional 2508

department: Genetics and Molecular Biology

country: Mexico

institute: CIVESTAV-IPN

hyb_protocol: DNA microarray chip was prepare for hybridization by washing extensively with 0.1% SDS, rinsed twice with double deionizer water and heated in double deionizer water for 3 min at 95° C. After blocking with prehybridization buffer (4X SSC, 1 %SDS nd 10 mg/ml BSA) for 45 min at 42° C, DNA microarray chip was washed with double deionizer water for 20 s and dried under filtered air flow. A volume of 5 µl containing specific primer for serotype was used. The microarray substrates and coverslips were sealed in a chamber from BIO-RAD (Bio-Rad Laboratories, Inc., Ca., USA) and incubated at 42o C for 16-18 h at high humidity. Coverslip and supports were gently removed (4× SSC in a wash bottle) and arrays were washed by immersion into 1× SSC, 0.1% SDS for 10 min (10 slides in 250 ml), 0.1× SSC, 0.1% SDS twice for 10 min and 0.1× SSC twice for 10 min. Finally, blow the slide dry with air by pushing the liquid away from the spots and towards the outer edges.

scan_protocol: Slides were scanned using Scanner GeneTac LS IV (Genomic Solutions, Molecular Dynamics Generation III) to detect Cy5 fluorescence. For the detection of DENV serotypes we used the excitation lines at 646 nm wavelength of a laser scanner (Scanner Gene TAC LSIV from Genomic Solutions) by adding pixel intensities of each spot image

data_processing: Data was normalized by experiment mean after background correction.

molecule: other

organism: Dengue virus

source_name: Specific primer for DENV-3

label_protocol: Peformed during the synthesis of the oligonucleotide by The Midland Certified reagent Company Inc. (Midland, TX, USA).

extract_protocol: The primer was synthesized with 5´ C6 amino linker by The Midland Certified reagent Company Inc. (Midland, TX, USA). Synthesis was validated using each pair of oligonucleotides by RT-PCR and found to yield PCR products of the expected size.

tag: primer


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 1 DNEV-3


title: Huvecs, Cold Control, 72h, Biological Rep2

value: exposed to 4°C for 2hours while perfused with LM5 and then left to incubate under normal growth conditions for 72h


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 3 DNEV-4

scan_protocol: Slides were scanned using Scanner GeneTac LS IV (Genomic Solutions, Molecular Dynamics Generation III) to detect Yakima yellow fluorescence. For the detection of DENV serotypes we used the excitation lines at 530 nm wavelength of a laser scanner (Scanner Gene TAC LSIV from Genomic Solutions) by adding pixel intensities of each spot image

label: Yakima Yelow

source_name: Specific primer for DENV-4

value: 5´-(_Yakima Yelow) CCTGGTTGATGACAAAAGTCTTG-3´, DENV-4


title: WT-48hr-replicate 3

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

country: USA

institute: University of Kentucky

description: Gene expression data from mouse oviducts

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: Microarray data were analyzed by importing raw expression intensity values (*.cel files) into Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO), where the GC-Robust Multiarray Analysis algorithm (GC-RMA), quantile normalization, and Median Polish was applied for GeneChip background correction, log base 2 transformation, conversion of expression values and probeset summarization.  Annotation was performed using NetAffx annotation database (Release 34) on December 3rd, 2014.  Quality of data was assessed using light intensity expression values on a per chip and per gene basis and visualized as box plots

label: Biotin

organism: Mus musculus

source_name: WT oviduct 48hr

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

extract_protocol: Oviducts were pooled from 3-4 mice per treatment group and genotype and total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) and purified through RNeasy columns (Qiagen, Valencia, CA).

treatment_protocol: Mice with a global deletion of ESR1 (ESR1KO) on a C57BL/6 background were generated.  Briefly, two transgenic mouse lines were used; male ESR1flox/flox were bred with female Zp3cre to produce a line expressing Cre recombinase in the oocyte.  The F1 heterozygotes (ESR1flox/+Zp3cre) were bred with ESR1flox/flox resulting in ESR1flox/floxZp3cre mice, where females produce oocytes that are ESR1-.  ESR1flox/floxZp3cre females were then bred with ESR1flox/- males to produce ESR1KO progeny (ESR1-/- and ESR1-/- ZP3Cre) or sibling controls (ESR1flox/- and ESR1flox/- ZP3Cre).  Genomic DNA was extracted from ear punches using the Easy DNA kit (Invitrogen, Carlsbad CA) to confirm genotypes.  Whole oviducts were collected for extraction of RNA from immature female mice (ESR1KO and WT) killed at 23 days of age, or ESR1KO and WT mice treated with 5 IU PMSG at 23 days of age and killed 48 h later.

tag: strain background

value: whole oviduct

tag: strain

value: ESR1 wildtype

value: PMSG


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 2 DNEV-3


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 2 DNEV-4


title: Huvecs, Untreated, 72h, Biological Rep 1

source_name: Huvecs under normal growth conditions after 72h

value: exposed to 4°C for 2hours while perfused with LM5 and increasing concentrations of Ethylene Glycol and then left to incubate under normal growth conditions for 24h


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 2 DNEV-2

scan_protocol: Slides were scanned using Scanner GeneTac LS IV (Genomic Solutions, Molecular Dynamics Generation III) to detect FAM, fluorescence. For the detection of DENV serotypes we used the excitation lines at 494 nm wavelength of a laser scanner (Scanner Gene TAC LSIV from Genomic Solutions) by adding pixel intensities of each spot image

label: 6 FAM

source_name: Specific primer for DENV-2

extract_protocol: Primer was synthesized with 5´ C6 amino linker by The Midland Certified reagent Company Inc. (Midland, TX, USA). Synthesis was validated using each pair of oligonucleotides by RT-PCR and found to yield PCR products of the expected size.

value: 5´-(_6 FAM) CCGGTGTGCTCRGCYCTGAT-3´, DENV-2


title: Huvecs, EG treated, 24h, Biological Rep2

source_name: Huvecs exposed to 4°C for 2hours while perfused with LM5 and increasing concentrations of Ethylene Glycol and then left to incubate under normal growth conditions for 24h


title: Huvecs, EG treated, 24h, Biological Rep1


title: Huvecs, Untreated, 72h, Biological Rep 2

value: under normal growth conditions after 72h


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 1 DNEV-4


title: Huvecs, EG treated, 24h, Biological Rep3

description: gene expression data from Huvecs exposed to 4°C for 2hours while perfused with LM5 and increasing concentrarions of Ethylene Glycol and then left to incubate under normal growth conditions for 24h


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 1 DNEV-2


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 3 DNEV-2


title: Huvecs, Untreated, 24h, Biological Rep 3

source_name: Huvecs under normal growth conditions after 24h


title: Huvecs, Cold Control, 24h, Biological Rep2

source_name: Huvecs exposed to 4°C for 2hours while perfused with LM5 and then left to incubate under normal growth conditions for 24h


title: Huvecs, Untreated, 24h, Biological Rep 2

value: under normal growth conditions after 24h


title: Huvecs, Cold Control, 24h, Biological Rep3

value: exposed to 4°C for 2hours while perfused with LM5 and then left to incubate under normal growth conditions for 24h


title: CD3_Transcripts-R.20_Tac.Mtx.F

status: Public on Nov 29 2015

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

description: CD3_Transcripts-R.20 Tac.Mtx.F

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Rhesus Macaque Genome Array.  GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 scanner with 7G upgrade.

data_processing: Data from .CEL files were uploaded to the Bioconductor for further analysis and normalized using RMA (‘affy’ package).  Resulting fluorescent intensities were normalized to account for batch effects using the ‘sva’ package.

organism: Macaca mulatta

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’IVT Plus protocol from 70-85 ng total RNA.

extract_protocol: CD3 T cells were lysed in RLT Buffer and total RNA was isolated using the RNAEasy kit per manufacturers instructions.

treatment_protocol: Cohorts of rhesus macaques received either an allogeneic or autologous HCT.  Allogeneic HCT recipients received various immunoprophylactic treatments for prevention of GVHD.  CD3 T cells were sorted by FACS from peripheral blood at various timepoints in the post transplant period and from healthy controls.

tag: individual

value: Allogeneic

tag: prophylaxis

value: Tac-Mtx

tag: group

value: Final

tag: batch


title: CD3_Transcripts-R.21_Tac.Mtx.F

description: CD3_Transcripts-R.21 Tac.Mtx.F


title: CD3_Transcripts-R.19_Tac.Mtx.F

description: CD3_Transcripts-R.19 Tac.Mtx.F


title: CD3_Transcripts-R.17_Siro.F

description: CD3_Transcripts-R.17 Siro.F

value: Siro


title: CD3_Transcripts-R.45_Healthy.Control

description: CD3_Transcripts-R.45 Healthy.Control


title: CD3_Transcripts-R.52_NoRx.F

description: CD3_Transcripts-R.52 NoRx.F


title: Huvecs, Untreated, 24h, Biological Rep 1


title: CD3_Transcripts-R.21_Tac.Mtx.D14

description: CD3_Transcripts-R.21 Tac.Mtx.D14


title: CD3_Transcripts-R.13_Siro.F

description: CD3_Transcripts-R.13 Siro.F


title: CD3_Transcripts-R.20_Tac.Mtx.D30

description: CD3_Transcripts-R.20 Tac.Mtx.D30


title: CD3_Transcripts-R.20_Tac.Mtx.D14

description: CD3_Transcripts-R.20 Tac.Mtx.D14


title: CD3_Transcripts-R.40_Healthy.Control

description: CD3_Transcripts-R.40 Healthy.Control


title: CD3_Transcripts-R.51_NoRx.F

description: CD3_Transcripts-R.51 NoRx.F


title: Lsd1 inhibited

city: Manchester

first: Roshana

middle: S

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

institute: CRUK Manchester

description: RNA expression value

hyb_protocol: Samples were hybridized with GeneChip mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the CRUK Manchester Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (Rma) for background correction and normalization.

source_name: Bry-GFP ES line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the Terminal Labeling Kit (Affymetrix).

growth_protocol: FLK1+ cells were isolated from day 3 Bry-GFP derived EB and CD41 comparment  from both samples were FACS isolated on day 2 after culture. EBs and Cultures grown as decribed in Lancrin et al, 2009 and Stefanska et al, 2014

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Flk+ positive were either treated with DMSO (Ctrl) or with 300nM of the LSD1 inhibitor compound B

tag: cell type

value: hemogenic endothelial cells

tag: agent

value: 300nM of the Lsd1 inhibitor


title: CD3_Transcripts-R.19_Tac.Mtx.D30

description: CD3_Transcripts-R.19 Tac.Mtx.D30


title: CD3_Transcripts-R.19_Tac.Mtx.D14

description: CD3_Transcripts-R.19 Tac.Mtx.D14


title: CD3_Transcripts-R.16_Siro.F

description: CD3_Transcripts-R.16 Siro.F


title: CD3_Transcripts-R.18_Siro.F

description: CD3_Transcripts-R.18 Siro.F


title: A_TBS45_45

value: CD14+ monocytes

value: male


title: CD3_Transcripts-R.50_NoRx.F

description: CD3_Transcripts-R.50 NoRx.F


title: CD3_Transcripts-R.35_Healthy.Control

description: CD3_Transcripts-R.35 Healthy.Control


title: CD3_Transcripts-R.48_Healthy.Control

description: CD3_Transcripts-R.48 Healthy.Control


title: CD3_Transcripts-R.34_Healthy.Control

description: CD3_Transcripts-R.34 Healthy.Control


title: CD3_Transcripts-R.31_Healthy.Control

description: CD3_Transcripts-R.31 Healthy.Control


title: CD3_Transcripts-R.47_Healthy.Control

description: CD3_Transcripts-R.47 Healthy.Control


title: CD3_Transcripts-R.53_NoRx.F

description: CD3_Transcripts-R.53 NoRx.F


title: CD3_Transcripts-R.54_Healthy.Control

description: CD3_Transcripts-R.54 Healthy.Control


title: DMSO ctrl

description: RNA expression value


title: CD3_Transcripts-R.60_Healthy.Control

description: CD3_Transcripts-R.60 Healthy.Control


title: CD3_Transcripts-R.13_Healthy.Control

description: CD3_Transcripts-R.13 Healthy.Control


title: CD3_Transcripts-R.39_Healthy.Control

description: CD3_Transcripts-R.39 Healthy.Control


title: Huvecs, Cold Control, 24h, Biological Rep1

value: Human Umbilical Vein


title: CD3_Transcripts-R.33_Healthy.Control

description: CD3_Transcripts-R.33 Healthy.Control


title: CD3_Transcripts-R.16_Healthy.Control

description: CD3_Transcripts-R.16 Healthy.Control


title: CD3_Transcripts-R.36_Healthy.Control

description: CD3_Transcripts-R.36 Healthy.Control


title: CD3_Transcripts-R.49_Healthy.Control

description: CD3_Transcripts-R.49 Healthy.Control


title: CD3_Transcripts-R.32_Healthy.Control

description: CD3_Transcripts-R.32 Healthy.Control


title: CD3_Transcripts-R.62_Healthy.Control

description: CD3_Transcripts-R.62 Healthy.Control


title: CD3_Transcripts-R.56_Healthy.Control

description: CD3_Transcripts-R.56 Healthy.Control


title: CD3_Transcripts-R.28_Healthy.Control

description: CD3_Transcripts-R.28 Healthy.Control


title: Corn Oil Control-Recovery, biological replicate 18

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

description: messenger RNA

hyb_protocol: Followed manufacturer's instructions.

scan_protocol: Followed manufacturer's instructions.

data_processing: The probe cell intensity data from the Affymetrix GeneChips was normalized and annotated following previously published methods (Pacheco, Houseman et al. 2011 (PMID 21674046)). The linear models of microarray analysis (LIMMA) procedure (Smyth, Yang et al. 2003) (R package limma) was used to fit a linear regression model for each transcript on the Affymetrix GeneChip Array for each pair of treatment and controls. The p-values were adjusted for multiple comparisons with the qvalue package in R (Storey 2002) and the log2 expression ratios were transformed into fold change values.

organism: Rattus norvegicus

source_name: sperm, corn oil, recovery

label_protocol: Followed manufacturer's instructions.

extract_protocol:
Sperm isolation protocol: The cauda epididymides were punctured repeatedly with 30 or 26 gauge needles and put into micro-centrifuge tubes containing 1 mL phosphate-buffered saline (PBS). The samples were incubated in a water bath at 37°C for 10 minutes to aid sperm diffusion from the tissue. The tubes were spun for 3 minutes at 300 xg to pellet the epididymal pieces and the supernatant containing sperm were put into a new tube. The tube was spun for an additional 5 minutes at 2000 xg to pellet the sperm and the supernatant was removed. One mL of lysis buffer (0.15 M ammonium chloride, 10 mM potassium bicarbonate, 0.1 mM EDTA) was added to the sperm pellet, incubated on the bench top for 30 seconds and spun at 16,100 xg for 1 minute. The pellet was washed with 1 mL of PBS and spun at 16,100 xg for 1 minute.

RNA was extracted from the fresh sperm using the mirVana miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA), which separated the RNA into large and small fractions, per manufacturer’s instructions.

value: Fischer 344

value: sperm

value: corn oil

tag: recovery

value: yes


title: Corn Oil Control-Recovery, biological replicate 20

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 19

description: messenger RNA


title: CD3_Transcripts-R.59_Healthy.Control

description: CD3_Transcripts-R.59 Healthy.Control


title: CD3_Transcripts-R.37_Healthy.Control

description: CD3_Transcripts-R.37 Healthy.Control


title: Corn Oil Control-Recovery, biological replicate 16

description: messenger RNA


title: CD3_Transcripts-R.18_Healthy.Control

description: CD3_Transcripts-R.18 Healthy.Control


title: CD3_Transcripts-R.53_Healthy.Control

description: CD3_Transcripts-R.53 Healthy.Control


title: CD3_Transcripts-R.30_Healthy.Control

description: CD3_Transcripts-R.30 Healthy.Control


title: Corn Oil Control-Recovery, biological replicate 17

description: messenger RNA


title: CD3_Transcripts-R.43_Healthy.Control

description: CD3_Transcripts-R.43 Healthy.Control


title: CD3_Transcripts-R.58_Healthy.Control

description: CD3_Transcripts-R.58 Healthy.Control


title: CD3_Transcripts-R.22_Healthy.Control

description: CD3_Transcripts-R.22 Healthy.Control


title: PBMC CD4&CD8 T cells-No GVHD.8

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 28 post transplant
No.GVHD.8

hyb_protocol: Following fragmentation, 4.5 ug of cDNA were hybridized for 18 hr at 45 degrees C on GeneChip Human Transcriptome Array 2.0.  GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450_0001.

scan_protocol: GeneChip arrays were scanned using the Affymetrix GeneChip 3000 scanner with 7G upgrade.

data_processing: Data from .CEL files were uploaded to the Expression Console Software for further analysis and normalized using RMA.  Resulting fluorescent intensities were normalized to account for batch effects using the ‘sva’ package in Bioconductor.

label_protocol: Amplified cDNA were prepared using the NuGen Ovation Pico WTA System V2 from 1 ng total RNA; Biotin labeling of the cDNA was performed with the NuGen Encore Biotin Module according to standard protocol.

extract_protocol: Total RNA was isolated from CD4/8 T lysates using the RNAEasy kit per manufacturers instructions.

treatment_protocol: PBMC were thawed and labeled with CD4, CD8, CD11c, CD14, CD16, CD20, CD56.  Cells positive for either CD4 or CD8 but negative for the remainder of markers were sorted and subsequently lysed/preserved in RLT buffer.

value: No

value: No GVHD

value: PBMC CD4&CD8 T cells


title: Corn Oil Control-Recovery, biological replicate 14

description: messenger RNA


title: DBCP-Recovery, biological replicate 18

description: messenger RNA

source_name: sperm, DBCP, recovery

value: 5 mg/kg/d DBCP


title: CD3_Transcripts-R.44_Healthy.Control

description: CD3_Transcripts-R.44 Healthy.Control


title: PBMC CD4&CD8 T cells-No GVHD.9

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 60 post transplant
No.GVHD.9


title: CD3_Transcripts-R.61_Healthy.Control

description: CD3_Transcripts-R.61 Healthy.Control


title: PBMC CD4&CD8 T cells-No GVHD.6

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 60 post transplant
No.GVHD.6


title: Corn Oil Control-Recovery, biological replicate 11

description: messenger RNA


title: CD3_Transcripts-R.41_Healthy.Control

description: CD3_Transcripts-R.41 Healthy.Control


title: PBMC CD4&CD8 T cells-No GVHD.7

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 28 post transplant
No.GVHD.7


title: DBCP-Recovery, biological replicate 17

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 13

description: messenger RNA


title: PBMC CD4&CD8 T cells-No GVHD.5

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 28 post transplant
No.GVHD.5


title: DBCP-Recovery, biological replicate 12

description: messenger RNA


title: CD3_Transcripts-R.201_Healthy.Control

description: CD3_Transcripts-R.201 Healthy.Control


title: DBCP-Recovery, biological replicate 16

description: messenger RNA


title: DBCP-Recovery, biological replicate 19

description: messenger RNA


title: DBCP-Recovery, biological replicate 15

description: messenger RNA


title: CD3_Transcripts-R.55_Healthy.Control

description: CD3_Transcripts-R.55 Healthy.Control


title: PBMC CD4&CD8 T cells-No GVHD.4

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 60 post transplant
No.GVHD.4


title: DBCP-Recovery, biological replicate 13

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 15

description: messenger RNA


title: DBCP-Recovery, biological replicate 14

description: messenger RNA


title: CD3_Transcripts-R.200_Healthy.Control

description: CD3_Transcripts-R.200 Healthy.Control


title: Corn Oil Control-Recovery, biological replicate 9

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 8

description: messenger RNA


title: CD3_Transcripts-R.28_FR104.Siro.F

description: CD3_Transcripts-R.28 FR104.Siro.F

value: Allogeneic


title: CD3_Transcripts-R.26_FR104.Siro.F

description: CD3_Transcripts-R.26 FR104.Siro.F


title: PBMC CD4&CD8 T cells-No GVHD.3

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 60 post transplant
No.GVHD.3


title: PBMC CD4&CD8 T cells-No GVHD.2

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 28 post transplant
No.GVHD.2


title: Corn Oil Control-Recovery, biological replicate 7

description: messenger RNA


title: DBCP-Recovery, biological replicate 11

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 10

description: messenger RNA


title: CD3_Transcripts-R.29_FR104.Siro.F

description: CD3_Transcripts-R.29 FR104.Siro.F


title: PBMC CD4&CD8 T cells-No GVHD.12

description:
PBMC CD4&CD8 T cells from Patient with No GVHD Day 28 post transplant
No.GVHD.12

source_name: PBMC CD4&CD8 T cells from patient with No GVHD


title: PBMC CD4&CD8 T cells-No GVHD.13

description:
PBMC CD4&CD8 T cells from Patient with No GVHD Day 28 post transplant
No.GVHD.13


title: Corn Oil Control-Recovery, biological replicate 4

description: messenger RNA


title: PBMC CD4&CD8 T cells-No GVHD.10

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 28 post transplant
No.GVHD.10


title: Corn Oil Control-Recovery, biological replicate 5

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 6

description: messenger RNA


title: PBMC CD4&CD8 T cells-No GVHD.11

description:
PBMC CD4&CD8 T cells from Patient with No GVHD Day 176 post transplant
No.GVHD.11


title: CD3_Transcripts-R.27_FR104.Siro.F

description: CD3_Transcripts-R.27 FR104.Siro.F


title: CD3_Transcripts-R.202_Healthy.Control

description: CD3_Transcripts-R.202 Healthy.Control


title: Corn Oil Control-Recovery, biological replicate 1

description: messenger RNA


title: DBCP-Recovery, biological replicate 9

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 3

description: messenger RNA


title: CD3_Transcripts-R.29_FR104.Siro.D14

description: CD3_Transcripts-R.29 FR104.Siro.D14


title: DBCP-Recovery, biological replicate 7

description: messenger RNA


title: CD3_Transcripts-R.26_FR104.Siro.D14

description: CD3_Transcripts-R.26 FR104.Siro.D14


title: DBCP-Recovery, biological replicate 3

description: messenger RNA


title: Corn Oil Control-Recovery, biological replicate 2

description: messenger RNA


title: DBCP-Recovery, biological replicate 10

description: messenger RNA


title: DBCP-Recovery, biological replicate 6

description: messenger RNA


title: DBCP-Recovery, biological replicate 1

description: messenger RNA


title: DBCP-Recovery, biological replicate 5

description: messenger RNA


title: DBCP-Recovery, biological replicate 2

description: messenger RNA


title: DBCP-Recovery, biological replicate 8

description: messenger RNA


title: CD3_Transcripts-R.24_FR104.F

description: CD3_Transcripts-R.24 FR104.F


title: CD3_Transcripts-R.28_FR104.Siro.D14

description: CD3_Transcripts-R.28 FR104.Siro.D14


title: DBCP-Recovery, biological replicate 4

description: messenger RNA


title: PBMC CD4&CD8 T cells-No GVHD.1

description:
PBMC CD4&CD8 T cells from patient with No GVHD Day 28 post transplant
No.GVHD.1


title: CD3_Transcripts-R.22_FR104.F

description: CD3_Transcripts-R.22 FR104.F


title: PBMC CD4&CD8 T cells-GVHD.9

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 60 post transplant
GVHD.9

value: Yes

value: GVHD


title: Corn Oil Control, biologial replicate 18

description: messenger RNA

source_name: sperm, corn oil

value: no


title: CD3_Transcripts-R.23_FR104.D14

description: CD3_Transcripts-R.23 FR104.D14


title: CD3_Transcripts-R.27_FR104.Siro.D14

description: CD3_Transcripts-R.27 FR104.Siro.D14


title: PBMC CD4&CD8 T cells-GVHD.8

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 28 post transplant
GVHD.8


title: Corn Oil Control, biologial replicate 20

description: messenger RNA


title: Corn Oil Control, biologial replicate 19

description: messenger RNA


title: PBMC CD4&CD8 T cells-GVHD.6

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 60 post transplant
GVHD.6


title: CD3_Transcripts-R.23_FR104.F

description: CD3_Transcripts-R.23 FR104.F

value: Final


title: PBMC CD4&CD8 T cells-GVHD.7

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 28 post transplant
GVHD.7


title: Corn Oil Control, biologial replicate 15

description: messenger RNA


title: Corn Oil Control, biologial replicate 12

description: messenger RNA


title: CD3_Transcripts-R.22_FR104.D14

description: CD3_Transcripts-R.22 FR104.D14


title: CD3_Transcripts-R.42_Bela.Siro.F

description: CD3_Transcripts-R.42 Bela.Siro.F

value: Bela-Siro


title: CD3_Transcripts-R.24_FR104.D14

description: CD3_Transcripts-R.24 FR104.D14


title: PBMC CD4&CD8 T cells-GVHD.4

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 60 post transplant
GVHD.4


title: PBMC CD4&CD8 T cells-GVHD.3

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 60 post transplant
GVHD.3


title: CD3_Transcripts-R.38_Bela.Siro.F

description: CD3_Transcripts-R.38 Bela.Siro.F


title: Corn Oil Control, biologial replicate 17

description: messenger RNA


title: Corn Oil Control, biologial replicate 13

description: messenger RNA


title: Corn Oil Control, biologial replicate 14

description: messenger RNA


title: Corn Oil Control, biologial replicate 11

description: messenger RNA


title: PBMC CD4&CD8 T cells-GVHD.5

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 28 post transplant
GVHD.5


title: Corn Oil Control, biologial replicate 16

description: messenger RNA


title: DBCP, biological replicate 18

description: messenger RNA

source_name: sperm, DBCP


title: PBMC CD4&CD8 T cells-GVHD.2

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 28 post transplant
GVHD.2


title: DBCP, biological replicate 17

description: messenger RNA


title: PBMC CD4&CD8 T cells-GVHD.10

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 28 post transplant
GVHD.10


title: DBCP, biological replicate 20

description: messenger RNA


title: CD3_Transcripts-R.49_Bela.Siro.D30

description: CD3_Transcripts-R.49 Bela.Siro.D30


title: DBCP, biological replicate 15

description: messenger RNA


title: DBCP, biological replicate 16

description: messenger RNA


title: PBMC CD4&CD8 T cells-GVHD.1

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 28 post transplant
GVHD.1


title: CD3_Transcripts-R.38_Bela.Siro.D30

description: CD3_Transcripts-R.38 Bela.Siro.D30


title: DBCP, biological replicate 14

description: messenger RNA


title: PBMC CD4&CD8 T cells-GVHD.11

description:
PBMC CD4&CD8 T cells from patient with GVHD Day 83 post transplant
GVHD.11


title: DBCP, biological replicate 19

description: messenger RNA


title: CD3_Transcripts-R.42_Bela.Siro.D30

description: CD3_Transcripts-R.42 Bela.Siro.D30


title: DBCP, biological replicate 13

description: messenger RNA


title: Murine colon carcinoma cell line CT26.WT treated with BSA

city: Changsha

first: Xuemei

last: Zhang

address: xiangya road #110

country: China

institute: Key Laboratory of Carcinogenesis, Ministry of Health, China

description:
Gene expression data from murine colon carcinoma cell line CT26.WT stimulated with normal saline .
CT26.WT_control

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: colon carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: Murine colon carcinoma cell line CT26.WT was purchased from Cell Bank of the Chinese Academy of Sciences (Shanghai,China). Cells were cultured in both RPMI1640 medium supplemented with 10% fetal bovine serum, 100 units/m of penicillin and streptomycin. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

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

treatment_protocol: Cells were grown in serum-free medium for 12 hours, and then 4 ug/ml of S100a8 or S100a9 mouse recombinant protein  was added for an additional 24 hours .

tag: cell line

value: colon carcinoma cell line CT26.WT

value: control


title: DBCP, biological replicate 12

description: messenger RNA


title: DBCP, biological replicate 11

description: messenger RNA


title: CD3_Transcripts-R.49_Bela.Siro.D14

description: CD3_Transcripts-R.49 Bela.Siro.D14


title: Corn Oil Control, biological replicate 9

description: messenger RNA


title: Corn Oil Control, biological replicate 8

description: messenger RNA


title: Murine colon carcinoma cell line CT26.WT treated with S100a9 mouse recombinant protein

description:
Gene expression data from  murine colon carcinoma cell line CT26.WTstimulated with S100a9 recombinant protein.
CT26.WT_S100a9

value: S100a9 mouse recombinant protein


title: CD3_Transcripts-R.42_Bela.Siro.D14

description: CD3_Transcripts-R.42 Bela.Siro.D14


title: Corn Oil Control, biological replicate 6

description: messenger RNA

value: Fischer 344


title: Corn Oil Control, biological replicate 3

description: messenger RNA

value: sperm


title: Corn Oil Control, biological replicate 5

description: messenger RNA

value: corn oil


title: Murine colon carcinoma cell line CT26.WT treated with S100a8 mouse recombinant protein

description:
Gene expression data from murine colon carcinoma cell line CT26.WTstimulated with S100a8 recombinant protein.
CT26.WT_S100a8

value: S100a8 mouse recombinant protein


title: CD3_Transcripts-R.46_Bela.F

description: CD3_Transcripts-R.46 Bela.F

value: Bela


title: CD3_Transcripts-R.38_Bela.Siro.D14

description: CD3_Transcripts-R.38 Bela.Siro.D14


title: CD3_Transcripts-R.57_Bela.F

description: CD3_Transcripts-R.57 Bela.F


title: DBCP, biological replicate 10

description: messenger RNA


title: DBCP, biological replicate 7

description: messenger RNA


title: Corn Oil Control, biological replicate 10

description: messenger RNA


title: Corn Oil Control, biological replicate 4

description: messenger RNA


title: CD3_Transcripts-R.202_Auto.D36

description: CD3_Transcripts-R.202 Auto.D36

value: Autologous


title: DBCP, biological replicate 9

description: messenger RNA


title: DBCP, biological replicate 8

description: messenger RNA


title: CD3_Transcripts-R.200_Auto.D36

description: CD3_Transcripts-R.200 Auto.D36


title: Corn Oil Control, biological replicate 1

description: messenger RNA


title: Corn Oil Control, biological replicate 2

description: messenger RNA


title: DBCP, biological replicate 5

description: messenger RNA


title: DBCP, biological replicate 6

description: messenger RNA


title: Corn Oil Control, biological replicate 7

description: messenger RNA


title: CD3_Transcripts-R.201_Auto.D36

description: CD3_Transcripts-R.201 Auto.D36


title: CD3_Transcripts-R.47_Bela.F

description: CD3_Transcripts-R.47 Bela.F


title: CD3_Transcripts-R.200_Auto.D14

description: CD3_Transcripts-R.200 Auto.D14


title: DBCP, biological replicate 4

description: messenger RNA


title: DBCP, biological replicate 1

description: messenger RNA


title: DBCP, biological replicate 3

description: messenger RNA


title: hiPSC line FiPS2-13, passage 12 ENSG

status: Public on Nov 28 2015

city: Tampere

first: Reija

last: Autio

address: Korkeakoulunkatu 1

department: SGN

country: Finland

institute: Tampere University of Technology

description: Hybridized in Finnish Microarray and  Sequencing Centre (Turku, Finland)

hyb_protocol: accordingly to the manufacturer's instructions (Affymetrix)

data_processing:
Probe values were directly linked to Ensembl genes (build 49) using alternative CDF-files provided by brainarray (http://brainarray.mbni.med.umich.edu/), version 11. RMA-pre-processing was used  to preprocess gene, transcript and exon values of Exon array values.
HuEx10stv2_Hs_ENSG, HuEx10stv2_Hs_ENST, HuEx10stv2_Hs_ENSE
HuEx10stv2_Hs_ENSG, HuEx10stv2_Hs_ENST, HuEx10stv2_Hs_ENSE

source_name: human induced pluripotent stem cell line  FiPS2-13, passage 12

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: RNA was isolated from cell pellets using Rneasy Kit (Qiagen). To eliminate genomic DNA from the samples Dnase I (Qiagen) digestion in column was included.

tag: cell line/clone

value: clone FiPS2-13

tag: passage

tag: cell origin

value: cell line is derived from Human embryonic lung fibroblast IMR90 cell, passage #14


title: hiPSC line FiPS5-3, passage 12 ENSG

scan_protocol: accordingly to the manufacturer's instructions (Affymetrix)

source_name: human induced pluripotent stem cell line FiPS5-3, passage 12

value: clone FiPS5-3

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: Parental Fibroblast line MRC5, passage 19 ENSG

source_name: human embryonic lung fibroblast line MRC5

label_protocol: accordingly to the manufacturer's instructions (Affymetrix)

value: human embryonic lung fibroblast

value: line MRC5


title: DBCP, biological replicate 2

description: messenger RNA

tag: tissue

value: 5 mg/kg/d DBCP

value: no


title: Parental Fibroblast line IMR90, passage 14 ENSG

source_name: human embryonic lung fibroblast line IMR90

value: line IMR90


title: hiPSC line FiPS5-7, passage 10 ENSG

source_name: human induced pluripotent stem cell line FiPS5-7, passage 10

value: clone FiPS5-7


title: hiPSC line FiPS6-3, passage 14 ENSG

source_name: human induced pluripotent stem cell line FiPS6-3, passage 14

value: clone FiPS6-3


title: hiPSC line FiPS6-12, passage 14 ENSG

source_name: human induced pluripotent stem cell line FiPS6-12, passage 14

value: clone FiPS6-12


title: hiPSC line FiPS3-12, passage 19 ENSG

source_name: human induced pluripotent stem cell line FiPS3-12, passage 19

value: clone FiPS3-12

value: cell line is derived from Human embryonic lung fibroblast MRC5 cell, passage #19


title: hiPSC line FiPS2-10, passage 16 ENSG

source_name: human induced pluripotent stem cell line FiPS2-10, passage 16

value: clone FiPS2-10


title: CD3_Transcripts-R.201_Auto.D14

description: CD3_Transcripts-R.201 Auto.D14


title: hiPSC line FiPS1-14, passage 13 ENSG

source_name: human induced pluripotent stem cell line FiPS1-14, passage 13

value: clone FiPS1-14


title: CD3_Transcripts-R.202_Auto.D14

description: CD3_Transcripts-R.202 Auto.D14

value: Autologous


title: Parental Fibroblast line HFF, passage 11 ENSG

source_name: human foreskin fibroblast line HFF

value: human neonatal foreskin fibroblast

value: line HFF


title: hiPSC line FiPS6-3, passage 14 ENST

value: human induced pluripotent stem cell line


title: hiPSC line FiPS3-12, passage 19 ENST


title: hiPSC line FiPS5-3, passage 12 ENST

value: clone FiPS5-3

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: SZ4 FOXP3+_rep1

city: Shanghai

first: Bin

last: Li

address: 320 Yueyang Road, Xuhui District,

institute: Institut Pasteur of Shanghai, CAS

description:
miRNA expression in cells under steady state
SZ4 FOXP3 Positive

hyb_protocol: Hybridization was prepared using the Agilent’s miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions. Cy3-labelled RNA hybridized to Agilent Human miRNA Microarrays for 20 hours at 55Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: FOXP3 positive SZ4 cells

label_protocol: Cyanine-3 (Cy3) label were prepared from 0.1 ug RNA using the Agilent’s miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions

growth_protocol: SZ4 cells were cultured in 1640 medium containing 10%FBS

extract_protocol: RNA was prepared using the Trizol Regent (Invitrogen) following the manufacturer's

value: T cell line

tag: genotype/variation

value: FOXP3+ (FOXP positive)


title: hiPSC line FiPS5-7, passage 10 ENST


title: WT+ P.indica, NP

city: Jena

first: Madhunita

last: Bakshi

address: Dornburger Str. 159

department: Plant physiology

institute: Friedrich-Schiller Universität Jena

description: SAMPLE 6

hyb_protocol: For the hybridisation the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) is used following the manufacture`s protocol. 600 ng cRNA are hybridised on a 8x60K microarray at 65°C for 17 h using Agilent`s recommended hybridisation chamber and oven. Finally the microarray is washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37°C) Gene Expression Wash Buffer 2 for one minute. Washed miroarray was scanned.

scan_protocol: Fluorescence signals on microarray were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 5 micron for HD Microarray formats, generating a 20 bit TIFF file respectively.

data_processing: The scanned images were analyzed with Feature Extraction Software 11 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded and quantile normalized.

organism: Arabidopsis thaliana

source_name: WT_NP_colonized roots

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) is used for generation of fuorescent cRNA (complementary RNA). cRNA is amplified by using oligo-dT primer and labeled with cyanine 3-CTP following the manufacture`s protocol.

growth_protocol: Arabidopsis thaliana WT (ecotype Columbia -0) and wrky6 mutant seeds were surface sterilized and placed on Petri dishes containing MS (Murashige and Skoog 1962) nutrient medium. After cold treatment for 48 h at 4°C, the plates were incubated for 10 days at 22°C under continuous illumination (100 μmol m–2 s–1). P. indica was cultured as described previously on Aspergillus minimal medium (Johnson et al. 2011; Hill and Kaefer 2001).

extract_protocol: Total RNA was isolated from roots of colonized and uncolonized seedlings, using the Trizol method (Invitrogen Inc., USA). Quality of RNA samples were checked by photometrical measurement with the Nanodrop 2000 spectrophotometer (Thermo Scientific) and then analyzed on agarose gel (2%) as well as by using 2100 Bioanalyser (Agilent Technologies, CA) for determining integrity and detection of potential contaminants.

treatment_protocol: Seedlings were grown on square Petri dishes and kept vertically under two different phosphate conditions (0.25mM, LP and 2.5mM, NP) for 3 dpi with or without P. indica.

tag: ecotype

value: Columbia -0

value: wild type

tag: phosphate condition

value: 2.5mM phosphate (normal P; NP)

tag: exposed to

value: Piriformospora indica

tag: time point

value: 3 dpi

value: roots


title: wrky6, NP

description: SAMPLE 7

source_name: wrky6_NP_uncolonized roots

value: wrky6 mutant

value: none (without P. indica)


title: WT, NP

description: SAMPLE 5

source_name: WT_NP_uncolonized roots


title: WT+ P.indica, LP

description: SAMPLE 2

source_name: WT_LP_colonized roots

value: 0.25mM phosphate (Low P; LP)


title: wrky6, LP

description: SAMPLE 3

source_name: wrky6_LP_uncolonized roots


title: hiPSC line FiPS2-13, passage 12 ENST

source_name: human induced pluripotent stem cell line  FiPS2-13, passage 12

value: clone FiPS2-13

value: cell line is derived from Human embryonic lung fibroblast IMR90 cell, passage #14


title: hiPSC line FiPS6-12, passage 14 ENST

value: clone FiPS6-12


title: Parental Fibroblast line HFF, passage 11 ENST

value: human neonatal foreskin fibroblast

value: line HFF


title: hiPSC line FiPS1-14, passage 13 ENST

value: human induced pluripotent stem cell line

value: clone FiPS1-14


title: hiPSC line FiPS2-10, passage 16 ENST

value: clone FiPS2-10


title: wrky6 + P. indica, LP

description: SAMPLE 4

source_name: wrky6_LP_colonized roots

value: Columbia -0


title: Parental Fibroblast line IMR90, passage 14 ENST

value: human embryonic lung fibroblast

value: line IMR90


title: wrky6 + P. indica, NP

description: SAMPLE 8

source_name: wrky6_NP_colonized roots

value: 2.5mM phosphate (normal P; NP)

value: Piriformospora indica


title: Parental Fibroblast line HFF, passage 11 ENSE


title: hiPSC line FiPS3-12, passage 19 ENSE

value: clone FiPS3-12

value: cell line is derived from Human embryonic lung fibroblast MRC5 cell, passage #19


title: WT, LP

description: SAMPLE 1

source_name: WT_LP_uncolonized roots

value: wild type

value: none (without P. indica)

value: 3 dpi

value: roots


title: Parental Fibroblast line MRC5, passage 19 ENSE

source_name: human embryonic lung fibroblast line MRC5

value: line MRC5


title: Parental Fibroblast line MRC5, passage 19 ENST


title: hiPSC line FiPS5-7, passage 10 ENSE

source_name: human induced pluripotent stem cell line FiPS5-7, passage 10

value: clone FiPS5-7

value: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #11


title: hiPSC line FiPS5-3, passage 12 ENSE

source_name: human induced pluripotent stem cell line FiPS5-3, passage 12

value: clone FiPS5-3


title: hiPSC line FiPS6-3, passage 14 ENSE

source_name: human induced pluripotent stem cell line FiPS6-3, passage 14

value: clone FiPS6-3


title: hiPSC line FiPS2-10, passage 16 ENSE

source_name: human induced pluripotent stem cell line FiPS2-10, passage 16

value: clone FiPS2-10

value: cell line is derived from Human embryonic lung fibroblast IMR90 cell, passage #14


title: SZ4 FOXP31_rep1

description:
miRNA expression in cells under steady state
SZ4 FOXP3 Negative

source_name: FOXP3 negative SZ4 cells

value: T cell line

value: FOXP3- (FOXP negative)


title: hiPSC line FiPS1-14, passage 13 ENSE

source_name: human induced pluripotent stem cell line FiPS1-14, passage 13

value: clone FiPS1-14


title: hiPSC line FiPS6-12, passage 14 ENSE

source_name: human induced pluripotent stem cell line FiPS6-12, passage 14

value: clone FiPS6-12


title: hiPSC line FiPS2-13, passage 12 ENSE

value: human induced pluripotent stem cell line

value: clone FiPS2-13


title: Parental Fibroblast line IMR90, passage 14 ENSE

source_name: human embryonic lung fibroblast line IMR90

value: human embryonic lung fibroblast

value: line IMR90


title: Sample182_Tumor

status: Public on Nov 27 2015

type: genomic

city: Oslo

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
Sentrix_ID: 5775446044
Sentrix_Position: R05C02

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Touleimat and Tost, Epigenomics 2012

label: Cy5 and Cy3

molecule: genomic DNA

source_name: lung adenocarcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: The tumor tissue and normal tissue were obtained at surgery and snap frozen in liquid nitrogen and stored at 80°C until DNA isolation. DNA was extracted using Maxwell 16 DNA Purification kit (http://www.promega.com) and the Maxwell 16 instrument after standard procedure.

tag: gender

value: Female

value: Tumor

tag: Stage

tag: p53 status

value: Mutated

tag: egfr status

value: WildType

tag: kras status


title: Sample183_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R02C02


title: Sample181_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R06C02


title: Sample177_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R01C01

value: Male


title: Sample180_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R04C02


title: Sample179_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R05C02


title: Sample175_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R06C01


title: Sample166_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R04C01


title: Sample168_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R01C01


title: Sample169_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R05C01


title: Sample158_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R01C01


title: Sample171_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R04C02


title: Sample178_Normal

description:
Sentrix_ID: 5775278003
Sentrix_Position: R04C02

source_name: normal lung

value: Normal


title: Sample160_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R06C01


title: Sample162_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R05C02


title: Sample156_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R03C02


title: Sample173_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R02C02


title: Sample172_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R03C02


title: Sample154_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R01C02


title: Sample167_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R04C02


title: Sample163_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R01C02


title: Sample170_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R05C02


title: Sample155_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R03C01


title: Sample165_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R04C02


title: Sample161_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R02C01


title: Sample174_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R01C01


title: Sample176_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R02C02


title: Sample159_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R04C01


title: Sample164_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R04C02


title: Sample152_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R05C01


title: Sample153_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R06C02


title: Sample150_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R05C01


title: Sample157_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R06C01


title: Sample149_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R03C02


title: Sample139_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R06C02


title: Sample134_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R01C01


title: Sample141_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R03C01


title: Sample144_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R05C01


title: Sample146_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R06C02


title: Sample140_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R06C02


title: Sample136_Normal

description:
Sentrix_ID: 5775278003
Sentrix_Position: R01C02


title: Sample137_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R02C02


title: Sample143_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R04C01


title: Sample138_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R03C01


title: Sample131_Normal

description:
Sentrix_ID: 5775278003
Sentrix_Position: R02C01


title: Sample128_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R04C02


title: Sample148_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R03C02


title: Sample151_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R05C02


title: Sample145_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R05C02


title: Sample133_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R04C01


title: Sample127_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R02C01


title: Sample132_Tumor

description:
Sentrix_ID: 5775278003
Sentrix_Position: R03C01


title: Sample130_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R03C01


title: Sample129_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R06C01


title: Sample121_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R01C02


title: Sample126_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R02C02


title: Sample125_Normal

description:
Sentrix_ID: 5775446044
Sentrix_Position: R03C02


title: Sample123_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R02C01


title: Sample122_Normal

description:
Sentrix_ID: 5775278034
Sentrix_Position: R06C01


title: Sample124_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R06C02


title: Sample135_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R02C01


title: Sample147_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R01C02


title: Sample116_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R02C01


title: Sample117_Normal

description:
Sentrix_ID: 5775446035
Sentrix_Position: R01C01


title: Sample118_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R02C01


title: Sample120_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R06C02


title: Sample115_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R03C01


title: Sample113_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R03C02


title: Sample100_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R01C01


title: Sample119_Normal

description:
Sentrix_ID: 5775278034
Sentrix_Position: R03C01


title: Sample109_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R05C02


title: Sample105_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R06C01


title: Sample108_Normal

description:
Sentrix_ID: 5775446011
Sentrix_Position: R04C02


title: Sample103_Tumor

description:
Sentrix_ID: 5775278028
Sentrix_Position: R06C02


title: Sample102_Normal

description:
Sentrix_ID: 5775278028
Sentrix_Position: R03C02


title: Sample142_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R05C01


title: Sample98_Normal

description:
Sentrix_ID: 5775446044
Sentrix_Position: R05C01


title: Sample99_Tumor

description:
Sentrix_ID: 5775446044
Sentrix_Position: R04C01


title: Sample114_Normal

description:
Sentrix_ID: 5775278030
Sentrix_Position: R05C01


title: Sample106_Normal

description:
Sentrix_ID: 5775446035
Sentrix_Position: R01C02


title: Sample110_Normal

description:
Sentrix_ID: 5775278030
Sentrix_Position: R06C01


title: Sample104_Normal

description:
Sentrix_ID: 5775446044
Sentrix_Position: R01C02


title: Sample111_Tumor

description:
Sentrix_ID: 5775278030
Sentrix_Position: R04C01


title: Sample97_Tumor

description:
Sentrix_ID: 5775446011
Sentrix_Position: R06C01


title: Sample96_Normal

description:
Sentrix_ID: 5775446011
Sentrix_Position: R02C02


title: Sample101_Tumor

description:
Sentrix_ID: 5775278034
Sentrix_Position: R04C01


title: Sample107_Tumor

description:
Sentrix_ID: 5775446035
Sentrix_Position: R02C02


title: Sample93_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R06C02


title: Sample95_Tumor

description:
Sentrix_ID: 5775446066
Sentrix_Position: R01C01


title: Sample94_Normal

description:
Sentrix_ID: 5775446066
Sentrix_Position: R02C01


title: Sample112_Normal

description:
Sentrix_ID: 5775278030
Sentrix_Position: R02C02


title: Sample90_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R01C02


title: Sample91_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R03C01


title: Sample89_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R06C01


title: Sample88_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R05C02


title: Sample76_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R05C01


title: Sample87_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R05C01


title: Sample79_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R01C02


title: Sample84_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R01C01


title: Sample80_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R06C01


title: Sample73_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R03C02


title: Sample71_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R01C01


title: Sample77_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R01C02


title: Sample81_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R02C02


title: Sample68_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R02C02


title: Sample69_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R02C02


title: Sample74_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R06C02


title: Sample78_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R06C02


title: Sample67_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R04C01


title: Sample85_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R05C02


title: Sample66_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R03C02


title: Sample65_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R03C01


title: Sample83_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R01C02


title: Sample75_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R04C01


title: Sample82_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R03C02


title: Sample70_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R05C01


title: Sample86_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R03C02


title: Sample92_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R06C01


title: Sample64_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R01C01


title: Sample72_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R03C02


title: Sample59_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R05C02


title: Sample60_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R05C01


title: Sample63_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R02C02


title: Sample61_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R03C01


title: Sample62_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R02C01


title: DKO

city: Jerusalem

first: Moshe

last: Biton

address: hadassah ein kerem

department: Lautenberg Center for immunology

country: Israel

institute: Hebrew University

description: Test

data_processing:
Applied Biosystem software
The samples were normalized to U6.
Fold change of each miRNA expression in CKIαΔgut or CKIα/p53Δgut was relatively quantified (RQ) to CKIα Het specimens- KO/Het and DKO/Het respectively

label: FAM

source_name: homozygus CKIα/p53Δgut

label_protocol: commercial kit for Applied Biosystem miRNA cards

growth_protocol: SPF mice

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Tamoxifen injection to induce KO to mice

tag: strain

value: small intestine

tag: cell type

value: enterocyte

value: DKO


title: KO

description: Test

source_name: homozygus CKIαΔgut

value: KO


title: Sample54_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R02C02


title: Sample53_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R06C02


title: Sample58_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R05C01


title: Sample47_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R03C01


title: Sample56_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R04C02


title: Sample50_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R01C02


title: Sample48_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R04C02


title: Het

description:
control
corresponding to WT

source_name: heterozygous CKIα+/Δgut

value: Het


title: Sample52_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R02C01


title: Sample44_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R02C01


title: Sample51_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R04C02


title: Sample55_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R05C01


title: Sample46_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R04C02


title: Hippocampus CM-414. Biological replica 4

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm (Affymetrix GeneChip Mouse Gene 2.0 ST (mogene20stv1cdf from Bioconductor))

source_name: Mouse hippocampi after chronic treatment with CM-414

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Hippocampus of mouse treated with different solutions during four weeks. The mouse underwent fear conditioning and Morris water maze test during week 3 and 4 of the treatment. Next, mouse reveived a 4-weeks washaout period and underwent to a reversal phase of MWM before sacrificed.

extract_protocol: The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Mice were sacrificed by cervical dislocation, brain was extracted and the hippocampus was dissected and kept in dry ice immediately. Tissue was stored at -80 C until RNA extraction.

tag: strain background

tag: age

value: 16-18 month-old

tag: sample group

value: chronic treatment with CM-414

value: hippocampus


title: Sample42_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R04C02


title: Sample34_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R04C01


title: Sample43_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R06C01


title: Sample39_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R05C01


title: Sample45_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R02C01


title: Sample40_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R05C02


title: Sample36_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R05C02


title: Sample57_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R02C01


title: Sample38_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R05C02


title: Sample37_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R01C02


title: Hippocampus CM-414. Biological replica 2


title: Sample49_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R06C02


title: Hippocampus SAHA and Tadalafil. Biological replica 4

source_name: Mouse hippocampi after chronic treatment with SAHA and Tadalafil


title: Hippocampus SAHA and Tadalafil. Biological replica 7

value: chronic treatment with SAHA and Tadalafil


title: Hippocampus SAHA and Tadalafil. Biological replica 5


title: Hippocampus CM-414. Biological replica 3


title: Hippocampus SAHA and Tadalafil. Biological replica 6


title: Sample33_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R04C01


title: Sample32_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R02C01


title: Hippocampus SAHA and Tadalafil. Biological replica 3


title: Sample30_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R06C01


title: Sample35_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R01C02


title: Hippocampus SAHA and Tadalafil. Biological replica 2


title: Hippocampus SAHA. Biological replica 3

source_name: Mouse hippocampi after chronic treatment with SAHA

value: chronic treatment with SAHA


title: Hippocampus SAHA and Tadalafil. Biological replica 1


title: Hippocampus Tadalafil. Biological replica 2

source_name: Mouse hippocampi after chronic treatment with Tadalafil

value: chronic treatment with Tadalafil


title: Hippocampus Tadalafil. Biological replica 1


title: Sample31_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R06C01

value: Female


title: Hippocampus vehicle. Biological replica 6

source_name: Mouse hippocampi after chronic treatment with saline

value: chronic treatment with saline


title: Hippocampus SAHA. Biological replica 1


title: Sample28_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R01C02

value: Tumor


title: Hippocampus vehicle. Biological replica 5


title: Sample29_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R02C02

value: WildType

value: Mutated


title: Hippocampus vehicle. Biological replica 4


title: Sample41_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R06C02

value: Male


title: Sample25_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R04C01


title: Hippocampus Tadalafil. Biological replica 3


title: Hippocampus vehicle. Biological replica 3


title: Sample27_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R01C01


title: Hippocampus vehicle. Biological replica 2


title: Sample22_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R02C01


title: Sample24_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R04C01


title: Hippocampus vehicle. Biological replica 1


title: Hippocampus CM-414. Biological replica 1


title: Sample26_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R06C01


title: Sample19_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R03C01


title: Control 4

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Lung

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Female MutaTMMouse, aged ~12 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed once a week for 4 consecutive weeks via intratracheal instillation. Two different doses of Mitsui XNRi-7 and NM 401 suspended in mouse serum  were selected to dose the animals: 42.7µg/mouse and 128µg/mouse. Control animals were gavaged with olive oil only.   Tissues were collected 56 days following the final dose.

tag: sampleID

value: MutaTMMouse

tag: time of dose

tag: treatment

value: olive oil only

source_name: Universal Mouse Reference RNA

tag: sample type

value: reference


title: Hippocampus SAHA. Biological replica 2

tag: tissue


title: Mitsui L2

tag: genotype/variation

value: 42.7µg/mouse of Mitsui XNRi-7


title: 401 H5

value: 128µg/mouse of NM 401


title: Mitsui H3

value: 128µg/mouse of Mitsui XNRi-7


title: Sample23_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R03C01


title: Control 3


title: Hippocampus vehicle. Biological replica 7

value: 16-18 month-old


title: 401 L5

value: 42.7µg/mouse of NM 401


title: Mitsui L5


title: 401 L3


title: 401 H4


title: Mitsui L5_2


title: Sample20_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R04C02


title: 401 H1


title: Sample21_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R05C02


title: Sample17_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R03C01


title: Mitsui L4


title: Control 2


title: Sample16_Tumor

description:
Sentrix_ID: 5808922060
Sentrix_Position: R01C01


title: Mitsui H2


title: Mitsui H1


title: 401 L1


title: Mitsui H5


title: 401 L2


title: Mitsui L3


title: e2-MSC

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: OB day2

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Bone marrow MSCs were cultured in advanced-minimal essential medium (MEM) supplemented with 5% fetal bovine serum, 100 micromolar ascorbic acid, 2 mM L-glutamine, 100 U/mL penicillin, and 100 ug/mL streptomycin.

extract_protocol: Total RNA was extracted using the QIAamp RNA Blood Mini Kit (Qiagen Japan).

treatment_protocol: To induce ostegenic differentiation of bone marrow MSCs, osteogenesis-inducing cocktails (OICS) of 1.8 mM potassium dihydrogen phosphate, 100 micromolar ascorbic acid, and 100 nM dexamethasone were added to culture media.

tag: cells

value: stimulated with OICS for 2 days


title: Sample15_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R01C01

tag: gender


title: Control 1


title: Sample13_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R03C02

tag: Stage


title: Control 5


title: 401 H3


title: Sample14_Tumor

description:
Sentrix_ID: 5808922088
Sentrix_Position: R02C02

tag: p53 status


title: Sample12_Tumor

description:
Sentrix_ID: 5775278085
Sentrix_Position: R05C01

tag: egfr status


title: 401 L4


title: Mitsui H4


title: e5-MSC

source_name: OB day5

value: stimulated with OICS for 5 days


title: Sample10_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R02C02

tag: kras status


title: 15580098

status: Public on Nov 26 2015

city: London

last: Brown

address: Du Cane Road, The Hammersmith Hospital-4th floor

institute: Imperial College London

description:
chipid: 5552218045_D
control sample 8

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing:
BeadStudio software v3.2

MISSING RAW DATA EXPLANATION: The raw data was not kept after conversion into beta values because of limitations of storage capacity.

source_name: genomic DNA from control sample 8

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions. Tumour DNA was bisulphite converted using the EZ-96 DNA Methylation™ Kit (Zymo) as per manufacturers protocol

tag: status

value: Control

tag: ChIP

tag: site

value: Fallopian Tube

tag: histology

value: Benign

tag: grade


title: 15580097

description:
chipid: 5552218045_K
control sample 7

source_name: genomic DNA from control sample 7

value: Ovary


title: ctrl-MSC

source_name: MSC control

value: ctrl-MSC


title: Sample9_Tumor

description:
Sentrix_ID: 5775278004
Sentrix_Position: R03C01

source_name: lung adenocarcinoma

value: Female

value: Tumor

value: WildType

value: Mutated


title: 15580072

description:
chipid: 5552218043_E
tumour sample 75

source_name: genomic DNA from tumour sample 75

value: Case

tag: tumour nuclei(%)

value: Ovarian

value: Serous


title: 15580074

description:
chipid: 5552218043_K
tumour sample 77

source_name: genomic DNA from tumour sample 77


title: 15580077

description:
chipid: 5552200031_D
control sample 1

source_name: genomic DNA from control sample 1


title: 15580080

description:
chipid: 5552200032_B
control sample 3

source_name: genomic DNA from control sample 3


title: 15580082

description:
chipid: 5552234050_I
control sample 5

source_name: genomic DNA from control sample 5


title: Mitsui L1

tag: sampleID

value: MutaTMMouse

tag: time of dose

value: 42.7µg/mouse of Mitsui XNRi-7

value: reference


title: 15580073

description:
chipid: 5552218043_G
tumour sample 76

source_name: genomic DNA from tumour sample 76


title: 15580083

description:
chipid: 5552234050_F
control sample 6

source_name: genomic DNA from control sample 6


title: 15580068

description:
chipid: 5552218043_A
tumour sample 73

source_name: genomic DNA from tumour sample 73


title: 15580076

description:
chipid: 5552234033_H
tumour sample 78

source_name: genomic DNA from tumour sample 78


title: 15580067

description:
chipid: 5552234050_L
tumour sample 72

source_name: genomic DNA from tumour sample 72


title: 15580081

description:
chipid: 5552200032_A
control sample 4

source_name: genomic DNA from control sample 4


title: 15580069

description:
chipid: 5552218043_C
tumour sample 74

source_name: genomic DNA from tumour sample 74


title: Sample11_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R02C01


title: Sample8_Tumor

description:
Sentrix_ID: 5808922086
Sentrix_Position: R04C02


title: 15580065

description:
chipid: 5552234050_J
tumour sample 71

source_name: genomic DNA from tumour sample 71


title: Sample5_Normal

description:
Sentrix_ID: 5775278017
Sentrix_Position: R06C02

source_name: normal lung

value: Normal


title: 15580078

description:
chipid: 5552200031_B
control sample 2

source_name: genomic DNA from control sample 2


title: Sample4_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R06C01

value: Male


title: Sample7_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R06C02


title: 15580061

description:
chipid: 5552218045_H
tumour sample 68

source_name: genomic DNA from tumour sample 68


title: Sample3_Tumor

description:
Sentrix_ID: 5808922089
Sentrix_Position: R01C01

source_name: lung adenocarcinoma


title: 15580063

description:
chipid: 5552234031_L
tumour sample 70

source_name: genomic DNA from tumour sample 70


title: 15580062

description:
chipid: 5552234050_H
tumour sample 69

source_name: genomic DNA from tumour sample 69


title: 15580059

description:
chipid: 5552234050_B
tumour sample 67

source_name: genomic DNA from tumour sample 67


title: Sample6_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R05C02


title: 15580053

description:
chipid: 5552234050_E
tumour sample 64

source_name: genomic DNA from tumour sample 64


title: 15580057

description:
chipid: 5552234050_K
tumour sample 66

source_name: genomic DNA from tumour sample 66


title: 15580027

description:
chipid: 5552200032_J
tumour sample 48

source_name: genomic DNA from tumour sample 48


title: 15580055

description:
chipid: 5552234050_G
tumour sample 65

source_name: genomic DNA from tumour sample 65


title: 15580033

description:
chipid: 5552234005_G
tumour sample 52

source_name: genomic DNA from tumour sample 52


title: 15580050

description:
chipid: 5552234050_A
tumour sample 62

source_name: genomic DNA from tumour sample 62


title: 15580048

description:
chipid: 5552234005_J
tumour sample 60

source_name: genomic DNA from tumour sample 60


title: 15580052

description:
chipid: 5552234050_C
tumour sample 63

source_name: genomic DNA from tumour sample 63


title: 15580029

description:
chipid: 5552200032_L
tumour sample 49

source_name: genomic DNA from tumour sample 49


title: 15580041

description:
chipid: 5552234005_A
tumour sample 57

source_name: genomic DNA from tumour sample 57


title: 15580031

description:
chipid: 5552218045_L
tumour sample 50

source_name: genomic DNA from tumour sample 50


title: 15580040

description:
chipid: 5552234005_F
tumour sample 56

source_name: genomic DNA from tumour sample 56


title: 15580045

description:
chipid: 5552218045_F
tumour sample 59

source_name: genomic DNA from tumour sample 59


title: 15580035

description:
chipid: 5552234031_F
tumour sample 53

source_name: genomic DNA from tumour sample 53


title: 15580043

description:
chipid: 5552234005_H
tumour sample 58

source_name: genomic DNA from tumour sample 58


title: 15580036

description:
chipid: 5552234031_H
tumour sample 54

source_name: genomic DNA from tumour sample 54


title: 15580049

description:
chipid: 5552234005_L
tumour sample 61

source_name: genomic DNA from tumour sample 61


title: 15580038

description:
chipid: 5552234031_J
tumour sample 55

source_name: genomic DNA from tumour sample 55


title: 401 H2

source_name: Lung

tag: treatment

value: 128µg/mouse of NM 401

source_name: Universal Mouse Reference RNA

tag: sample type


title: 15580032

description:
chipid: 5552234005_C
tumour sample 51

source_name: genomic DNA from tumour sample 51


title: Sample18_Tumor

description:
Sentrix_ID: 5775278017
Sentrix_Position: R04C02

source_name: lung adenocarcinoma

tag: tissue


title: 15580025

description:
chipid: 5552200031_E
tumour sample 46

source_name: genomic DNA from tumour sample 46


title: 15580024

description:
chipid: 5552200032_F
tumour sample 45

source_name: genomic DNA from tumour sample 45


title: Sample1_Tumor

description:
Sentrix_ID: 5775278068
Sentrix_Position: R01C01


title: 15580018

description:
chipid: 5552200032_I
tumour sample 43

source_name: genomic DNA from tumour sample 43


title: 15580026

description:
chipid: 5552200032_H
tumour sample 47

source_name: genomic DNA from tumour sample 47


title: 15580013

description:
chipid: 5552200031_J
tumour sample 38

source_name: genomic DNA from tumour sample 38


title: 15580016

description:
chipid: 5552218045_C
tumour sample 41

source_name: genomic DNA from tumour sample 41


title: 15580017

description:
chipid: 5552218045_E
tumour sample 42

source_name: genomic DNA from tumour sample 42


title: 15580006

description:
chipid: 5552218045_I
tumour sample 31

source_name: genomic DNA from tumour sample 31


title: 800075

description:
chipid: 5552218043_L
tumour sample 28

source_name: genomic DNA from tumour sample 28


title: 15580009

description:
chipid: 5552200031_I
tumour sample 34

source_name: genomic DNA from tumour sample 34


title: 800062

description:
chipid: 5552218043_J
tumour sample 27

source_name: genomic DNA from tumour sample 27


title: 15580012

description:
chipid: 5552200031_H
tumour sample 37

source_name: genomic DNA from tumour sample 37


title: 15580010

description:
chipid: 5552200031_K
tumour sample 35

source_name: genomic DNA from tumour sample 35


title: 15580014

description:
chipid: 5552200031_L
tumour sample 39

source_name: genomic DNA from tumour sample 39


title: 800108

description:
chipid: 5552234031_K
tumour sample 29

source_name: genomic DNA from tumour sample 29


title: 15580007

description:
chipid: 5552218045_B
tumour sample 32

source_name: genomic DNA from tumour sample 32


title: 15580022

description:
chipid: 5552200032_D
tumour sample 44

source_name: genomic DNA from tumour sample 44


title: 700399

description:
chipid: 5552234005_B
tumour sample 25

source_name: genomic DNA from tumour sample 25


title: 15580015

description:
chipid: 5552200032_C
tumour sample 40

source_name: genomic DNA from tumour sample 40


title: 15580011

description:
chipid: 5552200031_F
tumour sample 36

source_name: genomic DNA from tumour sample 36


title: Sample2_Normal

description:
Sentrix_ID: 5808922089
Sentrix_Position: R03C02

source_name: normal lung


title: 900028

description:
chipid: 5552218045_A
tumour sample 30

source_name: genomic DNA from tumour sample 30


title: 700383

description:
chipid: 5552234005_K
tumour sample 24

source_name: genomic DNA from tumour sample 24


title: 15580008

description:
chipid: 5552200031_G
tumour sample 33

source_name: genomic DNA from tumour sample 33


title: 800057

description:
chipid: 5552218043_H
tumour sample 26

source_name: genomic DNA from tumour sample 26


title: human fetal, biological rep 9

first: Kusum

middle: Vijay

last: Pandit

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
396_emb

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent 8X15K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters.

source_name: Lung tissue, human fetal, biological rep 9

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

value: whole lung

tag: developmental stage

value: 16-23 weeks of gestation


title: human fetal, biological rep 10

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
887_emb

source_name: Lung tissue, human fetal, biological rep 10


title: E18.5 mouse embryo #6 (WT)

city: Yokohama

first: Kohsuke

last: Kataoka

address: 1-7-29 Suehiro-cho, Tsurumi-ku

institute: Yokohama City University

description: Gene expression data from epidermis of WT mouse at E18.5

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained with an Affymetrix fluidix station.

scan_protocol: GeneChips were scanned with an Affymetrix argon-ion laser confocal scanner.

data_processing: The data were analyzed with GeneChip software Microarray Suite 5.0 (Affymetrix).

source_name: E18.5 epidermis, mouse embryo #6 (WT)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

extract_protocol: Total RNA was isolated using Trizol reagent (Life Technologies) and further purified using an RNeasy mini kit (Qiagen).

treatment_protocol: Epidermis was separated from dorsal skin tissues of E18.5 mouse embryos (MafB-/- and WT) by Dispase (Life Technologies) treatment.

value: epidermis

value: E18.5 embryo

tag: genotype

value: wild-type


title: human fetal, biological rep 8

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
359_emb

source_name: Lung tissue, human fetal, biological rep 8


title: R. sphaeroides 2.4.1 (lag90) vs. R. sphaeroides 2.4.1 (exp aerob) 1

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description:
1 lag90 vs exp (aerob)
biological sample 1-3

hyb_protocol: Total RNA of three independent experiments (biological replicates 1-3 or 4-6) of two different growth phases were pooled and hybridized to one array. Two arrays were hybridized with independent experimental runs. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: LOESS normalization log2 ratio (Cy3/Cy5) with Limma package (v.3.14.3; release date: 2012/11/29) for Bioconductor in R

organism: Cereibacter sphaeroides 2.4.1

source_name: lag phase (90min)_aerobic

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

treatment_protocol: R. sphaeroides strains grown under low aeration or aerobic conditions and cells were harvested at different growth phases

tag: growth phase

value: lag phase (90min)

tag: aeration condition

value: aerobic

source_name: exponential phase_aerobic

value: exponential phase


title: E18.5 mouse embryo #8 (WT)

source_name: E18.5 epidermis, mouse embryo #8 (WT)


title: R. sphaeroides 2.4.1 (lag90) vs. R. sphaeroides 2.4.1 (exp aerob) 2

description:
2 lag90 vs exp (aerob)
biological sample 4-6

growth_protocol: R. sphaeroides strains grown under low aeration or aerobic conditions


title: human fetal, biological rep 7

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
1994_emb

source_name: Lung tissue, human fetal, biological rep 7


title: 700324

first: Robert

description:
chipid: 5552218043_F
tumour sample 20

source_name: genomic DNA from tumour sample 20

value: Case


title: 700343

description:
chipid: 5552234031_B
tumour sample 21

source_name: genomic DNA from tumour sample 21

value: Ovarian


title: R. sphaeroides 2.4.1 (lag20) vs. R. sphaeroides 2.4.1 (exp aerob) 1

description:
1 lag20 vs exp (aerob)
biological sample 1-3

source_name: lag phase (20min)_aerobic

value: lag phase (20min)


title: human fetal, biological rep 6

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
1992_emb

source_name: Lung tissue, human fetal, biological rep 6


title: 700256

description:
chipid: 5552200031_C
tumour sample 19

source_name: genomic DNA from tumour sample 19

value: Serous


title: E18.5 mouse embryo #1 (mafB KO)

description: Gene expression data from epidermis of mafB KO mouse at E18.5

source_name: E18.5 epidermis, mouse embryo #1 (mafB KO)

value: mafB KO


title: E18.5 mouse embryo #9 (mafB KO)

source_name: E18.5 epidermis, mouse embryo #9 (mafB KO)


title: R. sphaeroides 2.4.1 (lag20) vs. R. sphaeroides 2.4.1 (exp aerob) 2

description:
2 lag20 vs exp (aerob)
biological sample 4-6


title: human fetal, biological rep 5

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
1804_emb

source_name: Lung tissue, human fetal, biological rep 5


title: R. sphaeroides 2.4.1 (trans) vs. R. sphaeroides 2.4.1 (exp aerob) 2

description:
2 trans vs exp (aerob)
biological sample 4-6

source_name: transition phase_aerobic

value: transition phase


title: 700230

description:
chipid: 5552234033_D
tumour sample 18

source_name: genomic DNA from tumour sample 18


title: OCI-LY10 CC-122_5

city: Summit

first: Anita

last: Gandhi

state: New Jersey

address: 86 Morris Avenue

department: Translational Development Ops

institute: Celgene Corporation

description:
DLBCL cell line treated with CC-122
314085

hyb_protocol: Illumina Direct Hybridization (ILDH) Method

scan_protocol: Illumina iScan instrument using the DirectHyb Tiff setting

data_processing: Processed with R statistical software environment (www.r-project.org; v3.02) using beadarray (v2.10) library and illuminaHumanv4.db (v1.18) annotation package from the Bioconductor suite (www.bioconductor.org; v2.20.1)

source_name: Flash-Frozen Cultured Cells

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

growth_protocol: Cells were obtained from ATCC and were grown in RPMI1640 supplemented with 10% fetal bovine serum and penicillin Streptomycin

extract_protocol: Qiagen miRNeasy Mini Kit (Qiagen, #217004)

treatment_protocol: Cells were treated with 1 micromolar CC-122 or vehicle control (DMSO) for 18 hours.  Cells were then harvested, washed with PBS and cell pellets were flash frozen and shipped to Expression Analyisis.

tag: cell line

tag: cell line origin

value: Ontario Cancer Institute

tag: compound dose

value: 1 micromolar

tag: treatment time

value: 18 hours

tag: replicate


title: R. sphaeroides 2.4.1 (trans) vs. R. sphaeroides 2.4.1 (exp aerob) 1

description:
1 trans vs exp (aerob)
biological sample 1-3


title: R. sphaeroides 2.4.1 (stat) vs. R. sphaeroides 2.4.1 (exp aerob) 1

description:
1 stat vs exp (aerob)
biological sample 1-3

source_name: stationary phase_aerobic

value: stationary phase


title: OCI-LY10 CC-122_4

description:
DLBCL cell line treated with CC-122
314074


title: 700382

description:
chipid: 5552234005_I
tumour sample 23

source_name: genomic DNA from tumour sample 23

tag: status

tag: ChIP

tag: site

tag: histology


title: 700217

description:
chipid: 5552234031_I
tumour sample 17

source_name: genomic DNA from tumour sample 17

tag: tumour nuclei(%)

tag: grade


title: 700189

description:
chipid: 5552234033_B
tumour sample 16

source_name: genomic DNA from tumour sample 16


title: OCI-LY10 CC-122_3

description:
DLBCL cell line treated with CC-122
314063

tag: treatment


title: 700351

description:
chipid: 5552234031_D
tumour sample 22

source_name: genomic DNA from tumour sample 22


title: R. sphaeroides 2.4.1 (stat) vs. R. sphaeroides 2.4.1 (exp aerob) 2

description:
2 stat vs exp (aerob)
biological sample 4-6

source_name: exponential phase_aerobic


title: OCI-LY10 CC-122_2

description:
DLBCL cell line treated with CC-122
314052


title: human fetal, biological rep 4

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
1662_emb

source_name: Lung tissue, human fetal, biological rep 4

tag: tissue

value: whole lung

value: 16-23 weeks of gestation


title: human fetal, biological rep 3

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
1304_emb

source_name: Lung tissue, human fetal, biological rep 3

tag: developmental stage


title: R. sphaeroides 2.4.1 (lag90_72h) vs. R. sphaeroides 2.4.1 (exp low) 1

description:
1 lag90_72h vs exp (low)
biological sample 1-3

source_name: lag phase (90min) after long stationary phase (57 h)_low aeration

value: low aeration

source_name: exponential phase_low aeration


title: human fetal, biological rep 1

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
1197_emb

source_name: Lung tissue, human fetal, biological rep 1


title: human fetal, biological rep 2

description:
Lung tissue samples obtained from the University of Pittsburgh  Tissue Bank. miRNA expression data from human fetal lung.
1302_emb

source_name: Lung tissue, human fetal, biological rep 2


title: R. sphaeroides 2.4.1 (lag90_72h) vs. R. sphaeroides 2.4.1 (exp low) 2

description:
2 lag90_72h vs exp (low)
biological sample 4-6

value: lag phase (90min) after long stationary phase (57 h)


title: 700050

description:
chipid: 5552218045_G
tumour sample 15

source_name: genomic DNA from tumour sample 15


title: R. sphaeroides 2.4.1 (lag20_72h) vs. R. sphaeroides 2.4.1 (exp low) 1

description:
1 lag20_72h vs exp (low)
biological sample 1-3

source_name: lag phase (20min) after long stationary phase (57 h)_low aeration


title: 700018

description:
chipid: 5552234033_I
tumour sample 13

source_name: genomic DNA from tumour sample 13


title: 700036

description:
chipid: 5552200032_G
tumour sample 14

source_name: genomic DNA from tumour sample 14


title: 600373

description:
chipid: 5552234033_G
tumour sample 12

source_name: genomic DNA from tumour sample 12


title: R. sphaeroides 2.4.1 (lag20_72h) vs. R. sphaeroides 2.4.1 (exp low) 2

description:
2 lag20_72h vs exp (low)
biological sample 4-6

value: lag phase (20min) after long stationary phase (57 h)


title: R. sphaeroides 2.4.1 (lag90) vs. R. sphaeroides 2.4.1 (exp low) 2

description:
2 lag90 vs exp (low)
biological sample 4-6

source_name: lag phase (90min)_low aeration

value: lag phase (90min)


title: OCI-LY10 DMSO_4

description:
DLBCL cell line with vehicle, DMSO
314073

source_name: Flash-Frozen Cultured Cells

value: DMSO

value: 0 micromolar


title: OCI-LY10 DMSO_3

description:
DLBCL cell line with vehicle, DMSO
314062


title: R. sphaeroides 2.4.1 (lag90) vs. R. sphaeroides 2.4.1 (exp low) 1

description:
1 lag90 vs exp (low)
biological sample 1-3

value: exponential phase


title: 600305

description:
chipid: 5552234031_C
tumour sample 10

source_name: genomic DNA from tumour sample 10

value: Case

value: Ovarian


title: 600359

description:
chipid: 5552234031_E
tumour sample 11

source_name: genomic DNA from tumour sample 11

value: Serous


title: OCI-LY10 DMSO_5

description:
DLBCL cell line with vehicle, DMSO
314084


title: OCI-LY10 CC-122_1

description:
DLBCL cell line treated with CC-122
314041


title: OCI-LY10 DMSO_2

description:
DLBCL cell line with vehicle, DMSO
314051


title: OCI-LY10 DMSO_1

description:
DLBCL cell line with vehicle, DMSO
314040


title: R. sphaeroides 2.4.1 (lag20) vs. R. sphaeroides 2.4.1 (exp low) 1

description:
1 lag20 vs exp (low)
biological sample 1-3

source_name: lag phase (20min)_low aeration

value: lag phase (20min)


title: 600280

description:
chipid: 5552234031_A
tumour sample 9

source_name: genomic DNA from tumour sample 9


title: R. sphaeroides 2.4.1 (stat) vs. R. sphaeroides 2.4.1 (exp low) 1

description:
1 stat vs exp (low)
biological sample 1-3

source_name: stationary phase_low aeration


title: R. sphaeroides 2.4.1 (lag20) vs. R. sphaeroides 2.4.1 (exp low) 2

description:
2 lag20 vs exp (low)
biological sample 4-6