title: K26 replicate 1

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

hyb_protocol: cRNA was purified and hybridized on Illumina HumanRef-8 V3.0 Expression BeadChips

data_processing:
Raw intensity data was taken from the Final Report produced by the GenomeStudio software version 1.6.0 (Illumina).
Variance‐stabilizing transformation (vst) and robust spline normalization (rsn) were applied to the raw data.

label_protocol: Biotinylated cRNA was prepared using the Illumina Total Prep RNA Amplification Kit (Ambion, Cat #4393543)

growth_protocol: Cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol: Total RNA was extracted using High Pure RNA isolation kit (Roche) according to the manufacturer's instructions. cDNA was obtained from 100 ng of total RNA using SuperScript VILO cDNA synthesis (Invitrogen). High RNA integrity was assessed by Bioanalyzer nano 6000 assay with RIN numbers 9.5

treatment_protocol: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated. Along a 6-day treatment with Dox, cells were passaged at day 3. Serum-containing media was replaced with serum-free media at day 4 for growth arrest.  Cells overexpressing WT or K26A HA-tagged H1.4 were grown without treatments.

value: human breast cancer cells

value: overexpressing HA-tagged K26A H1.4

tag: dox treatment

value: Untreated

tag: depletion/expression status

value: Histone H1.4K26A  expression


title: Control matched sample pair anterior cingulate cortex MD1_ACC #17

status: Public on May 16 2014

type: RNA

city: Pittsburgh

first: Etienne

last: Sibille

state: PA

address: 450 Technology Drive, Suite 231

department: Psychiatry

country: USA

institute: University of Pittsburgh

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: • Heat the hybridization cocktail to 99°C for 5 minutes in a heat block • Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation • Transfer the hybridization cocktail that has been heated at 99°C, to a 45°C heat block for 5 minutes • Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture • Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube • Place probe array into the hybridization oven, set to 45°C • To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm • Hybridize for 16 hours • During the latter part of the 16-hour hybridization, proceed to the GeneChip® Expression Wash, Stain and Scan User Manual, P/N 702731, to prepare reagents for the washing and staining steps required immediately after completion of hybridization

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing: Probeset signals (i.e., transcript levels) were extracted with the Affymetrix GCOS software. For statistical analysis, log2- transformed probeset signal intensities were extracted and normalized with the robust multiarray average (GC-RMA) algorithm

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Control sample, brain anterior cingulate cortex

label_protocol: According to standard affymetrix protocol: • 10ul  Purified cDNA10ul • DEPC H2O • 4ul  10x IVT Labeling Buffer • 12ul  IVT Labeling NTP mix • 4ul  IVT Labeling Enzyme mix - Incubate at 37C 16 hour in an incubating oven or thermal cycler with heated lid to avoid condensation. - Purify labeled cRNA generated from either IVT labeling reaction using RNeasy RNA Purification Mini kit (Qiagen) using the RNA Cleanup Protocol according to manufacturers instructions. - Quantitate Biotin labeled cRNA using 260nm/280nm spectrophotometric assay.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from frozen samples stored in TRIzol (Invitrogen, Carlsbad, Calif.) and processed for microarray analysis according to the microarray manufacturer’s protocol (Affymetrix, Santa Clara, Calif.)

treatment_protocol: not applicable

tag: tissue

value: brain anterior cingulate cortex

tag: disease state

value: Control


title: Control matched sample pair anterior cingulate cortex MD1_ACC #2


title: Control matched sample pair anterior cingulate cortex MD1_ACC #6


title: MDD matched sample pair amygdala MD1_AMY #4

source_name: MDD sample, brain amygdala

value: brain amygdala

value: MDD case


title: WT replicate 1

country: Spain

scan_protocol: Standard Illumina scanning protocol

source_name: WT

tag: cell line

tag: cell type

tag: genotype/variation

value: overexpressing HA-tagged wild type H1.4

value: Histone H1.4 expression


title: Control matched sample pair anterior cingulate cortex MD1_ACC #1


title: K26 replicate 2


title: 9377359016_E_raw_annot copy (5077175084009645852).tsv

city: Heidelberg

first: Vera

middle: C.

last: Martins

address: Im Neuenheimer Feld 280

department: Division of Cellular Immunology

country: Germany

institute: German Cancer Research Center

description: SAMPLE 25

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Data were normalized and analyzed with Chipster v2.9: Ilumina normalization for quantile, with consequent log2 transformation of the data

organism: Mus musculus

source_name: old wo competition

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

growth_protocol: All studies were performed in vivo.

extract_protocol: RNA was isolated using RNAzol B (IsoTex Diagnostics) according to the manufacturer’s recommendations and dissolved in RNase free water.

treatment_protocol: Samples were either prepared directly from single cell suspensions or sorted.

tag: strain background

tag: host strain type

value: donor origin TN2/3 cells

tag: cell phenotype


title: sh225 replicate 1

value: expressing Dox-inducible shRNAs against multiple H1 variants (sh225)

value: no depletion


title: WT replicate 2


title: 9377359016_D_raw_annot copy (6998081066301765375).tsv

description: SAMPLE 24


title: sh225 replicate 2


title: sh120 replicate 2

value: expressing Dox-inducible shRNAs against histone H1.4 (sh120)


title: sh225_Dox replicate 1

value: Treated

value: Histone H1 depletion


title: sh120_Dox replicate 1

value: Histone H1.4 depletion


title: sh225_Dox replicate 2

value: human breast cancer cells


title: 9377359070_B_raw_annot copy (8255379276798207645).tsv

description: SAMPLE 21


title: sh120_Dox replicate 2


title: 9377359016_F_raw_annot copy (7708514205978388778).tsv

description: SAMPLE 19


title: sh120 replicate 1


title: 9377359070_A_raw_annot copy (966766625532390149).tsv

description: SAMPLE 20


title: 9377359070_C_raw_annot copy (6958139940976984943).tsv

description: SAMPLE 22


title: Hip3/Cip3

type: genomic

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: dioxin-Hip sample 3 is compared to control-Cip sample 3

hyb_protocol: Roche Nimblegen's Rat DNA Methylation 3×720 K CpG Island Plus RefSeq Promoter Array was used, which contains three identical sub-arrays.  Three different comparative (MeDIP vs MeDIP) hybridizations experiments were performed by Nimblegen for each experimental group versus control, each encompassing DNA samples from 6 animals (3 treatment and 3 control groups) and 3 sub-arrays.

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing: For each comparative hybridization experiment, raw data from both the Cy3 and Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing), checked for quality and converted to MA values (M = Cy5-Cy3; A = (Cy5+Cy3)/2).  R-code for the data processing of these MeDIP-Chip data may be downloaded from http://skinner.wsu.edu/microarray.html.  The following normalization procedure was conducted. Within each array, probes were separated into groups by GC content and each group was separately normalized, between Cy3 and Cy5 using the loess normalization procedure. This allowed for GC groups to receive a normalization curve specific to that group. After each array was normalized within array, the arrays were then normalized across arrays using the A quantile normalization procedure. Following normalization each probe within each array was subjected to a smoothing procedure, whereby the probe's normalized M values were replaced with the median value of all probe normalized M values across all arrays within a 600 bp window. If the number of probes present in the window was less than 3, no value was assigned to that probe. Each probe's A values were likewise smoothed using the same procedure. Following normalization and smoothing each probe's M value represents the median intensity difference between vinclozolin lineage and control lineage of a 600 bp window. Significance was assigned to probe differences between lineage and generation samples by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the normalized M. A Z-score and P-value were computed for each probe from that distribution. The statistical analysis was performed in pairs of comparative IP hybridizations between treatment lineage (T) and control lineage (C) (e.g. T1-C1 and T2-C2; T1-C1 and T3-C3; T2-C2 and T3-C3). In order to assure the reproducibility of the candidates obtained, only the candidates showing significant changes in every one of the paired comparisons were chosen as having a significant change in DNA methylation between each of the experimental group and controls. This is a very stringent approach to select for changes, since it only considers repeated changes in all paired analysis.  Clustered Regions of interest were then determined by combining consecutive probes within 600 bases of each other, and based on whether their mean M values were positive or negative, with significance p-values less than 10−5. The statistically significant differential DNA methylated regions were identified and P-value associated with each region presented. Each region of interest was then annotated for gene and CpG content. This list was further reduced to those regions with an average intensity value exceeding 9.5 (log scale) and a CpG density ≥1 CpG/100 bp.

label: Cy 3

molecule: genomic DNA

organism: Rattus norvegicus

source_name: MeDIP ChIP DNA from F3 Dioxin (Hip) sperm

label_protocol: Samples from experimental groups were labeled with Cy3 and MeDIP DNA samples from the control groups were labeled with Cy5

growth_protocol: The F0 generation pregnant females were exposed to a Dioxin (Hip) treatment, during days 8 to 14 as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring, as previously described.

extract_protocol: DNA was extracted from purified sperm heads from a total of nine F3 generation rats per treatment lineage that were 120 days of age.  Equal concentrations of DNA from individual sperm samples were then used to produce pools of DNA material. Three DNA pools were produced in total per treatment, therefore a total of 45 animals were used for building three DNA pools per treatment for the 4 experimental groups plus controls. These DNA pools were then used for methylated DNA immunoprecipitation (MeDIP). MeDIP was performed as follows: 6 µg of genomic DNA was subjected to series of three 20 pulse sonications at 20% amplitude and the appropriate fragment size (200–1000 ng) was verified through 2% agarose gels; the sonicated genomic DNA was resuspended in 350 ul TE and denaturated for 10 min at 95°C and then immediately placed on ice for 5 min; 100 ul of 5× IP buffer (50 mM Na-phosphate pH 7, 700 mM NaCl, 0.25% Triton X-100) was added to the sonicated and denatured DNA. An overnight incubation of the DNA was performed with 5 ug of antibody anti-5-methylCytidine monoclonal from Diagenode S.A (Denville, NJ) at 4°C on a rotating platform. Protein A/G beads from Santa Cruz (Santa Cruz, CA) were prewashed on PBS-BSA 0.1% and resuspended in 40 ul 1× IP buffer. Beads were then added to the DNA-antibody complex and incubated 2 h at 4°C on a rotating platform. Beads bound to DNA-antibody complex were washed 3 times with 1 ml 1× IP buffer; washes included incubation for 5 min at 4°C on a rotating platform and then centrifugation at 6000 rpm for 2 min. Beads-DNA-antibody complex were then resuspended in 250 ul digestion buffer (50 mM Tris HCl pH 8, 10 mM EDTA, 0.5% SDS) and 3.5 ul of proteinase K (20 mg/ml) was added to each sample and then incubated overnight at 55°C on a rotating platform. DNA purification was performed first with phenol and then with chloroform:isoamyl alcohol. Two washes were then performed with 70% ethanol, 1 M NaCl and glycogen. MeDIP selected DNA was then resuspended in 30 ul TE buffer.

treatment_protocol: Dioxin

tag: generation

label: Cy 5

source_name: MeDIP ChIP DNA from F3 control (Cip) sperm

growth_protocol: The F0 generation pregnant females were exposed to a control vehicle (Cip) DMSO treatment, during days 8 to 14 as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring, as previously described.

treatment_protocol: Control


title: Jip3/Cip3

description: jet fuel-Jip sample 3 is compared to control-Cip sample 3

source_name: MeDIP ChIP DNA from F3 Jet fuel (Jip) sperm

growth_protocol: The F0 generation pregnant females were exposed to a Jet fuel (Jip) treatment, during days 8 to 14 as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring, as previously described.

treatment_protocol: Jet Fuel


title: 9377359016_B_raw_annot copy (2379105070518132026).tsv

description: SAMPLE 23


title: Vip1/Cip1

description: vinclozolin-Vip sample 1 is compared to control-Cip sample 1

source_name: MeDIP ChIP DNA from F3 Vinclozolin (Vip) sperm

growth_protocol: The F0 generation pregnant females were exposed to a vinclozolin (Vip) treatment, during days 8 to 14 as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring, as previously described.

treatment_protocol: Vinclozolin


title: 9377359048_A_raw_annot copy (3234637297748272875).tsv

description: SAMPLE 16

value: wild type control samples that correspond to TN2 from B6 mice


title: Pip1/Cip1

description: pesticides-Pip sample 1 is compared to control-Cip sample 1

source_name: MeDIP ChIP DNA from F3 Pesticides (Pip) sperm

growth_protocol: The F0 generation pregnant females were exposed to a pesticide (Pip) treatment, during days 8 to 14 as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring, as previously described.

treatment_protocol: Pesticides


title: Bip3/Cip3

description: plastics-Bip sample 3 is compared to control-Cip sample 3

source_name: MeDIP ChIP DNA from F3 Plastics (Bip) sperm

growth_protocol: The F0 generation pregnant females were exposed to a plastics (Bip) treatment, during days 8 to 14 as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring, as previously described.

treatment_protocol: Plastics


title: Ctrl_Dox replicate 1

value: expressing Dox-inducible random shRNA vector


title: 9377359041_E_raw_annot copy.txt

description: SAMPLE 13

source_name: old w competititon

value: competitive wild type hosts

tag: cell marker


title: Ctrl replicate 2

source_name: Ctrl

value: Untreated


title: 9377359016_A_raw_annot copy (2843628979840366694).tsv

description: SAMPLE 18


title: Ctrl_Dox replicate 2


title: Ctrl replicate 1


title: J1_Ino80e_siRNA_1

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: Gene expression 96 hours after transfection

hyb_protocol: Based on standard Agilent one-color protocol

scan_protocol: Images were scanned with an Agilent DNA Microarray Scanner (G2505B), and analyzed with Agilent Feature Extraction Software version 9.5.3.1 using default parameters (Protocol: GE1-v5_95_Feb07 and Grid: 014868_D_F_20060807.)

data_processing: Agilent signal intensities were loaded by Agi4x44PreProcess 1.20.0, the G signal was normalized to median log2 fold change of zero.

source_name: mouse J1 ESC, Ino80e siRNA, replicate 1

label_protocol: Quick Amp labeling kit

growth_protocol: J1 cell were maintianed in ESGRO medium. Cell were cultured in M15 medium when transfection or infection was performed.

extract_protocol: Total RNA were prepared using Therno RNA kit according to the manufacturer's instructions.

treatment_protocol: Cell were transfected with siRNAs against NT, Ino80, Ino80b, Ino80c or Ino80e, and harvested 96 hours after transfection. Cells were infected with shRNA-NT or shRNA-Ino80, and harvested 2, 4 or 6 days after infection.

value: Mouse embryonic stem cell line

value: Mouse J1 ESC

tag: agent

tag: time

tag: group

tag: control group


title: Bip1/Cip1

description: plastics-Bip sample 1 is compared to control-Cip sample 1


title: J1_Ino80e_siRNA_2

source_name: mouse J1 ESC, Ino80e siRNA, replicate 2


title: Pip2/Cip2

description: pesticides-Pip sample 2 is compared to control-Cip sample 2


title: Hip2/Cip2

description: dioxin-Hip sample 2 is compared to control-Cip sample 2


title: Jip2/Cip2

description: jet fuel-Jip sample 2 is compared to control-Cip sample 2


title: 9377359070_D_raw_annot copy (923973805842567135).tsv

description: SAMPLE 14


title: 9377359041_C_raw_annot copy (2296632680403852771).tsv

description: SAMPLE 12


title: Hip1/Cip1

description: dioxin-Hip sample 1 is compared to control-Cip sample 1


title: Jip1/Cip1

description: jet fuel-Jip sample 1 is compared to control-Cip sample 1


title: Vip2/Cip2

description: vinclozolin-Vip sample 2 is compared to control-Cip sample 2


title: 9377359070_E_raw_annot copy (6803971327400607688).tsv

description: SAMPLE 15

value: wild type control samples that correspond to TN3 from B6 mice


title: Vip3/Cip3

description: vinclozolin-Vip sample 3 is compared to control-Cip sample 3


title: 9377359054_E_raw_annot copy (7453569125425456996).tsv

description: SAMPLE 10


title: Pip3/Cip3

description: pesticides-Pip sample 3 is compared to control-Cip sample 3


title: J1_Ino80c_siRNA_1

source_name: mouse J1 ESC, Ino80c siRNA, replicate 1


title: Bip2/Cip2

description: plastics-Bip sample 2 is compared to control-Cip sample 2


title: J1_Ino80b_siRNA_1

source_name: mouse J1 ESC, Ino80b siRNA, replicate 1


title: 9377359041_A_raw_annot copy (8723057935475329246).tsv

description: SAMPLE 11


title: J1_Ino80b_siRNA_2

source_name: mouse J1 ESC, Ino80b siRNA, replicate 2


title: J1_Ino80c_siRNA_2

source_name: mouse J1 ESC, Ino80c siRNA, replicate 2


title: 9377359054_C_raw_annot copy (1333081922328109340).tsv

description: SAMPLE 9


title: 9377359054_A_raw_annot copy (1306846849228456421).tsv

description: SAMPLE 8


title: 9377359041_D_raw_annot copy (3094203962735328364).tsv

description: SAMPLE 7

source_name: young

value: host TN2/3 cells


title: J1_NT_siRNA_1

source_name: mouse J1 ESC, non-targeting siRNA, replicate 1


title: 9377359041_B_raw_annot copy (2291744759242529814).tsv

description: SAMPLE 6


title: 9377359048_B_raw_annot copy (7515721279976203595).tsv

description: SAMPLE 17


title: J1_Ino80_siRNA_2

source_name: mouse J1 ESC, Ino80 siRNA, replicate 2


title: J1_NT_siRNA_2

source_name: mouse J1 ESC, non-targeting siRNA, replicate 2


title: 9377359054_B_raw_annot copy (7878587681510785316).tsv

description: SAMPLE 3


title: 9377359041_F_raw_annot copy (3047035476514063444).tsv

description: SAMPLE 2


title: 9377359054_D_raw_annot copy (5180909687914071619).tsv

description: SAMPLE 4


title: J1_shRNA_Ino80_Day_6_2

description: Gene expression 144 hours after transfection

source_name: mouse J1 ESC, shRNA Ino80, day 6, replicate 2


title: 5993312001_F.raw (1977283945976947572)

value: WB

tag: tissue/cell type

value: total host splenocytes


title: J1_shRNA_NT_Day_6_2

source_name: mouse J1 ESC, shRNA non-targeting, day 6, replicate 2


title: J1_Ino80_siRNA_1

source_name: mouse J1 ESC, Ino80 siRNA, replicate 1


title: J1_shRNA_Ino80_Day_4_2

source_name: mouse J1 ESC, shRNA Ino80, day 4, replicate 2


title: 9377359016_C_raw_annot copy (1925624455275516602).tsv

description: SAMPLE 1

source_name: old wo competition


title: 5993312001_E.raw (3458140824901098868)


title: J1_shRNA_NT_Day_6_1

source_name: mouse J1 ESC, shRNA non-targeting, day 6, replicate 1


title: J1_shRNA_Ino80_Day_4_1

source_name: mouse J1 ESC, shRNA Ino80, day 4, replicate 1


title: 9377359054_F_raw_annot copy (8981497329535810521).tsv

description: SAMPLE 5


title: J1_shRNA_NT_Day_4_2

source_name: mouse J1 ESC, shRNA non-targeting, day 4, replicate 2


title: 5993312001_D.raw (4448606275287412591)

value: total wild type splenocytes


title: K83_treatment, biological rep2

city: Changchun

first: Yunhong

last: Zhang

state: Jilin province

address: Renmin street 5268

country: China

institute: Northeast Normal University

hyb_protocol: According to manufacture’s protocol (Affymetrix Technologies The Affymetrix, INC. Santa Clara, CA , USA)

scan_protocol: Microarray slides were scanned with an Affymetrix 3000 GeneArray scanner

data_processing: The raw data were normalized with the Robust Multichip Average (RMA) method. Differentially expressed genes were identified using the R software 'limma' package, and multiple test corrections were performed using the FDR

organism: Oryza sativa

source_name: shoots, treatment

growth_protocol: rice were grown in greenhouse with a 16/8 hour photoperiod at 27 °C during the day and 23 °C during the night.

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

treatment_protocol: Seven-day-old uniform-sized seedlings grown in hydroponic medium were transferred to fresh hydroponic medium alone or containing 50 mM alkali salts. Shoots were harvested 24 h after transfer and 10 shoots were pooled for microarray analysis.

value: shoot

tag: genotype

tag: stress

value: alkali


title: K83_treatment, biological rep1

label_protocol: According to manufacture’s protocol (Affymetrix Technologies The Affymetrix, INC. Santa Clara, CA , USA)

tag: tissue


title: 5993312001_C.raw (7176197924693476910)


title: J1_shRNA_Ino80_Day_6_1

source_name: mouse J1 ESC, shRNA Ino80, day 6, replicate 1


title: J1_shRNA_NT_Day_4_1

source_name: mouse J1 ESC, shRNA non-targeting, day 4, replicate 1


title: K83_treatment, biological rep3


title: K83_control, biological rep3

source_name: shoots, control

value: control


title: J1_shRNA_Ino80_Day_2_2

description: Gene expression 48 hours after transfection

source_name: mouse J1 ESC, shRNA Ino80, day 2, replicate 2


title: J1_shRNA_Ino80_Day_2_1

source_name: mouse J1 ESC, shRNA Ino80, day 2, replicate 1


title: K83_control, biological rep1


title: Jijing88_treatment, biological rep2


title: 5993312001_A.raw (7496073987975929990)

value: total wild type thymocytes


title: 5993312001_B.raw (227301842742843462)


title: Jijing88_control, biological rep3


title: Jijing88_control, biological rep1


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #12

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

source_name: MDD sample, brain orbital ventral prefrontal cortex

value: brain orbital ventral prefrontal cortex

tag: disease state

value: MDD case


title: Jijing88_treatment, biological rep1


title: Jijing88_treatment, biological rep3


title: 5535696071_B.raw (6916570179291862810) [re-analysis]

description: reanalysis of SAMPLE 9 Fig4a

value: T cell acute lymphoblastic leukemia


title: Jijing88_control, biological rep2


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #10


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #7


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #6


title: 5535696071_F.raw (4853230209989437418) [re-analysis]

description: reanalysis of SAMPLE 7 Fig4a

source_name: T-ALL


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #9


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #8


title: 5535696061_F.raw (7995091202440220546) [re-analysis]

description: reanalysis of SAMPLE 6 Fig4a


title: FLT3-ITD 1 (037)

city: Oxford

first: Sten Eirik

last: Jacobsen

address: Headington

department: Weatherall Institute

country: United Kingdom

institute: University of Oxford

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array MOE430A 2.0, using a  Genechip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed at the PAN Facility, Stanford)

scan_protocol: Chips were scanned using the Genechip Scanner 3000 7G

data_processing: Cel files were processed in R using RMA normalisation

label: Biotin

label_protocol: Nugen kit WT-Ovation Pico RNA Amplifications System for total RNA amplification. Uesd WT Ovation cDNA Biotin Module V2 for cDNA labeling and fragmentation.

tag: age

value: 8-10 weeks

tag: gender

value: female

tag: genetic background

tag: source tissue

value: Bone Marrow

value: Lineage negative, Sca-1 positive, cKit positive, CD48 positive, CD150 negative Lympho-myeloid Multipotent Progenitors


title: 5535696061_E.raw (3812411373257263762) [re-analysis]

description: reanalysis of SAMPLE 5 Fig4a

tag: strain background


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #11


title: J1_shRNA_NT_Day_2_2

source_name: mouse J1 ESC, shRNA non-targeting, day 2, replicate 2

tag: cell type

value: Mouse embryonic stem cell line

tag: cell line

value: Mouse J1 ESC


title: FLT3-ITD 1


title: 5535696061_D.raw (3566588110640980207) [re-analysis]

description: reanalysis of SAMPLE 4 Fig4a


title: K83_control, biological rep2


title: FLT3-ITD 2


title: FLT3-ITD 3


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #12

source_name: Control sample, brain orbital ventral prefrontal cortex

value: Control


title: WT 1 (037)

source_name: wild type

value: wild type


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #4


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #1


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #5


title: WT 3


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #11


title: 5535696061_B.raw (4758709639004682744)

source_name: 10 wk-thymus graft

value: autonomous thymus


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #10


title: WT 2


title: 5535696061_C.raw (2152376368016891227)


title: Control, CK2, biological rep1

city: Beijing

first: Jin

middle: Hui

last: Chen

state: Beijing

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Biotechnology, Beijing Forestry University

institute: Beijing Forestry University

description: Expression data from one year old leaves of Populus simonii

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Populus simonii

source_name: Populus simonii leaves from  controls.

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The cuttings were planted in basins (15 cm diameter × 10 cm depth) that contained sand, organic matter and vermiculite (3:1:1,v/v/v) in the greenhouse of Beijing Forestry University in March 2010. After sprouting and growth for about one year, healthy cuttings with approximately the same crown size and equal height were chosen and moved into growth chambers at the laboratory of Beijing Forestry University.

extract_protocol: Total RNA was extracted by the procedure of Chang et al(Chang, et al. 1993). mRNA was isolated from total RNA (~0.5 mg for each treatment) using the PolyAtract mRNA Isolation System (Promega). Double-stranded cDNA was then synthesized from mRNA with the Universal RiboClone cDNA Synthesis System (Promega) following the manufacturer’s protocol. The synthesized cDNA was dissolved in 50 μl TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: We took six plants obtained from one genotype, using three for chilling stress (4°C, 10h) and the other three as controls.

value: leaves

tag: treatment


title: 5535696049_E.raw (2009153553543611507) [re-analysis]

description: reanalysis of SAMPLE 2 Fig4a


title: Control, CK1, biological rep1


title: 5535696049_C.raw (1646110240412190961)


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #9


title: 5535696049_F.raw (1019341314213550024) [re-analysis]

description: reanalysis of SAMPLE 3 Fig4a


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #8


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #2


title: WT 1


title: 5535696049_D.raw (485867349740789808) [re-analysis]

description: reanalysis of SAMPLE 1 Fig4a


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #5


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #7


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #6


title: J1_shRNA_NT_Day_2_1

source_name: mouse J1 ESC, shRNA non-targeting, day 2, replicate 1

tag: agent


title: 5535696049_B.raw (8151562555714662367)


title: Chilling stress (4°C,  10h) treatment, BH11269-2_Zdqe 14_(Poplar), biological rep1

source_name: Populus simonii leaves from  chilling stress (4°C, 10h) treatments.

value: 4 C


title: starved L1 lin-35(n745), biological rep2

city: Boulder

first: Mingxue

last: Cui

address: Colorado Ave.

department: MDCB

institute: HHMI, University of Colorado at Boulder

description: lin-35(n745) replicant 2L; lin-35(n745)_rep 2

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: The data were analyzed with GeneSifter web-based software (VizX Labs) using the GC robust multi-array average (RMA) algorithm (Wu et al. 2003).

organism: Caenorhabditis elegans

source_name: Starved L1 lin-35(n745) worms

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

growth_protocol: L1 stage worms were incubated in S-basal buffer without cholesterol added at 20°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and then DNAseI treated before purification on RNEasy minicolumns from Qiagen.

tag: worm stage

value: starved L1 stage worms

tag: genotype/variation


title: SAMPLE 26_9423642035_E.raw (115736260223475576)

description: SAMPLE 26

source_name: TN4 thymocytes

value: triple negative 4 thymocytes

tag: cell phenotype


title: starved L1 lin-35(n745), biological rep3

description: lin-35(n745) replicant 3; lin-35(n745)_rep 3


title: 5535696071_D.raw (3340365011948158043) [re-analysis]

description: reanalysis of SAMPLE 10 Fig4a

tag: tissue/cell type


title: Chilling stress (4°C,  10h) treatment, BH11269-2_Zdqe 13_(Poplar), biological rep1


title: SAMPLE 25_9423642035_D.raw (6860378146913841166)

description: SAMPLE 25

source_name: TN3b thymocytes

value: triple negative 3b thymocytes


title: starved L1 lin-35(n745), biological rep1

description: lin-35(n745) replicant 1; lin-35(n745)_rep 1


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #4

value: brain orbital ventral prefrontal cortex


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #3


title: starved L1 wild type worm, biological rep3

description: wild type replicant 3; wild type_rep 3

source_name: Starved L1 wild type worms


title: Rat adrenal DEX-3

city: Palo Alto

first: Wen-Jun

last: Shen

state: CA

address: 3801 Miranda Avenue

department: Medicine

institute: Stanford University

description: miRNA expression data from rat adrenal gland treated with DEX.

hyb_protocol: Affymetrix® GeneChip® Hybridization, Wash and Stain Kit was used for the hybridization according the standard protocal. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G. The measurements were carried out by the Protein and Nucleic Acid (PAN) Microarray Facility of Stanford University.

data_processing: The microarray data were analyzed using Partek® Genome Suite software, version 6.3 Copyright© 2008 (Partek Inc., St. Louis, MO, USA)

source_name: Rat adrenal with DEX

label_protocol: 500 ng total RNA containing low molecular weight RNA was labled with FlashTag™ Biotin HSR RNA Labeling Kit according to the standard Affymetrix protocol.

growth_protocol: Three monthes male Sprague Dawley (SD) rats were purchased from Harlan Laboratories (Indianapolis, IN). They were allowed to acclimatize to a new controlled environment (25 ± 2oC, 55 ± 5% relative humidity with a 12h light-dark cycle) for approximately one week.

extract_protocol: Total RNA was purified with miRNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Subsequently rats were randomly divided into Four groups (3 rats in each group): 1) non-stressed controls (C), 2) rats treated with Cortrosyn (ACTH) (10 IU) every 24h for 4 days, with the last injection on day 4 given 1h prior to harvesting of adrenal tissues, 3) rats treated with 17α-ethinyl estradiol (17α-E2), 10 mg/kg BW sc every 24h for 5 days, and 4) rats treated with dexamethasone (DEX), a single injection of 100 ug, sc for a 24 h period. At the end of treatment, animals were euthanized and adrenal tissues collected for various molecular and biochemical measurements.

value: Male

value: Adrenal gland

tag: strain

value: Sprague Dawley

value: 3 monthes

tag: weight


title: 5535696071_A.raw (1732612041391734011) [re-analysis]

description: reanalysis of SAMPLE 8 Fig4a

value: T cell acute lymphoblastic leukemia


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #13

source_name: MDD sample, brain dorsolateral prefrontal cortex

tag: tissue

value: brain dorsolateral prefrontal cortex

value: MDD case


title: starved L1 wild type worm, biological rep1

description: wild type replicant 1; wild type_rep 1


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #10

tag: disease state


title: MDD matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #3


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #11


title: SAMPLE 21_9377359057_E.raw (2780359002668627929)

description: SAMPLE 21


title: SAMPLE 22_9423642035_A.raw (7060318066108016723)

description: SAMPLE 22

source_name: ISP thymocytes

value: immature single positive


title: SAMPLE 23_9423642035_B.raw (1098371799171665091)

description: SAMPLE 23

source_name: DP thymocytes

value: double positive thymocytes


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #12


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #1

value: Control


title: starved L1 wild type worm, biological rep2

description: wild type replicant 2; wild type_rep 2

value: wild type


title: Control matched sample pair brain orbital ventral prefrontal cortex NY_BA47 #2


title: xyl-grown cell culture- 1h 1mM Fru_3

city: UMEÅ

first: Leszek

last: Kleczkowski

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

hyb_protocol: The hybridization of the Arabidopsis ATH1 Genome Array occured for 16 hours in a 45°C incubator, rotating at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev3, Affymetrix Inc., Santa Clara, CA) the arrays were subsequently washed and stained using the Fluidics Station 450.

scan_protocol: The scanning of the  Arabidopsis ATH1 Genome Arrays was done using the GeneChip® Scanner 3000 7G.

data_processing:
Normalization of the raw data was achieved by using the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method. Subsequent analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org).
In order to search for the differentially expressed genes between X and the Y groups an empirical Bayes moderated t-test was then applied (1), using the ‘limma’ package (2). To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg (3). 1. Smyth GK, Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004.  2. Smyth, G. K. Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, edited by R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420, 2005.  3. Benjamini Y HY. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B: 289-300, 1995.

organism: Arabidopsis thaliana

source_name: Xyl-grown cell culture_ 1h 1mM Fru

label_protocol: 250 ng of total RNA per sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® 3’ IVT Express Kit Manual (PN 702646 Rev8, Affymetrix Inc., Santa Clara, CA).

growth_protocol: Arabidopsis thaliana cell suspension culture was grown for 7 d after sub-culturing in a hormone-free full strength MS (Murashige and Skoog) media supplied with 87 mM Xylose as the only carbon source. The culture was maintained by shaking on an orbital shaker in the dark.

extract_protocol: The total RNA was isolated by applying TRI Reagent® (Sigma-Aldrich) and chloroform to frozen and ground plant material. Phase separation was reached by centrifugation at full speed for 15 min. The aqueous fraction was mixed with half a volume isopropanol and the nucleic acids were pelleted by a 10 min centrifugation at full speed. The pellet was washed 2 times with 70% ethanol, air-dried and subsequently taken up in sterile water. The total RNA samples were DNase-treated using RQ1 RNase-Free DNase (Promega Biotech AB) and RNA was re-extracted as described above. RNA concentration was assessed using the ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA).

treatment_protocol: 7 day old xyl-grown cell culture was subjected to a 1 hour treatment with 1 mM of either Fru, Glc, Suc or Xyl (control). The treatment was conducted on an orbital shaker in the dark. After removal of the treatment solution, cells were washed three times in sugar free MS-media using vacuum filtration and immediately snap frozen in liquid nitrogen.

tag: cell culture

value: xyl-grown cell culture

tag: sugar species

value: Fru


title: xyl-grown cell culture- 1h 1mM Glc_3

source_name: Xyl-grown cell culture_ 1h 1mM Glc

value: Glc


title: xyl-grown cell culture- 1h 1mM Xyl_3

source_name: Xyl-grown cell culture_ 1h 1mM Xyl

value: control (Xyl)


title: Rat adrenal DEX-2

tag: gender

tag: age


title: Rat adrenal DEX-1


title: xyl-grown cell culture- 1h 1mM Xyl_2


title: xyl-grown cell culture- 1h 1mM Suc_3

source_name: Xyl-grown cell culture_ 1h 1mM Suc

value: Suc


title: SAMPLE 18_9377359057_B.raw (7774462146196586741)

description: SAMPLE 18

source_name: TN2 thymocytes

tag: strain background

value: triple negative 2 thymocytes


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #9


title: xyl-grown cell culture- 1h 1mM Suc_2


title: SAMPLE 17_9377359057_A.raw (792089525828312591)

description: SAMPLE 17

source_name: ETP thymocytes

tag: cell type

value: early thymic progenitor


title: Rat adrenal 17-2

description: miRNA expression data from rat adrenal gland treated with 17α-E2.

source_name: Rat adrenal with 17α-E2

value: Male

value: Adrenal gland


title: Rat adrenal 17-3

value: Sprague Dawley

value: 3 monthes


title: Rat adrenal 17-1


title: Rat adrenal ACTH-2

description: miRNA expression data from rat adrenal gland treated with ACTH.

source_name: Rat adrenal with ACTH


title: Rat adrenal ACTH-3


title: xyl-grown cell culture- 1h 1mM Glc_2


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #7

value: brain dorsolateral prefrontal cortex


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #6

value: MDD case


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #4


title: SAMPLE 16_9377359040_D.raw (4092413543864261998)

description: SAMPLE 16


title: xyl-grown cell culture- 1h 1mM Fru_2


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #5


title: SAMPLE 13_9249051071_C.raw (6671337448010325989)

description: SAMPLE 13

source_name: TN3a thymocytes

value: triple negative 3a thymocytes


title: Rat adrenal ACTH-1


title: xyl-grown cell culture- 1h 1mM Glc_1


title: xyl-grown cell culture- 1h 1mM Suc_1


title: SAMPLE 15_9249051071_E.raw (5106207831138327857)

description: SAMPLE 15

value: immature single positive


title: xyl-grown cell culture- 1h 1mM Xyl_1


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #2


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #3


title: SAMPLE 14_9249051071_D.raw (5524432068414700764)

description: SAMPLE 14

value: triple negative 4 thymocytes


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #8


title: SAMPLE 24_9423642035_C.raw (1328852387672780694)

description: SAMPLE 24


title: Rat adrenal CON-2

description: miRNA expression data from rat adrenal gland treated with phosphate buffered saline (PBS).

source_name: Rat adrenal with vehicle


title: SAMPLE 10_5535696071_D.raw (6764307601211763101)

description: SAMPLE 10

value: T cell acute lymphoblastic leukemia

value: Rag-defficient


title: SAMPLE 11_9249051071_A.raw (1121386549896968282)

description: SAMPLE 11


title: MDD matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #1


title: Rat adrenal CON-3


title: Rat adrenal CON-1


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #13

source_name: Control sample, brain dorsolateral prefrontal cortex

value: Control


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #12


title: xyl-grown cell culture- 1h 1mM Fru_1

value: xyl-grown cell culture

value: Fru


title: SAMPLE 9_5535696071_B.raw (4185212996052893539)

description: SAMPLE 9


title: Cast_2

city: Boston

first: Haydn

last: Kissick

state: MA

address: 3 Blackfan Circle, CLS 4/430

institute: Beth Israel Deaconess Medical Ceter

hyb_protocol: cRNA (15 μg) was fragmented and hybridized to arrays according to the manufacturer's (Ambion® | Life Technologies) protocols.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 and GeneChip Operating Software acquired raw fluorescence signal.

data_processing: Scanned array images were analyzed by dChip and CEL file data were normalized using RMAexpress.

source_name: CD3+CD4+GFP- cells from spleens of Foxp3-GFP mice

label_protocol: Biotin-UTP was incorporated during the overnight in vitro transcription step according to the manufacturer's (Ambion® | Life Technologies) protocol.

extract_protocol: CD3+CD4+GFP- cells isolated from the spleens of mice 4 weeks after surgery. RNA extracted using Trizol.

treatment_protocol: Mice were castrated or received sham surgery.

tag: surgery

value: castrated

value: CD3+CD4+ GFP- Splenocytes


title: SAMPLE 12_9249051071_B.raw (2190114702802723125)

description: SAMPLE 12

value: triple negative 2 thymocytes


title: SAMPLE 8_5535696071_A.raw (9171181181707023462)

description: SAMPLE 8


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #10


title: Sham_1

value: sham


title: Sham_2


title: SAMPLE 6_5535696061_F.raw (559346980960210059)

description: SAMPLE 6

source_name: T-ALL

value: Rag-proficient


title: SAMPLE 7_5535696071_F.raw (8172316186769384052)

description: SAMPLE 7


title: Cast_1


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #7


title: SAMPLE 3_5535696049_F.raw (1042052480121112783)

description: SAMPLE 3


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #11


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #8


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #5


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #6


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #4


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #2


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #3


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #9


title: SAMPLE 1_5535696049_D.raw (3780495822042598432)

description: SAMPLE 1


title: SAMPLE 5_5535696061_E.raw (166451866509421572)

description: SAMPLE 5


title: SAMPLE 2_5535696049_E.raw (5211611422918482139)

description: SAMPLE 2


title: Control matched sample pair brain dorsolateral prefrontal cortex NY_BA9 #1


title: Bronchi-high-3R4F 5

status: Public on May 15 2014

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

country: Switzerland

institute: Philip Morris Products SA

hyb_protocol: The biotin-labeled RNA was hybridized on Affymetrix Rat230_2 microarrays. The wash and stain procedures were performed according to Affymetrix protocols (GeneChip(R) Expression Wash, Stain and ScanUser Manual, Affymetrix).

scan_protocol: Cartridges were scanned using the GeneChip Scanner 3000 (Affymetrix). Scanned image files were visually inspected for artifacts and the generated Cel files was used as input for data analysis. The Affymetrix Command Console Software (AGCC, Affymetrix, Santa Clara, CA) was used to control the fluidics station and the scanner.

data_processing: Data processing was implemented in the R statistical environment. Raw RNA expression data was analyzed using the affy and gcrma packages of the Bioconductor suite of microarray analysis tools available in the R statistical environment. GC Robust Microarray Analysis (GCRMA) (including background correction and quantile normalization) was used to generate probe set expression values.

label_protocol: GeneChip(R) 3’ IVT Express Kit (Affymetrix, Santa Clara, USA) with 100 ng RNA.

extract_protocol: Whole tissue for nasal epithelia or laser microdissected (LCM) tissue for bronchi and lung parenchyma was used to extract total RNA using miRNAeasy Mini Kit (Qiagen).

treatment_protocol: Animals were exposed to mainstream smoke smoke through nose-only inhalation for 28 days with varying doses (0, 8, 15, 23 ug nicotine/l) and different tobacco products (pMRTP and 3R4F).

value: male

value: Bronchus

tag: tissue source

value: Left Lung

tag: treatment

tag: treatment concentration [ug nicotine/l]

tag: treatment duration [days]

tag: daily exposure [hours]

tag: exposure path

value: nose-only

tag: smoking regimen

value: Health Canada


title: Bronchi-high-3R4F 2


title: Bronchi-high-3R4F 4


title: Bronchi-high-3R4F 1


title: Bronchi-low-3R4F 4


title: Bronchi-high-3R4F 3


title: Bronchi-low-3R4F 5


title: Bronchi-low-3R4F 3


title: Bronchi-low-3R4F 1


title: Bronchi-med-3R4F 4


title: Bronchi-low-3R4F 2


title: Bronchi-med-3R4F 5


title: Bronchi-med-3R4F 2


title: Bronchi-sham 5

source_name: Bronchi-sham

value: fresh air


title: Bronchi-pMRTP 2

source_name: Bronchi-pMRTP

value: pMRTP


title: Bronchi-med-3R4F 3


title: Bronchi-pMRTP 1


title: Bronchi-pMRTP 5


title: Bronchi-sham 1


title: Bronchi-sham 4


title: Bronchi-pMRTP 4


title: Bronchi-med-3R4F 1


title: Bronchi-sham 3


title: Bronchi-pMRTP 3


title: Parenchyma-high-3R4F 5

value: Parenchyma


title: Bronchi-sham 2


title: SAMPLE 4_5535696061_D.raw (7110080857427187297)

description: SAMPLE 4

value: T cell acute lymphoblastic leukemia

tag: cell phenotype


title: Parenchyma-high-3R4F 4

tag: tissue


title: SAMPLE 19_9377359057_C.raw (6992047728549652256)

description: SAMPLE 19

value: triple negative 3a thymocytes


title: Parenchyma-high-3R4F 3


title: Parenchyma-high-3R4F 2


title: Parenchyma-low-3R4F 5


title: Parenchyma-low-3R4F 3


title: Parenchyma-low-3R4F 4


title: SAMPLE 20_9377359057_D.raw (7674970820789243426)

description: SAMPLE 20

source_name: TN3b thymocytes

value: triple negative 3b thymocytes


title: Parenchyma-low-3R4F 2


title: Parenchyma-high-3R4F 1


title: Parenchyma-med-3R4F 3


title: Parenchyma-med-3R4F 4


title: Parenchyma-pMRTP 5

source_name: Parenchyma-pMRTP


title: Parenchyma-pMRTP 4


title: Parenchyma-sham 3

source_name: Parenchyma-sham


title: Parenchyma-low-3R4F 1


title: Parenchyma-med-3R4F 1


title: Parenchyma-sham 5


title: RNE-low-3R4F 5

value: Nasal Cavity Respiratory Epithelium

value: Nose


title: RNE-high-3R4F 2


title: Parenchyma-pMRTP 3


title: Parenchyma-sham 4


title: Parenchyma-med-3R4F 2


title: Parenchyma-sham 1


title: RNE-low-3R4F 3


title: Parenchyma-pMRTP 1


title: Parenchyma-med-3R4F 5


title: RNE-high-3R4F 5


title: RNE-low-3R4F 4


title: Parenchyma-sham 2


title: RNE-high-3R4F 4


title: RNE-high-3R4F 1


title: RNE-high-3R4F 3


title: RNE-med-3R4F 5


title: Parenchyma-pMRTP 2


title: RNE-med-3R4F 4


title: RNE-low-3R4F 1


title: RNE-low-3R4F 2


title: RNE-med-3R4F 2


title: RNE-med-3R4F 3


title: RNE-pMRTP 3

source_name: RNE-pMRTP


title: RNE-pMRTP 4


title: RNE-med-3R4F 1


title: RNE-pMRTP 2


title: PFp_presen_3_HG-U133A+2

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip Scanner 3000

data_processing: RMA express was used to generate the RMA file

source_name: Human skeletal muscle myoblasts (HSMMs)

label_protocol: MessageAmp(tm) Premier RNA Amplification Kit

growth_protocol: Human skeletal muscle myoblasts (HSMMs) stably expressing PAX3-FOXO1 as described previously (Naini et al., 2008), and were maintained in defined media (SkGM-2 Bullet Kit, Lonza).

extract_protocol: RNA was isolated using an RNeasy kit according to the manufacturer’s protocol

treatment_protocol: Human skeletal muscle myoblasts (HSMMs) transduced with indicated genetic constructs.

tag: cell line

value: HSMMs

tag: expressing

value: no glutamine


title: PFp_presen_2_HG-U133A+2


title: RNE-pMRTP 5


title: Vp_Presen_3_HG-U133A+2

value: pK1 plasmid (empty vector)

value: 4mM glutamine


title: RNE-sham 5

source_name: RNE-sham

value: male


title: RNE-sham 3


title: RNE-pMRTP 1


title: Vp_Presen_2_HG-U133A+2


title: PFp_postsen_2_HG-U133A+2

value: PAX3-FOXO1 that passed the senescence checkpoint


title: RNE-sham 1


title: RNE-sham 2


title: PFp_presen_1_HG-U133A+2


title: RNE-sham 4


title: PFp_postsen_3_HG-U133A+2


title: Vehicle Repeat 4

city: St. Louis

first: David

last: DeNardo

state: MO

address: 425 S. Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

description: 10128 - 515

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

source_name: Mouse pancreatic tumor

growth_protocol: C57BL6 mice were purchased from Jackson Laboratory and maintained in specific pathogen-free facilities at Washington University before surgical implantation.

extract_protocol: RNA was extracted with EZNA kit, followed by clean-up and DNase I treatment with Promega RQ1 DNase kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Orthotopic pancreatic ductal adenocarcinomas were established by surgical implantation using syngenic tumor cell lines (MAP-free and mycoplasma-negative) mixed with matrigel. Upon the establishment of orthotopic tumors (~1cm in diameter), mice were treated with vehicle or CSF1R inhibitor, both administered through chow, for 8 days. Mice were perfused with PBS-heparin; tumor tissues were obtained and digested with collagenase.

tag: strain

value: Female

tag: developmental stage

value: Adult

value: Vehicle

value: pancreatic tumor


title: PFp_postsen_1_HG-U133A+2


title: Vp_Presen_1_HG-U133A+2


title: CSF1Ri Repeat 1 Hyb_B

description: 10130 - 493_Hyb_B

tag: gender


title: CSF1Ri Repeat 5

description: 10129 - 425


title: Vehicle Repeat 3 Hyb_B

description: 10124 - 423_Hyb_B


title: Sertoli Cell Line AR17_3

city: Giessen

first: Melanie

last: Markmann

state: Hessen

address: Rudolf-Buchheim-Str. 7

department: Anaesthesiology

institute: University of Giessen

description:
Sertoli cells derived from rat testis.
Biological replicate 3 of 3. Sertoli cells (93RS2) transfected with full-length human AR, harvested after 24h growth after last passage.

hyb_protocol: Biotin-labeled cRNA was hybridized on the CodeLink Human Whole Genome using the CodeLink Expression Assay Kit (GE Healthcare) according to manufacturer's instructions. Bioarrays were stained with Cy5™-streptavadin (GE Healthcare). http://www.fda.gov/downloads/scienceresearch/bioinformaticstools/microarrayqualitycontrolproject/ucm132970.pdf

scan_protocol: GenePix® 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA).

data_processing: Data were median normalized (normalized to median = 1; intra-slide normalization) and local background subtracted using CODELINK Version 5.1.

source_name: Sertoli cell line, expressing AR

label_protocol: Extracted RNA was subjected to cRNA synthesis and cRNA fragmentation using the CodeLink Expression Assay Kit (GE Healthcare) according to manufacturer's instructions.

extract_protocol: RNA was extracted with the "peqGOLD total RNA kit" (#12-6634-01) from  PEQLab according to the manufacturer's protocol.

treatment_protocol: A full-length human AR was introduced into the expression vector pcDNA 6.2 C-EmGFP, and AR-deficient rat Sertoli cells (93RS2) were transfected by electroporation. Cells were harvested after 24h growth after last passage.

value: Sertoli cell line

tag: androgen receptor expression

value: yes


title: CSF1Ri Repeat 2

description: 10133 - 513


title: Vehicle Repeat 1 Hyb_B

description: 10127 - 514_Hyb_B


title: Sertoli Cell Line AR17_2

description:
Sertoli cells derived from rat testis.
Biological replicate 2 of 3. Sertoli cells (93RS2) transfected with full-length human AR, harvested after 24h growth after last passage.

tag: cell type


title: TLDA-29

city: tokyo

first: ohtsuki

last: kazushige

country: Japan

institute: tokyo medical university

description: SAMPLE 16

data_processing:
RNU6B were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data (raw Ct values) from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).
fold_change.txt: deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])

label: TaqMan probe (FAM-MGB)

source_name: healthy Control_PBMC

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA). RT reaction products from the exosome sample were further amplified using the Megaplex PreAmp Primers (Primers A v2.1).

extract_protocol: Total RNA was isolated with the mirVana PARIS kit (Ambion, Austin, TX, USA).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were harvested form 10ml of whole blood.

tag: disease status

value: healthy volunteers

tag: sample group

value: healthy volunteers (controls)


title: TLDA-30

description: SAMPLE 17

value: chronic myeloid leukemia (CML) patients

value: receiving imatinib with CMR; undetermined minimal disease (UMD)

value: Peripheral blood mononuclear cells (PBMCs)


title: TLDA-28

description: SAMPLE 15


title: Sertoli Cell Line noAR_2

description:
Sertoli cells derived from rat testis.
Biological replicate 2 of 3. Sertoli cells lacking any AR (93RS2), harvested after 24h growth after last passage.

source_name: Sertoli cell line, not expressing AR

treatment_protocol: Cells were not transfected and were harvested after 24h growth after last passage.

value: no


title: Vehicle Repeat 3

description: 10124 - 423

tag: treatment


title: CSF1Ri Repeat 4

description: 10132 - 512


title: CSF1Ri Repeat 3

description: 10131 - 494


title: TLDA-27

description: SAMPLE 14


title: TLDA-26

description: SAMPLE 13


title: Vehicle Repeat 2

description: 10125 - 470


title: Vehicle Repeat 1

description: 10127 - 514


title: Sertoli Cell Line noAR_1

description:
Sertoli cells derived from rat testis.
Biological replicate 1 of 3. Sertoli cells lacking any AR (93RS2), harvested after 24h growth after last passage.


title: Sertoli Cell Line AR17_1

description:
Sertoli cells derived from rat testis.
Biological replicate 1 of 3. Sertoli cells (93RS2) transfected with full-length human AR, harvested after 24h growth after last passage.


title: CSF1Ri Repeat 1

description: 10130 - 493


title: TLDA-25

description: SAMPLE 12


title: TLDA-21

description: SAMPLE 11


title: Sertoli Cell Line noAR_3

description:
Sertoli cells derived from rat testis.
Biological replicate 3 of 3. Sertoli cells lacking any AR (93RS2), harvested after 24h growth after last passage.


title: TLDA-19

description: SAMPLE 9


title: TLDA-20

description: SAMPLE 10


title: TLDA-17

description: SAMPLE 8


title: TLDA-14

description: SAMPLE 5

value: sustained CMR for more than 6 months after discontinuation of imatinib (STOP-IM group)


title: TLDA-15

description: SAMPLE 6


title: TLDA-16

description: SAMPLE 7


title: TLDA-13

description: SAMPLE 4


title: TLDA-12re

description: SAMPLE 3


title: MCF-7 cells

city: Taichung

first: Jer-Yuh

last: Liu

address: Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

description:
MCF-7
Gene expression data from MCF-7 cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip Human Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Resulting data was analysed using Expression Console software (Affymetrix) with default RMA parameters. Among the differentially expressed genes, those designated as 'up-regulated' were ones which over-expressed by at least two-fold in comparison with the untreated control (p<0.05), whereas those designated as 'down-regulated' were ones which under-expressed by at least 0.75-fold compared with the untreated control (p<0.05).

source_name: MCF-7 cells

growth_protocol: The human breast cancer Hs578T, MDA-MB-231, MDA-MB-231-M(V4), Hs578T-M(S3), MDA-MB-468 and MCF-7 cells were maintained in DMEM supplemented with 10% FBS and 100 μg/ml penicillin/streptomycin at 37oC in a humidified atmosphere containing 5% CO2. Cells were seeded in culture plates at an initial density of 1x10^5 cells/ml and grown to approximately 80% confluence.

treatment_protocol: The cells were grown to approximately 80% confluence and then collected for following analyses.

value: breast adenocarcinoma cell line

tag: transfection

value: female


title: MDA-MB-468 cells

description:
MDA-MB-468
Gene expression data from MDA-MB-468 cells.

source_name: MDA-MB-468 cells


title: Hs578T cells with MZF-1 fragment

description:
Hs578T-M(S3)
Gene expression data from Hs578T cells transfected with MZF-1 fragment.

value: breast carcinoma cell line

value: MZF-1 fragment


title: MDA-MB-231 cells with MZF-1 fragment

description:
MDA-MB-231-M(V4)
Gene expression data from MDA-MB-231 cells transfected with MZF-1 fragment.


title: TLDA-11

description: SAMPLE 2


title: TLDA-10

description: SAMPLE 1


title: Hs578T cells

description:
Hs578T
Gene expression data from Hs578T cells.

source_name: Hs578T cells transfected with empty vector

value: empty vector


title: Nutlin replicate 2

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

description: Gene expression data

hyb_protocol: followd the affymetrix insructions in GeneChip® WT Terminal  Labeling and Hybridization  User Manual  for use with the Ambion® WT  Expression Kit

scan_protocol: followed the affymetic manual GeneChip® Expression Wash, Stain and Scan  User Manual  For Cartridge Arrays

data_processing: Partek. 1. Import CEL files (Nutlin-3, replicates 1-3; DMSO, replicates 1-3)   a. Use Partek default RMA import settings  2. Add a categorical attribute (found under Workflows, Gene Expression, Import, Add sample attributes)  a. Attribute Name: Treatment  i. Group 1 Name: Nutlin  ii. Group 2 Name: DMSO  3. Detect differentially expressed genes (found under Workflows, Gene Expression, Analysis, Detect differentially expressed genes)  a. Add Factor: Treatment  b. Add Contrast  i. Group 1: Nutlin  ii. Group 2: DMSO  c. Output file saved as:   i. ANOVA - 120612  4. Create Gene Lists (found under Tools, Create Gene List)  a. Cutoffs:  Fold change > |+/-1.5|, p-value with FDR <0.05  b. Output files saved as:   i. Gene List - Increase 1_5 fold - FDR 0_05 – 120612  1. 413 genes up, 45 with no gene symbol = 368 genes  ii. Gene List - Decrease 1_5 fold - FDR 0_05 - 120612   1. 407 genes down, 25 with no gene symbol = 382 genes  5. Save ANOVA and Gene Lists in txt format

growth_protocol: HCT116 cells were grown in McCoy's 5A and passaged the day prior to treatment. Cells were plated at a concentration of 300,000 cells per well of 6 well plate and treated 24 hours later with either Nutlin-3R (10M) or the equivalent amount of vehicle (DMSO) for 12 hour.

extract_protocol: Total RNA was harvested with an RNeasy kit (Qiagen)

treatment_protocol: 12 hours 10microM Nutlin-3 vs DMSO

value: Nutlin


title: MDA-MB-231 cells

description:
MDA-MB-231
Gene expression data from MDA-MB-231 cells.

source_name: MDA-MB-231 cells transfected with empty vector


title: 24h_50UVA (G5)

city: London

first: Angela

last: Tewari

address: 9th Floor Tower Wing, Guys Hospital

department: St. John's Institute of Dermatology

institute: King`s College London

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (44K) 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 and a final wash step with acetonitrile for 30 sec at RT.

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. The background corrected raw data were further proecessed by quantile normalization and log2 transformation.

source_name: skin biopsy

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

treatment_protocol: 4 skin type I/II individuals were given 50J/cm2 UVA1 (after a UVR sensitivity test) and biopsies taken at 6h and 24h, after analysis as below, a further 5 skin type I/II volunteers were UVR sensitivity tested and had a dose response of UVA1 (12.5J/cm2, 25J/cm2, 50J/cm2 and biopsies taken at 6h post irradiation.  A further dose of 50J/cm2 was also given and a biospy taken at 24h) as well as 30mJ/cm2 of UVB and biopsies taken at 6h and 24h.

tag: donor

tag: stress

value: UVA

tag: dose

tag: time


title: DMSO replicate 3

description: Gene expression data

label_protocol: followd the affymetrix insructions in GeneChip® WT Terminal  Labeling and Hybridization  User Manual  for use with the Ambion® WT  Expression Kit

value: DMSO


title: Nutlin replicate 3

description: Gene expression data


title: 24h_50UVA (G4)


title: DMSO replicate 2

description: Gene expression data


title: 24h_50UVA (G3)


title: Nutlin replicate 1

description: Gene expression data


title: 24h_50UVA (G_7T)


title: 24h_50UVA (G_5T)


title: 24h_50UVA (G_6T)


title: 24h_50UVA (G_4T)


title: wholeblood_woman_T-260

city: Toronto

first: Jan

last: Heng

state: ON

address: 25 Orde Street

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix U133 plus 2.0 arrays (EukGE-WS2v5)

scan_protocol: Affymetrix GeneChip Scanner 2000

data_processing: Data were normalised using GCRMA (v.2.30.0) and differential expression was determined using Limma with multiple hypothesis testing (Benjamini and Hochberg); Bioconductor (v.1.8.3 )/R

source_name: did not deliver within 48 hr of hospital admission

label_protocol: Labeling was performed according to standard Affymetrix protocols (Affymetrix one-cycle kit with PNAs; Affymetrix IVT kit)

extract_protocol:
Peripheral maternal blood collected using PAXgene tubes
PAXgene Blood RNA system kit was used to isolate total RNA

tag: preterm delivery within 48 hours

value: No

value: whole blood, maternal peripheral


title: 24h_50UVA (G2)


title: 24h_UVB (F2)

value: UVB

value: 30 mJ/cm2


title: 24h_UVB (F5)


title: DMSO replicate 1

description: Gene expression data


title: 24h_50UVA (G1)


title: wholeblood_woman_T-065

tag: tissue


title: 6h_UVB (E3)


title: 24h_UVB (F3)


title: 6h_UVB (E4)


title: wholeblood_woman_T-261


title: 24h_UVB (F4)


title: wholeblood_woman_T-214


title: 6h_UVB (E5)


title: wholeblood_woman_T-199

source_name: delivered within 48 hr of hospital admission

value: Yes


title: 6h_UVB (E1)


title: 24h_UVB (F1)


title: 6h_UVB (E2)


title: wholeblood_woman_T-050


title: 6h_50UVA (D2)


title: 6h_50UVA (D5)


title: wholeblood_woman_T-179


title: wholeblood_woman_T-105


title: 6h_50UVA (D4)


title: 6h_50UVA (D1)


title: wholeblood_woman_T-057


title: wholeblood_woman_T-112


title: 6h_50UVA (D3)


title: wholeblood_woman_T-039


title: 6h_50UVA (D_5T)


title: wholeblood_woman_T-239


title: wholeblood_woman_T-009


title: wholeblood_woman_T-015


title: 6h_50UVA (D_7T)


title: 6h_25UVA (C4)


title: 6h_25UVA (C5)


title: 6h_25UVA (C1)


title: 6h_50UVA (D_4T)


title: 6h_25UVA (C2)


title: 6h_25UVA (C3)


title: wholeblood_woman_T-162


title: wholeblood_woman_T-058


title: wholeblood_woman_T-195


title: 6h_12.5UVA (B2)


title: wholeblood_woman_T-116


title: wholeblood_woman_T-226


title: wholeblood_woman_T-008


title: 6h_12.5UVA (B4)


title: control (A4)

value: control


title: 6h_12.5UVA (B3)


title: wholeblood_woman_T-094


title: wholeblood_woman_T-005


title: wholeblood_woman_T-113


title: wholeblood_woman_T-132


title: wholeblood_woman_T-011


title: wholeblood_woman_T-111


title: 6h_12.5UVA (B5)


title: wholeblood_woman_T-134


title: control (A5)


title: 6h_12.5UVA (B1)


title: wholeblood_woman_T-107


title: control (A3)


title: control (A_7C)


title: wholeblood_woman_T-251


title: wholeblood_woman_T-104


title: wholeblood_woman_T-232


title: wholeblood_woman_T-231


title: control (A_6C)


title: wholeblood_woman_T-071


title: control (A2)


title: wholeblood_woman_T-078


title: wholeblood_woman_T-165


title: wholeblood_woman_T-066


title: wholeblood_woman_T-017


title: wholeblood_woman_T-279


title: wholeblood_woman_T-286


title: wholeblood_woman_T-018


title: wholeblood_woman_T-021


title: control (A_5C)


title: wholeblood_woman_T-148


title: wholeblood_woman_T-103


title: wholeblood_woman_T-029


title: wholeblood_woman_T-025


title: wholeblood_woman_T-147


title: wholeblood_woman_T-120


title: wholeblood_woman_T-001


title: wholeblood_woman_T-069


title: wholeblood_woman_T-031


title: wholeblood_woman_T-054


title: wholeblood_woman_T-133


title: control (A1)


title: control (A_4C)


title: wholeblood_woman_T-161


title: 6h_50UVA (D_6T)


title: wholeblood_woman_T-030


title: wholeblood_woman_T-020


title: wholeblood_woman_T-075


title: wholeblood_woman_T-041


title: wholeblood_woman_T-180


title: wholeblood_woman_T-140


title: wholeblood_woman_T-123


title: wholeblood_woman_T-275


title: wholeblood_woman_T-003


title: wholeblood_woman_T-067


title: wholeblood_woman_T-287


title: wholeblood_woman_T-218


title: wholeblood_woman_T-106


title: wholeblood_woman_T-064


title: wholeblood_woman_T-124


title: wholeblood_woman_T-077


title: wholeblood_woman_T-270


title: wholeblood_woman_T-051


title: wholeblood_woman_T-089


title: wholeblood_woman_T-044


title: wholeblood_woman_T-248


title: wholeblood_woman_T-170


title: wholeblood_woman_T-012


title: wholeblood_woman_T-173


title: wholeblood_woman_T-252


title: wholeblood_woman_T-203


title: wholeblood_woman_T-278


title: wholeblood_woman_T-144


title: wholeblood_woman_T-014


title: wholeblood_woman_T-183


title: wholeblood_woman_T-217


title: wholeblood_woman_T-096


title: wholeblood_woman_T-055


title: wholeblood_woman_T-068


title: wholeblood_woman_T-237


title: wholeblood_woman_T-042


title: wholeblood_woman_T-224


title: wholeblood_woman_T-300


title: wholeblood_woman_T-119


title: wholeblood_woman_T-155


title: wholeblood_woman_T-288


title: wholeblood_woman_T-274


title: wholeblood_woman_T-169


title: wholeblood_woman_T-172


title: wholeblood_woman_T-049


title: wholeblood_woman_T-284


title: wholeblood_woman_T-197


title: wholeblood_woman_T-175


title: wholeblood_woman_T-013


title: wholeblood_woman_T-263


title: wholeblood_woman_T-212


title: wholeblood_woman_T-035


title: wholeblood_woman_T-262


title: wholeblood_woman_T-097


title: wholeblood_woman_T-136


title: wholeblood_woman_T-142


title: wholeblood_woman_T-022


title: wholeblood_woman_T-221


title: wholeblood_woman_T-272


title: wholeblood_woman_T-002


title: wholeblood_woman_T-154


title: wholeblood_woman_T-079


title: wholeblood_woman_T-070


title: wholeblood_woman_T-249


title: wholeblood_woman_T-127


title: wholeblood_woman_T-255


title: wholeblood_woman_T-290


title: wholeblood_woman_T-193


title: wholeblood_woman_T-016


title: wholeblood_woman_T-234


title: wholeblood_woman_T-168


title: wholeblood_woman_T-225


title: wholeblood_woman_T-006


title: wholeblood_woman_T-273


title: wholeblood_woman_T-158


title: wholeblood_woman_T-028


title: wholeblood_woman_T-166


title: wholeblood_woman_T-204


title: wholeblood_woman_T-004


title: wholeblood_woman_T-085


title: wholeblood_woman_T-188


title: wholeblood_woman_T-268


title: wholeblood_woman_T-023


title: wholeblood_woman_T-048


title: wholeblood_woman_T-243


title: wholeblood_woman_T-109


title: wholeblood_woman_T-157


title: wholeblood_woman_T-007


title: wholeblood_woman_T-053


title: wholeblood_woman_T-194


title: wholeblood_woman_T-153


title: wholeblood_woman_T-160


title: wholeblood_woman_T-090


title: wholeblood_woman_T-072


title: wholeblood_woman_T-102


title: wholeblood_woman_T-238


title: wholeblood_woman_T-129


title: Patient_09_miRNA

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

description: miRNA expression profile of surgically resected material

hyb_protocol: Hybridization to the miRNA microarrays were performed following the procedure described by the manufacturer.

scan_protocol: Hybridization signals were detected using the Genepix 4000B Scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Scanned images were analyzed using the Array-Pro Analyzer ver.4.5 software (Media Cybernetics, Rockville, MD). Because two different probe desigins (lot numbers 31015 and 31078) were used, the common probes between them were extracted. The obtained miRNA microarray datasets were then normalized by the quantile normalization method using R statistical software version 2.12.1.

source_name: Liver tissue

label_protocol: Total RNA was labeled with Hy3 fluorescent label using the miRCURY LNA microRNA Power Labeling kit (Exiqon).

extract_protocol: A global miRNA expression analysis was performed using 1 µg of total RNA and the miRCURY LNA microRNA Array series (Exiqon, Vedbaek, Denmark).

treatment_protocol: miRNA expression profiles of liver tissues from 12 patients with chronic hepatitis C were used.

value: Liver biopsy sample

tag: Sex

value: M

tag: outcome

value: SVR


title: Patient_08_miRNA

value: F

value: VR


title: Patient_10_miRNA

value: NVR


title: wholeblood_woman_T-141


title: Patient_06_miRNA


title: wholeblood_woman_T-046


title: Patient_05_miRNA


title: Patient_07_miRNA


title: Patient_11_miRNA


title: wholeblood_woman_T-150


title: wholeblood_woman_T-045


title: Patient_12_miRNA


title: Patient_01_miRNA


title: Patient_03_miRNA


title: Patient_02_miRNA


title: SB-3

type: protein

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: SB-216763 lysate replicate 3

hyb_protocol: Human protein microarrays (ProtoArray 5.0; Invitrogen) were washed 3 times in TBST, blocked for 4 h at 4 ºC using Microarray Blocking solution (Arrayit), followed by a wash in swelling buffer. HeLa extracts (1 ml) were pre-warmed, treated with 30 μM SB-216763 or DMSO (control), and incubated on the microarrays under coverslips at RT for 1 h. Microarrays were washed and incubated with anti-polyubiquitin antibody FK1 (4 μg/ml; Enzo Life Sciences) overnight at 4ºC, washed again and incubated with Alexa Fluor 680 anti-mouse antibody (Invitrogen). The microarrays were washed 3 times in TBST and 2 times in water and dried.

scan_protocol: The microarrays were scanned in an Oddysey scanner (LI-COR) using the following parameters: Channel 700; Grid = 8x3, 21.17; Intensity = 5; Offset = 0.

data_processing: Raw ProtoArray signal data from GenePix Pro (version 5.0.0.49; Molecular Devices) were pre-processed following the manufacturer's recommendations using the ProtoArray Prospector software (version 5.2; Invitrogen) with the following options: background subtraction, outlier detection and Z-factor calculation per sub-array.

label: Alexa Fluor 680

molecule: protein

source_name: SB-216763-treated HeLa lysate supplemented with ubiquitin

label_protocol: Cleared extracts (2 mg/ml) were supplemented with 0.5 mg/ml ubiquitin (Boston Biochem), 30 mM creatine phosphate, 20 mM ATP, 2 mM EGTA and 20 mM MgCl2.

growth_protocol: HeLa cells were cultured in 15-cm dishes at 37°C with 5% CO2 in RPMI medium supplemented with 10% fetal calf serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Cells were harvested in ice-cold PBS, resuspended in 50 mM Hepes-KOH, pH 7.5, 1.5 mM MgCl2, 5 mM KCl, 2 mM DTT and 1x protease inhibitor mixture tablet (Roche), and homogenized by freeze-thawing followed by Dounce homogenization.

tag: cell line

value: HeLa

value: GSK3 inhibitor SB-216763


title: Patient_04_miRNA


title: Co-3

description: Control lysate replicate 3

source_name: Control (DMSO-treated) HeLa lysate supplemented with ubiquitin

value: DMSO control


title: SB-1

description: SB-216763 lysate replicate 1


title: Co-2

description: Control lysate replicate 2


title: HumanMacrophage_6hr_LPS1ug_rep2

city: Helsinki

first: Tiina

last: Öhman

address: P.O.Box 65

country: Finland

institute: Institute of Biotechnology

description: Gene expression after 6hr stimulation with LPS 1 µg in human primary macrophages

hyb_protocol: Hybridization time 17 hours, temperature 65ºC and rounds 10 rpm.

scan_protocol: Agilent  Scanner model G2505C, Agilent Scan Control Version A.8.3.1.

data_processing: Protocol GE1_105_Dec08, Grid 014850_D_F_20080627, Feature Extraction  Software 10.5.1.1 (Agilent).

source_name: Human primary macrophages, 6hr, LPS 1 ug

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.7 ug of total RNA. Labeling, hybridization and scanning were performed according to the Agilent´s protocol:   One-Color  Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Version 5.7.

growth_protocol: Human monocytes were isolated from healthy blood donors and were allowed to differentiate into macrophages for six days by maintenance in the Macrophage-SFM medium supplemented with 10 ng/ml rh GM-CSF and antibiotics.

extract_protocol: Total RNA from 2 x 10E6 cells (1 x 12-well plate) including three different donors was isolated using RNeasy Plus Mini Kit (Qiagen) according to the protocol provided by the manufacturer.

treatment_protocol: Macrophages were stimulated 6 h with 1 µg LPS, 10 µg curdlan or 100 µg GBY at day 6.

value: primary macrophages


title: Co-1

description: Control lysate replicate 1


title: HumanMacrophage_6hr_Curdlan10ug_rep3

description: Gene expression after 6hr stimulation with Curdlan 10 µg in human primary macrophages

source_name: Human primary macrophages, 6hr, Curdlan 10 ug


title: HumanMacrophage_6hr_0_rep2

description: Gene expression after 6hr in 0-group in human primary macrophages

source_name: Human primary macrophages, 6hr, CTR


title: HumanMacrophage_6hr_0_rep1


title: HumanMacrophage_6hr_LPS1ug_rep3


title: QF-PF-3

city: Montevideo

first: Tamara

last: Fernandez-Calero

state: Montevideo

address: Mataojo 2020

department: Bioinfomatics Unit

country: Uruguay

institute: Institut Pasteur de Montevideo

hyb_protocol: We amplified and labeled 500ng of total RNA using the Cy5-CTP or Cy3-CTP dyes. Equal amounts of labeled samples (quiescent and proliferative) were hybridized to the arrays at 65°C for 17 hours in a rotating oven (Agilent). Arrays were washed with the wash buffers 1 and 2 and the stabilization and drying solutions from Agilent.

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner, and microarray data were extracted with Agilent’s Feature Extraction software (v9.5). Four biological dye swap replicates were performed

data_processing: Scanned on an Agilent G2565AA scanner. Data analysis was accomplished using ‘R', mainly through packages in the Bioconductor suite. Probes were flagged for filtering considering saturation, signal above background and uniformity. Probes that had any of the replicates flagged were eliminated. After probe filtering normalization was performed within and between arrays using loess and Aquantile methods, respectively. Differential expression was assayed using the limma software package.

source_name: CLL B cells QF (3)

label_protocol: Low RNA Input Linear Amplification Kit (Agilent) was used to generate fluorescent complementary RNA (cRNA) for the microarray hybridizations.

extract_protocol: Total RNA from CLL B-cells was isolated from 0,5-1x106 cells using mirVana isolation kit (Applied Biosystems, Ambion, U.S.). Total RNA were used to perform the array . The concentration and integrity of RNA was determined using a NanoDrop-1000 Spectrophotometer (NanoDrop Technologies) and a 2100 Bioanalyzer (Agilent) with an RNA 6000 Nano LabChip Kit, using the Eukaryote Total RNA Nano assay according to the manufacturer’s instructions. RNAs with an RNA integrity number (RIN) greater than 8 were used.

tag: sorted cell

value: quiescent fraction

value: whole blood

source_name: CLL B cells PF (3)

value: proliferating fraction


title: 8-DAC_chr11-1chr17-1_rep3

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: 8 refers to 8-DAC

hyb_protocol: Fragmentation of the labeled aRNA prepares the target for hybridization to GeneChip® 3’ expression arrays with GeneChip® hybridization oven 640.

scan_protocol: Wash and stain the arrays with GeneChip® fluidics station 450, Scan the arrays with the GeneArray scanner 3000 by the GeneChip® Operating  Software (GCOS) or Command Console® (AGCC) Software.

data_processing: RMA data were obtained by using Partek GS 6.4.

label_protocol: In Vitro Transcription to Synthesize Biotin-Modified aRNA with IVT Labeling Master Mix generates multiple copies of biotin-modified aRNA from  the double-stranded cDNA templates; this is the amplification step.aRNA Purification removes unincorporated NTPs, salts, enzymes, and  inorganic phosphate to improve the stability of the biotin-modified aRNA.

growth_protocol: 16 h light, 8 h dark, 22°C for seedlings; 24 h dark, 22°C for callus

extract_protocol: Extract and purify the total RNA by the Qiagen RNeasy Mini Kit.Reverse Transcription to Synthesize First-Strand cDNA is primed with  T7 oligo(dT) primer to synthesize cDNA containing a T7 promoter sequence.Second-Strand cDNA Synthesis converts the single-stranded cDNA into  a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA polymerase and RNase H to simultaneously degrade the RNA  and synthesize second strand cDNA.

treatment_protocol: Leaf explants were cultured on callus-inducing medium (CIM).

tag: days after culture

value: leaf explants

tag: genotype

value: chr11-1 chr17-1 mutant


title: SB-2

description: SB-216763 lysate replicate 2


title: HumanMacrophage_6hr_Curdlan10ug_rep1

tag: cell type


title: HumanMacrophage_6hr_GBY100ug_rep2

description: Gene expression after 6hr stimulation with GBY 100 µg in human primary macrophages

source_name: Human primary macrophages, 6hr, GBY 100 ug


title: 8-DAC_chr11-1chr17-1_rep1

description: 8 refers to 8-DAC


title: 8-DAC_Col-0_rep2

description: 8D refers to 8-DAC

value: wildtype

tag: cultivar


title: Time-0_chr11-1chr17-1_rep3

description: 0 refers time-0


title: 8-DAC_chr11-1chr17-1_rep2

description: 8 refers to 8-DAC


title: HumanMacrophage_6hr_LPS1ug_rep1


title: QF-PF-4

source_name: CLL B cells QF (4)

source_name: CLL B cells PF (4)


title: 8-DAC_Col-0_rep1

description: 8D refers to 8-DAC


title: HumanMacrophage_6hr_Curdlan10ug_rep2


title: HumanMacrophage_6hr_GBY100ug_rep3


title: Time-0_chr11-1chr17-1_rep2

description: 0 refers time-0


title: QF-PF-2

source_name: CLL B cells QF (2)

source_name: CLL B cells PF (2)


title: Time-0_chr11-1chr17-1_rep1

description: 0 refers time-0


title: QF-PF-1

source_name: CLL B cells QF (1)

source_name: CLL B cells PF (1)


title: HumanMacrophage_6hr_GBY100ug_rep1


title: HumanMacrophage_6hr_0_rep3


title: Time-0_Col-0_rep3

description: 0D refers time-0


title: 8-DAC_Col-0_rep3

description: 8D refers to 8-DAC


title: Time-0_Col-0_rep2

description: 0D refers time-0


title: Dkk1_G2/M_rep3

description: replicate 3

hyb_protocol: Microarrays were hybridized following Illumina's standard hybridization protocol on HumanHT-12 v4 expression BeadChips.

scan_protocol: Processed arrays were scanned on Illumina iScan System array reader according to the manufacturer's instructions.

data_processing: Raw microarray data were imported and preprocessed in GenomeStudio V2011.1 software (Illumina) using background subtraction and quantile normalization. Differential expression analysis of the grouped replicate samples was performed within GenomeStudio on the probe level utilizing the Illumina custom error model with FDR multiple-testing correction.

source_name: G2/M phase HeLa cells_Dkk1 CM

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep kit for Illumina arrays.

growth_protocol: HeLa cells were cultured at 37°C with 5% CO2 in RPMI medium supplemented with 10% fetal calf serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) with on-column DNase digestion following the manufacturer's protocol, quantified with a Thermo NanoDrop and the RNA quality was tested on agarose gel and on Agilent Bioanalyzer.

treatment_protocol: Cells in 15-cm dish plates at 80% confluency were treated for 3 h with either Control, Wnt3a or Dkk1 conditioned media (1:5 dilutions), live-stained with 10 μM Hoechst 33342 in the last 1 h of the treatment, resuspended in ice-cold sorting buffer (DMEM supplemented with 1 μM Hoechst, 5% serum and 1 mM EDTA) and FACS-sorted directly into RLT lysis buffer (Qiagen) on a FacsAria I (BD).

value: cervical carcinoma cells

tag: cell cycle phase

tag: treated with

value: Dkk1 conditioned medium (CM) for 3hr


title: KO TNF 2

city: Los Angeles

middle: A

last: Rodgers

address: 1450 Biggy St, NRT 5517

department: Molecular Microbiology and Immunology

institute: University of Southern California

description: Gene expression

hyb_protocol: Hybridization was done by standard protocol.

scan_protocol: Slides were scanned by standard protocol on an Agilent scanner.

data_processing: Data were analyzed using Partek Genomics Suite 6.4. We used the RMA algorithm for data normalization.  Thresholds for selecting significant genes were set at >= 2-fold and FDR p<0.05. Genes met both criteria simultaneously were considered as significant changes.

source_name: HOIL-1L-/- BMDM treated with TNFa 4 hours

label_protocol: Cy3 labeling of RNA was done by standard protocol.

growth_protocol: Bone marrow was collected from 6 week old male mice and plated at a density of 2x10^7 per 10cm dish. One dish was used for each sample. Differentiated with 10% L929 supernatant for 1 week with media changes every 3 days. The experiment was performed on day 7 of differentiation.

extract_protocol: RNA was extracted by a QIAeasy kit (QIAgen) and analyzed for integrity by agarose gel

treatment_protocol: Cells were untreated (plain media) or treated with 10ng/ml LPS or 1ng/ml TNFa for 4 hours in differentiation media (DMEM + pen/strep + 10% FBS + 10% L929 supernatant).

tag: age

value: 6 week

tag: strain

tag: treatment

value: 1ng/ml TNFa


title: Dkk1_G2/M_rep1

description: replicate 1


title: Dkk1_G2/M_rep4

description: replicate 4


title: Dkk1_G2/M_rep2

description: replicate 2


title: KO LPS 1

description: Gene expression

source_name: HOIL-1L-/- BMDM treated with LPS 4 hours

value: 10ng/ml LPS


title: KO TNF 1

description: Gene expression


title: S17_3

city: SAS Nagar

first: Ram

middle: Kishor

last: Yadav

state: Punjab

address: Sector 81

department: Biology

country: India

institute: Indian Institute of Science Education and Research Mohali

description: Gene expression data from ~28 days old plant

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Affymetrix Hybridization oven 640

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 with 7G upgrade

data_processing: MAS 5

source_name: Phloem cell type

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

growth_protocol: Arabidopsis thaliana ap1-1;cal1-1 plants were grown in growth room for 28 days. The shoot apices from these plants were used for isolating the cells.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen).

treatment_protocol: Protoplasting

tag: sample type

value: sorted cells

value: Phloem


title: Wnt3a_G2/M_rep4

description: replicate 4

source_name: G2/M phase HeLa cells_Wnt3a CM

value: HeLa

value: Wnt3a conditioned medium (CM) for 3hr


title: KO LPS 2

description: Gene expression


title: Wnt3a_G2/M_rep2

description: replicate 2


title: WT TNF 1

description: Gene expression

source_name: WT BMDM treated with TNFa 4 hours

value: WT


title: Wnt3a_G2/M_rep3

description: replicate 3


title: KAN1_3

source_name: Organ circumference

value: Organ circumference


title: Control_G2/M_rep4

description: replicate 4

source_name: G2/M phase HeLa cells_Control CM

value: Control conditioned medium (CM) for 3hr


title: LAS_1

source_name: Adaxial cell type

value: Adaxial


title: S17_1


title: Wnt3a_G2/M_rep1

description: replicate 1


title: Control_G2/M_rep2

description: replicate 2


title: Time-0_Col-0_rep1

description: 0D refers time-0


title: KO Un 2

description: Gene expression

source_name: HOIL-1L-/- BMDM untreated

value: untreated


title: Control_G2/M_rep3

description: replicate 3


title: S17_2


title: WT TNF 2

description: Gene expression


title: Control_G2/M_rep1

description: replicate 1


title: Dkk1_G1_rep3

description: replicate 3

source_name: G1 phase HeLa cells_Dkk1 CM


title: WT LPS 2

description: Gene expression

source_name: WT BMDM treated with LPS 4 hours


title: PF (4)

hyb_protocol: The Hybridization was perfomes according to the  Microarray System with miRNA Complete Labeling and Hyb Kit  (Agilent).  The slides were hybridize at 55°C for 20 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to Hi100%, and Lo 5%).

data_processing: Data analysis was accomplished using ‘R’ mainly through packages in the Bioconductor suite. Probes were flagged for filtering considering saturation, signal above background and uniformity. Probes that had more than one replicate flagged where eliminated. After probe filtering, arrays were background corrected using normexp methodology. Signal intensity was standardized across arrays via quantile normalization algorithm.

source_name: CLL B cells

value: whole blood

value: proliferating fraction


title: LAS_2


title: KAN1_1


title: Dkk1_G1_rep4

description: replicate 4


title: KAN1_2


title: Dkk1_G1_rep1

description: replicate 1


title: WT Un 1

description: Gene expression

source_name: WT BMDM untreated


title: WT Un 2

description: Gene expression


title: HMG_1

source_name: Epidermal cell type

value: Epidermal


title: Dkk1_G1_rep2

description: replicate 2

value: cervical carcinoma cells


title: WT LPS 1

description: Gene expression


title: HMG_3


title: QF (4)

value: quiescent fraction


title: HDG4_3

source_name: Subepidermal cell type

value: Subepidermal


title: PF (3)


title: HDG4_4


title: QF (3)


title: KO Un 1

description: Gene expression

value: 6 week


title: PF (2)


title: liver_HSC+6.5Gy_rep2

city: ShangHai

first: Jian-Zhong

last: Li

address: Guo He Road 325#

institute: Second Military Medical University

description:
Gene expression after 24hr in 6.5Gy-irradiated rat liver pre-treated with HSC
H22

hyb_protocol: The 4×44K Whole Rat Genome Oligo Microarray (Agilent technologies, Santa Clara, CA, US) was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Raw data were obtained by Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) and normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

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

extract_protocol: Total RNA was extracted from the liver tissue of rat using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: The rats were randomly assigned to one of the three following treatment groups (10-12 animals per group): normal control, radiation and HSC dose (30 mg/kg body weight/day) + radiation. HSC dissolved in double distilled water were administered intragastrically to the male animals for 3 consecutive days before irradiation. Radiation was delivered by the 60Co source. Radiation doses were 6.5 Gy at a rate 2 Gy/min.

value: liver

tag: gender

value: male

value: HSC,6.5Gy radiation


title: liver_HSC+6.5Gy_rep1

description:
Gene expression after 24hr in 6.5Gy-irradiated rat liver pre-treated with HSC
H21


title: Wnt3a_G1_rep2

description: replicate 2

source_name: G1 phase HeLa cells_Wnt3a CM

value: HeLa


title: HMG_2

value: sorted cells


title: liver_HSC+6.5Gy_rep3

description:
Gene expression after 24hr in 6.5Gy-irradiated rat liver pre-treated with HSC
H23


title: Wnt3a_G1_rep3

description: replicate 3

value: Wnt3a conditioned medium (CM) for 3hr


title: QF (2)


title: HDG4_1


title: liver_6.5Gy_rep2

description:
Gene expression after 24hr in 6.5Gy-irradiated rat liver
M3

value: 6.5Gy radiation


title: QF (1)


title: AtHB8_2

source_name: Xylem cell type, stem

value: Xylem , stem


title: AtHB8_3


title: PF (1)


title: Wnt3a_G1_rep1

description: replicate 1


title: liver_6.5Gy_rep3

description:
Gene expression after 24hr in 6.5Gy-irradiated rat liver
M5


title: AtML1_3


title: AtML1_1


title: liver_0Gy_rep3

description:
Gene expression after 24hr in 0Gy-irradiated rat liver
C43

value: control


title: liver_6.5Gy_rep1

description:
Gene expression after 24hr in 6.5Gy-irradiated rat liver
M1


title: Control_G1_rep1

description: replicate 1

source_name: G1 phase HeLa cells_Control CM

value: Control conditioned medium (CM) for 3hr


title: liver_0Gy_rep2

description:
Gene expression after 24hr in 0Gy-irradiated rat liver
C42


title: Control_G1_rep4

description: replicate 4


title: Control_G1_rep3

description: replicate 3


title: liver_0Gy_rep1

description:
Gene expression after 24hr in 0Gy-irradiated rat liver
C41


title: Control_G1_rep2

description: replicate 2


title: AtHB8_1


title: Xenograft from patient 53

status: Public on May 14 2014

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

hyb_protocol: Hybridisation was performed as outlined in standard Illumina protocols

scan_protocol: Scanning was performed as outlined in standard Illumina protocols

data_processing: Data was exported from Illumina BeadStudio V3.0.14 with no normalisation and no background correction performed (non-normalised). Data was pre-processed using quantile normalisation (normalised) within the LIMMA package in R. Differential gene expression analysis was then performed using LIMMA in R.

source_name: CD45+ MNC from spleen

label_protocol: Total RNA was amplified using TotalPrep RNA amplification kit (Ambion) and labelled according to standard Illumina protocols with included chemistry for this array. Arrays were analysed in house at Children's Cancer Institute of Australia, Sydney.

extract_protocol: TriZol Reagent extraction for total RNA.

tag: prednisolone response

value: Good

value: M