title: H1.5 in H1.5 knockdown IMR90 cells IP vs INPUT slide2

description: H1.5 knockdown


title: H1.5 in keratinocytes IP vs INPUT slide2

status: Public on Sep 18 2012

type: genomic

city: Los Angeles

first: Jing-Yu

last: Li

address: 615 Charles E. Young Dr. South BSRB 357

country: USA

institute: University of California, Los Angeles

description: wild-type

hyb_protocol: Labeled DNA were mixed with human Cot-1 DNA, Agilent aCGH Blocking solution, and Agilent aCGH hybridization buffer. After 5-minute denaturing, and 30-minute incubation at 37 degree, mixed solution was added to array, and hybridized for 40 hours at 65 degree.

scan_protocol: Scanned on Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction 10.5.1.1

data_processing: Agilent ChIP Analytics was used for inter-array median normalization. Background subtraction, common features median normalization, and dye bias normalization were performed by using MATLAB.

molecule: genomic DNA

organism: Homo sapiens

source_name: human keratinocytes

label_protocol: DNA were labeled with Cy3- or Cy5-dCTP by using Invitrogen BioPrime DNA Labeling kit following manufacturere's instructions.

growth_protocol: H1 hESCs were plated on Matrigel (BD Biosciences)-coated plates, and maintained in mTeSR (StemCell). Before purification, cells were trypsinized to single cells and TRA-1-60 expressing cells were isolated by using MACS cell separation columns (Miltenyi Biotec). Isolated cells were tested by flow cytometry, and samples with >99% purity were used. IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO2. Growing cells with 50~70% confluence were used for further analysis. Human primary hepatocytes (Zen-bio #HP-F) were grown in Hepatocyte Maintenance Medium (Zen-Bio #HM-2), and passage 4 was used. Human ESCs (HSF1) were differentiated to neural progenitor cells (NPCs) in DMEM:F12 (Gibco) plus B27 (Gibco), N2-supplement (Gibco), 20ng/ml bFGF (R and D systems), 1µM Retinoic Acid (Sigma), and 1µM Smoothened Agonist (Calbiochem). NPCs were mechanically isolated from culture based on rosette morphology as described(Elkabetz et al., 2008) and expanded in DMEM:F12 plus B27, N2-supplement, 20ng/ml bFGF, and 50ng/ml EGF (Gibco).  NPCs were further differentiated to neurons and glia by withdrawal of the maintenance factors (bFGF and EGF) for 10 days.  Human keratinocytes were cultured per manufacturer’s protocol in KSFM (Invitrogen).  To induce differentiation, calcium chloride was added to 1.5mM for 48 hours(Lowry et al., 2005).

extract_protocol: Cells were fixed with 1% formaldehyde for 10 minutes at 37 degree followed by incubation with 140 mM glycine for 15 minutes at room temperature. Nuclear extracts were sonicated to get 150 ~ 500 bp genomic DNA fragments, diluted, precleared with 50 µl of Invitrogen Dynabeads Protein A (for Rabbit IgG) or Dynabeads Protein G (for mouse IgG) for 1 hour at 4 degree, and the supernatant was incubated with primary antibody overnight at 4 degree. Appropriate Dynabeads were then added to the solution and incubated for another 3 hours before washing steps. Reverse crosslinking of the precipitated complex was performed at 65 degree overnight followed by RNase A digestion, proteinase K treatement, phenol/chlorform extraction, and ethanol precipitation. DNA pelletes were air dried, and disolved in ddH2O.

tag: antibody

tag: cell type

value: human keratinocytes

value: H1.5 antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #


title: H1.5 in hepatocytes IP vs INPUT slide2

description: wild-type

source_name: primary hepatocytes

value: primary hepatocytes


title: Falcorosso 0h-rep1

type: RNA

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

country: Italy

institute: University of Verona

description:
Heat-sensitive; 0h; rep1
raw data file: F0a.txt

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 °C.    Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).    Hybridization washings were performed as the following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST wash solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software, and a median normalization of raw medians and log2 transformation were performed. Further statistical processing was performed using the SAM analysis (T-Mev 3.4).  Hybridization signals with a variability coefficient higher than 0.5 were filtered out.

label: Alexa Fluor 647

molecule: total RNA

organism: Solanum lycopersicum

source_name: Meiotic anther of FR heat-sensitive tomato

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions.

growth_protocol: Seeds were germinated in potting compost in trays and transferred after two weeks to a growth chamber under standard temperature (ST) conditions, with a 16-h light (26°C) / 8-h dark (18°C) cycle. Fluorescent and incandescent lighting provided a photosynthetic photon flux density of 450-500 μmol m-2 sec-1.

extract_protocol: Anther cones ranging in size from 2-4mm were isolated, immediately frozen in liquid N2 and pooled for RNA extraction. Tissues were homogenized using glass rods and RNA was extracted using a Plant RNA isolation kit (Plant RNeasy Mini Kit, Qiagen Benelux BV, Venlo the Netherlands) according to the manufacturer’s recommendations.

treatment_protocol: Six-week-old plants were heat stressed by raising the temperature to a regime of MHS (32°C /26°C; day/night).

tag: genotype/variation

value: Falcorosso

tag: heat tolerance

value: Heat-sensitive

tag: tissue

value: anther

tag: stress

value: control

tag: time


title: Falcorosso 2h-rep2

description:
Heat-sensitive; 2h; rep2
raw data file: F2b.txt

value: heat stress [raising the temperature to a regime of MHS (32°C /26°C; day/night)]


title: H1.5 in IMR90 IP vs INPUT rep1slide2

description: wild-type

source_name: human fetal lung fibroblasts

value: human fetal lung fibroblasts

tag: cell line


title: H1.5 in neurons IP vs INPUT slide2

description: in vitro differentiated from HSF1 cells

source_name: neuron

value: neuron


title: Primary_Fibroblast_p7_166.411.4.1

city: La Jolla

first: Rathi

middle: D

last: Thiagarajan

state: CA

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

description:
Primary_Fibroblast_p7_166.411.4.1wq
SAMPLE 25

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The unnormalized data (for both v3 and v4 platform) were filtered in GenomeStudio for pvalue<=0.01 using OR clause. This resulted in 19015 probes for v3 platform and 25413 probes for v4 platform. The common probes between the 2 platforms were matched by sequence \(100% match\) and one single file was produced for all the samples under study. Only the common probes between the two platforms were normalized using robust spline normalisation (RSN) with lumi in R. The processed data are on the Series record.

label: Biotin

source_name: primary fibroblast

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

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

value: primary fibroblast

tag: gender

value: FEMALE

tag: passage number

tag: loring pipeline sample id


title: H37Rv, 4 hours, Rep C

city: Seattle

first: Molly

last: Nixon

state: WA

address: 307 Westlake Ave N Ste 500

institute: Seattle Biomedical Research Institute

description: _Molly 8_N18A12cy 3

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all arrays.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and quantile normalization (Bolstad et al. Bioinformatics 19(2):185).

organism: Mycobacterium tuberculosis H37Rv

source_name: H37Rv treated with 100 uM WR99210 for 4 hrs

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: M. tuberculosis strain H37Rv cultures were grown in 7H9+GAT.  Samples for microarray were harvested in mid-log phase (OD600 = 0.3)

extract_protocol: Total RNA was extracted TRIzol chloroform:isopropanol phase separation using phaselock gels to separate the aqueous phase.  Samples were isolated by immobilization on Qiagen RNeasy columns as per manufacturer's instructions.  On- and off-column DNase treatments were performed to minimuze genomic or plasmid nucleic acid contamination of the final sample.

treatment_protocol: Cultures were treated with 100 uM WR99210 for 0, 4, and 24 hours prior to RNA isolation.

tag: treated with

value: 100 uM WR99210 for 4 hrs


title: H1.5 in H1 hESC IP vs INPUT slide2

description: wild-type

source_name: human H1 embryonic stem cells

value: human H1 embryonic stem cells


title: Primary_HUVEC_HUVEC632_p17_632.1769.1.1

description:
Primary_HUVEC_HUVEC632_p17_632.1769.1.1wq
SAMPLE 23

source_name: primary human umbilical vein endothelial cells

value: UNKNOWN


title: Primary_Fibroblast_p7_166.411.1.1

description:
Primary_Fibroblast_p7_166.411.1.1wq
SAMPLE 24


title: H37Rv, 24 hours, Rep C

description: _Molly 9_N18A12cy 5

source_name: H37Rv treated with 100 uM WR99210 for 24 hrs

value: 100 uM WR99210 for 24 hrs


title: H1.5 in IMR90 IP vs INPUT rep2 slide1

description: wild-type


title: H3K9me2 in SIRT1 knockdown IMR90 cells IP vs INPUT slide1

description: SIRT1 knockdown

value: H3K9me2 antibody

value: Millipore


title: RNA polymerase II in H1 hESC IP vs INPUT slide1

description: wild-type

value: RNA polymerase II ChIP

value: Abcam


title: H3K9me2 in H1.5 knockdown IMR90 cells IP vs INPUT slide1

description: H1.5 knockdown


title: H1.5 in calcium induced keratinocytes IP vs INPUT slide2

description: human keratinocytes induced by 1.5 mM calcium chloride for 48 hours

value: human keratinocytes

value: H1.5 antibody


description:
hiPS.diff_K633IPS1_p4_Smooth.Muscle_633.1772.1.1wq
SAMPLE 21

source_name: human induced pluripotent stem cells differentiated smooth muscle

value: smooth muscle


description:
Primary_SMOOTHMUSCLE_HASMC_p5_629.1759.1.1wq
SAMPLE 22

source_name: primary smooth muscle

value: primary smooth muscle


title: RNA polymerase II in IMR90 cells IP vs INPUT slide1

description: wild-type


title: H37Rv, 0 hours, Rep C

description: _Molly 7_N18A11cy 5

source_name: H37Rv treated with WR99210 for 0 hr

value: WR99210 for 0 hr


title: hiPS.diff_K633IPS1_p4_endothelial_633.1771.1.1

description:
hiPS.diff_K633IPS1_p4_Endothelial_633.1771.1.1wq
SAMPLE 20

source_name: human induced pluripotent stem cells differentiated endothelial cells

value: endothelial cells


title: H37Rv, 24 hours, Rep B

description: _Molly 6_N18A11cy 3


title: hES.diff_Hues9_p13_endothelial_628.1761.1.1

description:
hES.diff_Hues9_p13_Endothelial_628.1761.1.1wq
SAMPLE 18

source_name: human embryonic stem cells differentiated endothelial cells


title: H37Rv, 4 hours, Rep B

description: _Molly 5_N18A10cy 5


title: H3K9me2 in IMR90 cells IP vs INPUT rep1 slide1

description: wild-type

value: human fetal lung fibroblasts


title: H3K9me2 in knockdown control IMR90 cells IP vs INPUT slide1

description: knockdown control


title: SIRT1 in H1.5 knockdown IMR90 cells IP vs INPUT rep1 slide1

description: H1.5 knockdown

value: SIRT1 antibody


title: SIRT1 in H1.5 knockdown IMR90 cells IP vs INPUT rep2 slide1

description: H1.5 knockdown


title: H37Rv, 0 hours, Rep B

description: _Molly 4_N18A10cy 3


title: H3K9me2 in IMR90 cells IP vs INPUT rep2 slide1

description: wild-type


title: hES_Hues9_p49_628.1763.1.1

description:
hES_Hues9_p49_628.1763.1.1wq
SAMPLE 17

source_name: human embryonic stem cell

value: human embryonic stem cells

value: FEMALE


title: H37Rv, 24 hours, Rep A

description: _Molly 3_N18A09cy 5


description:
trans.diff_4F_HFF637.1_p5_Smooth.Muscle_630.1767.1.1wq
SAMPLE 16

source_name: transdifferentiated fibroblasts to smooth muscle

value: MALE


title: SIRT1 in IMR90 cells IP vs INPUT rep2 slide1

description: wild-type


title: H37Rv, 4 hours, Rep A

description: _Molly 2_N18A09cy 3

value: 100 uM WR99210 for 4 hrs


title: SIRT1 in knockdown control IMR90 cells IP vs INPUT slide1

description: knockdown control


title: H37Rv, 0 hours, Rep A

description: _Molly 1_N18A08cy 5


title: trans.diff_4F.mIR_HFF637.1_p4_endothelial_630.1765.1.1

description:
trans.diff_4F.mIR_HFF637.1_p4_Endothelial_630.1765.1.1wq
SAMPLE 14

source_name: transdifferentiated endothelial cells

value: transdifferentiated fibroblasts to endothelial cells


title: SIRT1 in IMR90 cells IP vs INPUT rep1 slide1

description: wild-type


title: mutant_pH 7.5-6.5_rep3

city: Guangzhou

first: Gu

last: CHEN

address: 381 Wushan Road

country: China

institute: South China University of Technology

hyb_protocol: Hybridization was conducted at 65 1C for 16 h. After incubation, the microarrays were rinsed with 2 x SSC (1 x SSC is 150 mM NaCl and 15 mM sodium citrate) at room temperature, with 2 x SSC at 60 1C for 10 min, with 0.2 x SSC, 0.1% SDS at 60 1C for 10 min, and finally with distilled water at room temperature for 2 min. Moisture was removed with an air spray prior to analysis in the array scanner

scan_protocol: Images were acquired with GMS418 array scanner (Affimetrix, USA)

data_processing: Scanned images were quantified by ImaGene V.4.2 software (BioDiscovery, USA). Spot signal intensity was determined after local background subtraction and normalization

organism: Synechocystis sp. PCC 6803

source_name: mutant at pH 7.5

label_protocol: Dye-labeled cDNA was synthesized using RNA Fluorescence Labeling Core Kit (M-MLV Version) Ver.2.0 (TAKARA Biotech, China).

growth_protocol: The original Synechocystis sp. PCC 6803 wild type strain was derived from ATCC, namely ATCC27184. Standard growth condition was at 30°C in BG11 medium containing 20 mM HEPES-NaOH (pH 7.5) under continuous illumination of 30 μmol m−2 s−1, with oscillation at 130rpm. Kanamycin at 40ug mL-1 was supplemented in BG11 medium for slr0643 mutant.

extract_protocol: Cells were broken in Mini-Bead Beater-1 (Biospec, USA) and total RNA was extracted using RNA extraction kit (DongSheng Biotech, China). RNase-free DnaseⅠ (TAKARA Biotech, China) was used to remove contaminant of genomic DNA.

treatment_protocol: For the acid stress experiments, cells of wild type and slr0643 mutant were grown at standard condition before harvesting by centrifugation at 2000g for 5min. The collected cells were then resuspended in fresh BG11 medium containing 20 mM HEPES-NaOH, pH 7.5 or pH6.5.

value: partial disrupted slr0643 mutant

tag: strain

tag: ph

source_name: mutant at pH 6.5


title: mutant_pH 7.5-6.5_rep4


title: mutant_pH 7.5-6.5_rep2


title: mutant_pH 7.5-6.5_rep1


title: H1.5 in SIRT1 knockdown IMR90 cells IP vs INPUT slide1

description: SIRT1 knockdown

source_name: human fetal lung fibroblasts


title: wt_pH 7.5-6.5_rep4

source_name: wild type at pH 7.5

value: wild type

source_name: wild type at pH 6.5


title: wt_pH 7.5-6.5_rep3


title: H1.5 in knockdown control IMR90 cells IP vs INPUT slide1

description: knockdown control


description:
trans.diff_4F.mIR_HFF637.1_p4_Smooth.Muscle_630.1766.1.1wq
SAMPLE 15

value: transdifferentiated fibroblasts to smooth muscle


title: H1.5 in H1.5 knockdown IMR90 cells IP vs INPUT slide1

description: H1.5 knockdown

value: Abcam


title: H1.5 in neural progenitor cells IP vs INPUT slide1

description: in vitro differentiated from HSF1 cells

source_name: neural progenitor cells

value: neural progenitor cells


title: H1.5 in keratinocytes IP vs INPUT slide1

description: wild-type

source_name: human keratinocytes

value: human keratinocytes

value: H1.5 antibody


title: wt_pH 7.5-6.5_rep2


title: HPL2 N2 L3 Hybridization Rep.1 array

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: FP00001 HPL2;target name: HPL-2;host: Rabbit;antigen: C-terminus;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Francesca Palladino;short description: An affinity purified rabbit polyclonal antibody to HPL-2 (C-terminus) obtained from Francesca Palladino was used for ChIP.
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip normalization standard MA2C:JL:2 protocol. ChIP-chip_normalization_standard_MA2C_v2. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means that the INPUT or IP values for any probes which have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In a single experiment, median within the sliding window defined by 2x bandwidth parameter is assigned as MA2C score at the center of each probe. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by 2x bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190

label: Cy5 dye

organism: Caenorhabditis elegans

source_name: FP00001_HPL2_N2_L3 channel_1 ChIP DNA

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (20-30 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
Worm_Whole_Genome_Amplification_for_ChIP-chip_v1. Samples were amplified using a modified Whole Genome Amplification Kit protocol (Sigma).

tag: developmental stage

value: L3 Larva

tag: genotype

tag: Sex

value: mixed Male and Hermaphrodite population

label: Cy3 dye

source_name: FP00001_HPL2_N2_L3 channel_2 input DNA


description:
hES.diff_Hues9_p4_Smooth.Muscle_628.1762.1.1wq
SAMPLE 19

source_name: human embryonic stem cells differentiated smooth muscle

value: smooth muscle


title: wt_pH 7.5-6.5_rep1


title: Primary_Fibroblast_p4_631.1768.1.1

description:
Primary_Fibroblast_p4_631.1768.1.1wq
SAMPLE 12

source_name: primary fibroblast

value: primary fibroblast


title: trans.diff_4F.MIM_HFF637.1_p5_endothelial_630.1764.1.1

description:
trans.diff_4F.MIM_HFF637.1_p5_Endothelial_630.1764.1.1wq
SAMPLE 13


title: wt-mutant_pH 6.5-rep8


title: H1.5 in neurons IP vs INPUT slide1

description: in vitro differentiated from HSF1 cells

source_name: neuron

tag: antibody

tag: cell type

value: neuron

tag: antibody manufacturer


title: wt-mutant_pH 6.5-rep7

tag: genotype/variation


title: wt-mutant_pH 6.5-rep5


title: wt-mutant_pH 6.5-rep6


title: H1.5 in IMR90 IP vs INPUT rep1 slide1

description: wild-type

value: human fetal lung fibroblasts

tag: antibody catalog #


title: H1.5 in calcium induced keratinocytes IP vs INPUT slide1


title: H1.5 in HSF1 hESC IP vs INPUT slide1

description: wild-type

source_name: human HSF1 embryonic stem cells

value: human HSF1 embryonic stem cells


title: wt-mutant_pH 6.5-rep4


title: H1.5 in hepatocytes IP vs INPUT slide1

description: wild-type

source_name: primary hepatocytes

value: primary hepatocytes


title: wt-mutant_pH 6.5-rep3


title: Scurfy-CD4-LN-Biological replicate 3

city: Charlottesville

first: Rahul

last: Sharma

state: VA

address: Room 5768, Old Medical School Building, 21 Hospital Drive

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

description: Gene expression data from Foxp3 mutant Scurfy (Sf) mice

hyb_protocol: The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.

scan_protocol: The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.

data_processing: The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.

organism: Mus musculus

source_name: FACS sorted CD4+ T cells

label_protocol: RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.

growth_protocol: Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-

extract_protocol: Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.

treatment_protocol: Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.

value: Scurfy (Sf; B6.Cg-Foxp3sf/J)

tag: sex

value: male

tag: age

value: 3-week old

tag: tissue

value: peripheral lymph nodes


title: wt-mutant_pH 6.5-rep2

value: wild type

value: partial disrupted slr0643 mutant


title: wt-mutant_pH 7.5-rep8


title: wt-mutant_pH 6.5-rep1


title: Sf.Il2-/--CD4-LN-Biological replicate 2

description: Gene expression data from IL-2 deficienct Scurfy (Sf.Il2-/-) mice

value: Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) [Sf.Il2-/-]


title: Scurfy-CD4-LN-Biological replicate 2


title: ULL-D-053

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41614.gif

hyb_protocol: 1. Prepare the reaction for each aRNA sample.   aRNA Rhx Primer(8?ug/?ul) ddH2O Total  Cy5 X ul(3 ug) 1 ul 16-(X+1) 16 ul  Cy3 Y ul(3 ug) 1 ul 16-(Y+1) 16 ul   2. Heat to 70?C for 10 min and cool on ice.   3. Prepare reaction mixture for each Cye dye.   5X First-Strand Buffer 6 ?l   50X dNTPs 0.7 ul   Cye Dyes 3 ul   0.1 M DTT 3 ul   Superscript II 1.7 ul   Total Volume 14.4 ul   4. Add 14.4 ul of reaction mixture to the 16 ul reaction tube, mix well, and incubate at 42?C for 1 hour.   5. Add another 1 ul of SSII to each sample and incubate at 42?C for 1 hour.   6. Add 15 ul of 0.1 N NaOH (with 2mM EDTA) and incubate at 65?C for 8 min.   7. Neutralize by adding 15 ul of 0.1 HCl.   8. Add 450 ?l of TE to a Microcon YM-30 Microcon. Add 15 ul of COT1 (1 mg/ml) DNA.   9. Add Cy5 and Cy3 labeled probe to the same Microcon.   10. Wash 1: Spin column for 7 min at 14,000 x g.   Wash 2. Remove flow through and add 500 ?l TE Spin for 7 min.   Wash 3. Repeat Wash 2 and concentrate probe to less than or equal to 30-35 ul.   11. Invert the Microcon into a clean 1.5 ml tube and spin for 2 min. at 14,000 RPM to recover  the probe.   12. Transfer 26.1 ul of probe to new PCR tube:   Sample 26.1ul   Poly (A) DNA 2 ul (10 ug/ul)   Yeast tRNA 1 ul (10 ug/ul)   20X SSC 5.3 ul   10% SDS 0.6 ul   Total hybridization volume 35 ul   13. Denature probe by heating for 2 min at 92?C and 42?C for 20-30 min.   14. Spin briefly and place 35 ul to on array.   15. Place a coverslip (24 X 60 mm size) on to array and add 20-30 ul of 3X SSC to each corner of the hybridization chamber.   16. Hybridize at 65?C for 14-18 hours.   17. Wash slide once with 2X SSC/ 0.05% SDS, for 2 min.   18. Transfer slide to 1X SSC for 2 min.   19. Wash slide in 50?C 0.2X SSC for 2 min, twice.   20. Spin slide in 600RPM for 5min.

scan_protocol: Scanner Model: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Reference, ampl. totRNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Reference, amplified total RNA

source_name: ULL-D-053, ampl. totRNA

label_protocol: Jeffrey Lab RNA Amplification Protocol   First strand cDNA synthesis   Mix the following contents in 0.2 ml PCR tube and spin briefly:  N microl (3 mg) Total RNA 1 microl (0.5 mg/ml) Eberwine primer* 9-N microl RNase-free H2O   * Eberwine primer = T7-oligo-dT(15) (5?-AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC TTT TTT TTT TTT TTT-3?)   Incubate in PCR machine at 70?C for 3 min, cool on ice for 2 min. Spin briefly.    Add the following contents:   4 microl 5X first strand buffer 2 microl 0.1M DTT 1 microl RNasin 2 microl 10mM dNTP mix 2 microl Superscript?II   Mix contents, spin briefly, and incubate at 42?C for 1.5 hours.   Second strand cDNA synthesis   Add the following contents to the first strand synthesis reaction:   RNase-free H2O 106 microl  10X Advantage? PCR buffer (Clontech) 15 microl  10mM dNTP mix 3 microl  RNase H (2U/microl) 1 microl  Advantage? Polymerase Mix (Clontech) 3 microl   Incubate in PCR machine at 37?C for 5 min, 94?C for 2 min, 65?C for 1 min, 75?C for 30 min. Stop reaction by adding 7.5 microl of 1M NaOH with 2mM EDTA and incubate in PCR machine at 65?C for 10 min.   ds cDNA cleanup   If necessary, transfer to a larger tube. Add 150 microl phenol:chloroform:isoamyl alcohol 25:24:1 and mix by pipetting. Transfer to phase lock gel tube and spin at ~16,000g for 5min. Transfer aqueous layer to new tube. Add 1 microl acrylamide (0.1 mg/ml), 70 microl 7.5M NH4Ac, 1 ml 100% EtOH. Spin at ~16,000g for 20 min at room temperature (not at 4?C). Wash pellet with 500 microl 75% EtOH, spin at ~16,000g for 5 min. Air dry, and suspend the pellet in 16 microl RNase-free H2O.   In vitro transcription (IVT)   Mix at room temperature (the spermidine in the 10X transcription buffer can coprecipitate the template DNA if  the reaction is assembled on ice):   16 microl cDNA  4 microl 10X reaction buffer (room temperature)  16 microl 75mM NTP mix (on ice)  4 microl T7 enzyme mix*   *Ambion T7 MEGAscript? kit  Incubate at 37?C for 5 hours (we have tried incubating for 2-6 hours and achieved the highest correlation between amplified and unamplified samples at 5 hours incubation).   aRNA cleanup (using Qiagen RNeasy? mini kit)   Add 10 microl b-mercaptoethanol to 1ml buffer RLT before use (stable for 1 month).   Transfer IVT reaction into a 1.5 ml new tube, add 60 microl RNase-free H2O, add 350 microl buffer RLT, mix by pipetting. Add 250 microl 100% EtOH, mix by pipetting. Apply sample to RNeasy? column, spin at ~12,000g for 15 sec at room temperature. Transfer column to new collection tube. Add 500 microl buffer RPE, spin at ~12,000g for 15 sec. Discard flow through, add 500 microl buffer RPE, spin at ~12,000g for 2 min. Transfer column to new collection tube, add 30 microl RNase-free H2O to the membrane, spin at ~12,000g for 1 min to elute   Measure aRNA yield at A260;

growth_protocol: A Series of 212 primary breast cancer cases were studied; 80 of these tumors were analyzed using cDNA microarrays, along with one normal breast tissue sample collected from breast reduction surgery. Patient samples were sequentially collected at Ullev?l University Hospital from 1990 to 1994 (IRB approval 350, protocol 75026). The last update of patient information was done in 2006, providing an observation time of 12 to 16 years. Patients were followed until death or emigration, and only 12 patients were lost to follow-up. The average age of the 80 cases analyzed by cDNA microarrays was 65.0 years at time of primary surgery (range 28.2 to 87.7 years), similar to the average age of 64.4 years (range 28.2 to 91.5 years) for the total series. The 80 cases were selected from the total series based only on sufficient amount of fresh frozen tissue for microarray analysis. Consequently, a slightly higher fraction of patients with larger tumor size was observed in this subcohort. A summary of the clinical and histopathological data of the patients is shown in Table 1 (see Additional file 1 for more detailed information). All patients were treated according to Norwegian national guidelines at the time of diagnosis [19]. Patients receiving adjuvant systemic therapy were given nine courses of CMF (cyclophosphamide, methotrexate, 5-fluorouracil) and/or Tamoxifen for two years. Dosage of radiation given as adjuvant treatment was dependent on indication; after breast conserving therapy the mammary gland was given 50 Gy (2 Gy ? 25). The number of samples entered into the survival analyses is smaller than 212 (full dataset) and 80 (subset with gene expression data); excluding patients with missing information or distant metastases at the time of diagnosis and primary surgery, leaves us with a maximum number of 200 (full set) and 77 (subset) patients. <br>  Primary breast carcinoma tissue was snap frozen and stored at -80?C. Frozen sections stained with hematoxylin/eosin were reviewed to confirm tumor content, and specimens in which at least 5% of the cells were carcinoma cells were included in this study. The majority of samples (80%) analyzed using microarrays had at least 40% tumor cell content.

extract_protocol: Total RNA was isolated from snap frozen tumor tissue using TRIzol? solution (Invitrogen?, Carlsbad, California, USA). The concentration of total RNA was determined using an HP 8453 spectrophotometer (Hewlett Packard) and the integrity of the RNA was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).

value: primary breast carcinoma

tag: ID


title: Sf.Il2-/--CD4-LN-Biological replicate 1


title: Sf.Il2-/--CD4-LN-Biological replicate 3


title: ULL-T-123

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41609.gif

source_name: ULL-T-123, ampl. totRNA


title: H1.5 in H1 hESC IP vs INPUT slide1

description: wild-type

source_name: human H1 embryonic stem cells

value: human H1 embryonic stem cells

tag: cell line

value: H1.5 antibody

value: Abcam


title: wt-mutant_pH 7.5-rep7

source_name: mutant at pH 7.5


title: wt-mutant_pH 7.5-rep6

source_name: wild type at pH 7.5


title: B6-CD4-LN-Biological replicate 1

description: Gene expression data from B6 mice

value: pooled peripheral lymph nodes of two mice


title: wt-mutant_pH 7.5-rep4


title: wt-mutant_pH 7.5-rep5


title: wt-mutant_pH 7.5-rep3


title: Scurfy-CD4-LN-Biological replicate 1


title: ULL-D-144

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41880.gif

source_name: ULL-D-144, ampl. totRNA


title: ULL-D-113

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41608.gif

source_name: ULL-D-113, ampl. totRNA


title: ULL-DCIS-199

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42022.gif

source_name: ULL-DCIS-199, ampl. totRNA


title: DNR-N-AO100

description:
Simple annotation: Breast, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44394.gif

scan_protocol: Scanner Model: G2505B

source_name: DNR-N-AO100, ampl. totRNA (Ambion)

value: normal breast tissue

value: DNR-N-AO100 (Ambion)


title: ULL-D-183

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42019.gif

source_name: ULL-D-183, ampl. totRNA


title: ULL-D-085

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41615.gif

source_name: ULL-D-085, ampl. totRNA


title: Wild type mechanical damaged vs Myzus persicae feeding. Replicate 3

city: Turin

first: Cinzia

middle: Margherita

last: Bertea

state: To

address: via Quarello 11/A

department: Department of Life Sciences and Systems Biology

institute: University of Turin

description: Biological replicate 3 of 4. WT mechanical damaged (control)  vs WT aphid wounded leaves (treatment). Harvested 5 h after the treatments

hyb_protocol: Hybridization buffer (Agilent Gene Expression Hybridization Kit ) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: WT rosette leaves mechanical damaged

label_protocol: 500 ng of total RNA  were separately reverse-transcribed into double-strand cDNAs by the Moloney murine leukemia virus reverse transcriptase (MMLV-RT) and amplified for 2 h at 40°C using the Agilent Quick Amp Labelling Kit, two-color (Agilent Technologies). Subsequently, cDNAs were transcribed into antisense cRNA and labeled with either Cy3-CTP or Cy5-CTP fluorescent dyes for 2 h at 40°C following the manufacturer’s protocol. Cyanine-labeled cRNAs were purified using RNeasy Minikit (Qiagen). Purity and dye incorporation were assessed with the NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Arabidopsis plants (Col-0) were grown as a single plant in plastic pots filled with soil. Growth chamber was set up at 23°C, 60% humidity, 16h in the light (120 μE m-2 s-1) and 8 in the dark for 22 days

extract_protocol: Total RNA extracted from rosette leaves using Agilent Plant RNA Isolation Mini kit including RNAse-free DNase (Qiagen) treatment

treatment_protocol: Mechanical damage: microforged glass micropipettes (to mimic aphid stinging); aphid wounding: Myzus persicae feeding

value: WT

value: day 22 (growth stage 3)

value: rosette leaves

tag: ecotype

source_name: WT rosette leaves aphid wounded


title: ULL-MU-063

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41875.gif

source_name: ULL-MU-063, ampl. totRNA


title: ULL-D-016

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41606.gif

source_name: ULL-D-016, ampl. totRNA


title: ULL-L-138

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35567.gif

source_name: ULL-L-138, ampl. totRNA


title: ULL-D-134

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41884.gif

source_name: Stratagene Reference, ampl. totRNA

source_name: ULL-D-134, ampl. totRNA


title: wt-mutant_pH 7.5-rep2

tag: strain


title: ULL-L-222

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35568.gif

source_name: ULL-L-222, ampl. totRNA


title: Wild type mechanical damaged vs Myzus persicae feeding. Replicate 4

description: Biological replicate 4 of 4. WT mechanical damaged (control)  vs WT aphid wounded leaves (treatment). Harvested 5 h after the treatments


title: wt-mutant_pH 7.5-rep1

tag: ph


title: ULL-D-135

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43902.gif

source_name: ULL-D-135, ampl. totRNA


title: ULL-D-038

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41876.gif

source_name: ULL-D-038, ampl. totRNA


title: ULL-D-143

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41611.gif

source_name: ULL-D-143, ampl. totRNA


title: ULL-D-139

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41879.gif

source_name: ULL-D-139, ampl. totRNA


title: ULL-D-044

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41613.gif

source_name: ULL-D-044, ampl. totRNA


title: ULL-D-132

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41610.gif

source_name: ULL-D-132, ampl. totRNA


title: ULL-D-048

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41877.gif

source_name: ULL-D-048, ampl. totRNA


title: ULL-TL-107

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/40128.gif

source_name: ULL-TL-107, ampl. totRNA


title: ULL-D-101

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41119.gif

source_name: ULL-D-101, ampl. totRNA


title: ULL-D-057

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41118.gif

source_name: ULL-D-057, ampl. totRNA


title: ULL-TL-055

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41117.gif

source_name: ULL-TL-055, ampl. totRNA


title: ULL-D-167

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42018.gif

source_name: ULL-D-167, ampl. totRNA


title: ULL-D-184

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42020.gif

source_name: ULL-D-184, ampl. totRNA


title: Wild type mechanical damaged vs Myzus persicae feeding. Replicate 2

description: Biological replicate 2 of 4. WT mechanical damaged (control)  vs WT aphid wounded leaves (treatment). Harvested 5 h after the treatments

source_name: WT rosette leaves mechanical damaged

source_name: WT rosette leaves aphid wounded


title: Wild type mechanical damage vs herbivore wounding Replicate 4

description: Biological replicate 4 of 4. WT mechanical damaged (control)  vs WT herbivore wounding leaves (treatment). Harvested 2 h after the treatments

extract_protocol: Total RNA extracted from rosette leaves using the Agilent Plant RNA Isolation Mini kit including RNAse-free DNase (Qiagen) treatment

treatment_protocol: Mechanical damage: made by pattern wheel mimicking herbivore; Herbivore wounding: Spodoptera littoralis feeding

source_name: WT rosette leaves herbivore wounded


title: ULL-L-136

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35569.gif

source_name: Stratagene Reference, ampl. totRNA

source_name: ULL-L-136, ampl. totRNA


title: ULL-L-190

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35570.gif

source_name: ULL-L-190, ampl. totRNA


title: ULL-D-037

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41116.gif

source_name: ULL-D-037, ampl. totRNA


title: ULL-D-188

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42021.gif

source_name: ULL-D-188, ampl. totRNA


title: PE-7

city: Amsterdam

first: Sarah

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

country: Netherlands

institute: Netherlands Institute for Neuroscience

description: Biological replicate 7 of 7 of PE cells of healthy human ciliary body tissue, same donor as for NPE-7

hyb_protocol: Labeled RNA of interest (NPE of PE) and labeled common reference sample togheter with hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner, protocol GE2-v5_95_Fec07

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files.
Further data processing was done in R (version 2.14.0 for Windows, R Development Core Team, 2009), with package Limma. We read in the raw data (RG <-read.maimage). Next we normalized within arrays (method 'loess', resulating in MA) and than we normalized the red signals between arrays to make it possible to compare the red channels (method "q", resulting in MA.s). In the matrix table, we listed these normilized red channels of each NPE and PE sample (log2). These data were used to identify the highly expressed genes of the NPE and PE (based in 90th percentile).

source_name: healthy human donor eye

label_protocol: aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier. Cy3-labeled common reference sample.

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Qiagen Benelux, Venlo, The Netherlands). Subsequently, the mRNA component was amplified with Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion Applied Biosystems Europe B.V.).

treatment_protocol: By using laser dissection microscopy, the NPE and PE cells were specifically cut out from the ciliary body cryosection (20um) mounted on PEN-membrane slides

value: ciliary body

value: PE

tag: cell sampling

value: laser dissection microscopy

source_name: Total RNA from pooled healty human RPE/choroid cells labeled with Cy3

value: RPE/chodoid [common reference]


title: Wild type mechanical damage vs herbivore wounding Replicate 3

description: Biological replicate 3 of 4. WT mechanical damaged (control)  vs WT herbivore wounding leaves (treatment). Harvested 2 h after the treatments

tag: genotype


title: PE-6

description: Biological replicate 6 of 7 of PE cells of healthy human ciliary body tissue, same donor as for NPE-6


title: ULL-D-230

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42023.gif

source_name: ULL-D-230, ampl. totRNA


title: NPE-5

description: Biological replicate 5 of 7 of NPE cells of healthy human ciliary body tissue, same donor as for PE-5

value: NPE


title: ULL-D-075

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41607.gif

source_name: ULL-D-075, ampl. totRNA


title: PE-5

description: Biological replicate 5 of 7 of PE cells of healthy human ciliary body tissue, same donor as for NPE-5


title: Wild type Magnesium chloride infiltrated  vs Pseudomonas syringae infected. Replicate 1

description: Biological replicate 1 of 4. WT Magnesium chloride infiltrated (control)  vs WT Pseudomonas syringae infected leaves (treatment). Harvested 16 h after the treatments

source_name: WT rosette leaves Magnesium chloride infiltrated

treatment_protocol: Control: made by syringe injection of MgCl2, the solution in which bacteria are resuspended; Treatment: Pseudomonas syringae pv Tomato DC3000 (Pst DC3000 AvrRPM) inoculation

source_name: WT rosette leaves Pseudomonas syringae infected


title: Wild type Magnesium chloride infiltrated  vs Pseudomonas syringae infected. Replicate 2

description: Biological replicate 2 of 4. WT Magnesium chloride infiltrated (control)  vs WT Pseudomonas syringae infected leaves (treatment). Harvested 16 h after the treatments


title: Wild type Magnesium chloride infiltrated  vs Pseudomonas syringae infected. Replicate 4

description: Biological replicate 4 of 4. WT Magnesium chloride infiltrated (control)  vs WT Pseudomonas syringae infected leaves (treatment). Harvested 16 h after the treatments


title: PE-3

description: Biological replicate 3 of 7 of PE cells of healthy human ciliary body tissue, same donor as for NPE-3

label_protocol: aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier.  Cy3-labeled common reference sample.


title: ULL-L-036

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35563.gif

source_name: ULL-L-036, ampl. totRNA


title: ULL-D-150

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41612.gif

source_name: ULL-D-150, ampl. totRNA


title: PE-4

description: Biological replicate 4 of 7 of PE cells of healthy human ciliary body tissue, same donor as for NPE-4


title: ULL-D-013

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41115.gif

source_name: ULL-D-013, ampl. totRNA


title: NPE-6

description: Biological replicate 6 of 7 of NPE cells of healthy human ciliary body tissue, same donor as for PE-6


title: ULL-D-165

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42017.gif

source_name: ULL-D-165, ampl. totRNA


title: Wild type mechanical damaged vs Myzus persicae feeding. Replicate 1

description: Biological replicate 1 of 4. WT mechanical damaged (control)  vs WT aphid wounded leaves (treatment). Harvested 5 h after the treatments

source_name: WT rosette leaves mechanical damaged

source_name: WT rosette leaves aphid wounded


title: hES_WA09_p41_87.304.7.4

description:
hES_WA09_p41_87.304.7.4wq
SAMPLE 10

source_name: human embryonic stem cells undifferentiated

tag: gender

value: FEMALE

tag: passage number

tag: loring pipeline sample id


title: PE-2

description: Biological replicate 2 of 7 of PE cells of healthy human ciliary body tissue, same donor as for NPE-2

tag: cell type


title: hES_WA09_p43_87.304.7.5

description:
hES_WA09_p43_87.304.7.5wq
SAMPLE 11

value: human embryonic stem cells undifferentiated


title: Primary_HUVEC_HUVECWF8_p4_171.252.1.1

description:
Primary_HUVEC_HUVECWF8_p4_171.252.1.1wq
SAMPLE 9

source_name: primary human umbilical vein endothelial cells

value: UNKNOWN


title: NPE-7

description: Biological replicate 7 of 7 of NPE cells of healthy human ciliary body tissue, same donor as for PE-7


title: ULL-L-062

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35564.gif

source_name: Stratagene Reference, ampl. totRNA

value: Stratagene Reference, amplified total RNA

source_name: ULL-L-062, ampl. totRNA

value: primary breast carcinoma


title: ULL-D-067

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43903.gif

source_name: ULL-D-067, ampl. totRNA


title: Wild type mechanical damage vs herbivore wounding Replicate 1

description: Biological replicate 1 of 4. WT mechanical damaged (control)  vs WT herbivore wounding leaves (treatment). Harvested 2 h after the treatments

source_name: WT rosette leaves herbivore wounded


title: Primary_HUVEC_HUVECBF2_p4_169.250.1.1

description:
Primary_HUVEC_HUVECBF2_p4_169.250.1.1wq
SAMPLE 8

value: primary human umbilical vein endothelial cells


title: hiPS.EARLY_HDF51IPS10_p6_155.490.2.1

description:
hiPS.EARLY_HDF51IPS10_p6_155.490.2.1wq
SAMPLE 7

source_name: human induced pluripotent stem cells undifferentiated


title: Wild type Magnesium chloride infiltrated  vs Pseudomonas syringae infected. Replicate 3

description: Biological replicate 3 of 4. WT Magnesium chloride infiltrated (control)  vs WT Pseudomonas syringae infected leaves (treatment). Harvested 16 h after the treatments


title: NPE-4

description: Biological replicate 4 of 7 of NPE cells of healthy human ciliary body tissue, same donor as for PE-4

source_name: healthy human donor eye

source_name: Total RNA from pooled healty human RPE/choroid cells labeled with Cy3


title: NPE-3

description: Biological replicate 3 of 7 of NPE cells of healthy human ciliary body tissue, same donor as for PE-3


title: hiPS.EARLY_HDF51IPS1_p6_153.488.2.1

description:
hiPS.EARLY_HDF51IPS1_p6_153.488.2.1wq
SAMPLE 6

value: human induced pluripotent stem cells undifferentiated


title: NPE-2

description: Biological replicate 2 of 7 of NPE cells of healthy human ciliary body tissue, same donor as for PE-2


title: hiPS_KIPS4F1_p32_249.667.1.1

description:
hiPS_KIPS4F1_p32_249.667.1.1wq
SAMPLE 4

source_name: human induced pluripotent stem cells

value: human induced pluripotent stem cells


title: Wild type mechanical damage vs herbivore wounding Replicate 2

description: Biological replicate 2 of 4. WT mechanical damaged (control)  vs WT herbivore wounding leaves (treatment). Harvested 2 h after the treatments


title: SIRT1KD_vs_control_rep2

description: biological replicate 2 of 2

hyb_protocol: Labelled cDNAs were hybridized to the Agilent Human Whole-genome array (G2534-60011) as per manufacturer's instructions.

scan_protocol: standard Agilent protocol

data_processing: Raw data was natural log (ln) transformed. All samples were median normalized and standard deviation scaled so that the medians are zero and standard deviations are one.

source_name: IMR90 fetal lung fibroblasts

label_protocol: cDNAs from H1.5KD (or SIRT1KD) and control knockdown cells were labelled with Cy5 and Cy3, respectively, using Agilent Two-Colour Low RNA Input Linear Amplification Labelling Kit according to Manufacturer’s instructions.

growth_protocol: IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO2. Growing cells with 50~70% confluence were used for further analysis.

extract_protocol: ~200 ng of total RNA were extracted from ~50 million cells by using Trizol (Invitrogen) according to manufacturer’s instructions, and further purified by RNeasy Plus Mini Kit (QiaGen). cDNA libraries were prepared by using SuperScript III First-strand Synthesis SuperMix with random haxamers (Invitrogen).

treatment_protocol: pGIPZ lentiviral shRNAmir vectors (Open Biosystems) containing shRNAs targeting human H1.5 or SIRT1 were packaged into lentivirus and infected into IMR90 cells according to manufacturer’s instruction. shRNA expressed cells were selected by puromycin for 7 days before harvesting.

tag: knockdown

value: knockdown control

value: SIRT1 knockdown by shRNA


title: NPE-1

description: Biological replicate 1 of 7 of NPE cells of healthy human ciliary body tissue, same donor as for PE-1


title: H1.5KD_vs_control_rep1

description: biological replicate 1 of 2

value: H1.5 knockdown by shRNA


title: H1.5KD_vs_control_rep2

description: biological replicate 2 of 2


title: SIRT1KD_vs_control_rep1

description: biological replicate 1 of 2


title: hiPS_KIPS4F8_p27_250.668.1.1

description:
hiPS_KIPS4F8_p27_250.668.1.1wq
SAMPLE 5


title: Hepa_rep2

description: biological replicate 2 of 2

data_processing: standard Agilent protocol

source_name: Primary Hepatocytes

label_protocol: Synthesized cDNAs were amplified and labelled with Cy3 (Perkin Elmer) by using Agilent One Colour Low RNA Input Linear Amplification Labelling Kit according to manufacturer’s instructions.

treatment_protocol: Human keratinocytes were treated with 1.5 mM of calcium chloride for 48 hours.

tag: treatment

value: Primary Hepatocytes


description:
Primary_SMOOTHMUSCLE_HSkMC268_pUNK_208.561.1.2wq
SAMPLE 3

source_name: primary human skeletal smooth muscle

value: primary human skeletal smooth muscle


title: A1555A 1

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

description: culture cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

label: biotin

source_name: 143B cybrids

label_protocol: standard Affymetrix protocol

growth_protocol: HeLa cells, DMEM+10% BGS; cybrids, DMEM+10% FBS

extract_protocol: cells pelleted, RNA extracted from pellet using Qiagen kit

tag: state

value: basal


title: A1555A 2

description: culture cells


description:
Primary_SMOOTHMUSCLE_HBVSMC266_pUNK_203.556.1.2wq
SAMPLE 1

source_name: primary human brain vascular smooth muscle


title: ULL-D-071

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43895.gif

source_name: ULL-D-071, ampl. totRNA


title: Hepa_rep1

description: biological replicate 1 of 2


description:
Primary_SMOOTHMUSCLE_HESMC267_pUNK_207.560.1.2wq
SAMPLE 2

source_name: primary human human esophageal smooth muscle

value: primary human esophageal smooth muscle


title: posterior Fp_rep3

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

data_processing: Prior to normalization probes not detected (Illumina detection p-value <0.01) on any sample within the experiment were removed from the analysis. The remaining data was quantile normalized in R with the LIMMA package.

source_name: Immortalized E10.5 posterior limb cell line

label_protocol: Amplified, biotinylated cRNA was synthesized using Illumina® TotalPrep Amplification Kit (Ambion, Austin, Texas)

extract_protocol: Total RNA was extracted from immortalized murine E10.5  anterior and posterior cell lines using Trizol (Invitrogen) followed by acid phenol:chloroform:isopropyl alcohol extraction and treatment with DNaseI (Ambion) and cleanup using an RNeasy Mini Kit (Qiagen)

value: Posterior limb derived mesenchyme cells that express a temperature sensitive SV40 T antigen

value: immortalized murine E10.5 posterior limb cell line


title: ULL-D-096

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43900.gif

source_name: ULL-D-096, ampl. totRNA


title: ULL-D-065

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43894.gif

source_name: Stratagene Reference, ampl. totRNA

source_name: ULL-D-065, ampl. totRNA


title: hiPS.diff_K633IPS1_p4_Smooth.Muscle_633.1772.1.2

description: SAMPLE 15

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HD Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using IScan using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2010.3

label: Cy5 and Cy3

source_name: differentiated smooth muscle human induced pluripotent stem cell

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions


title: ULL-D-099

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43901.gif

source_name: ULL-D-099, ampl. totRNA


title: HeLa + mtTFB1[G65A] 2

description: culture cells

source_name: HeLa cells

value: HeLa

tag: overexpression


title: HKCa_rep2

description: biological replicate 2 of 2

source_name: Keratinocytes

value: CaCl2 treated

value: Keratinocytes


title: posterior Fp_rep2


title: HeLa + mtTFB1[G65A] 1

description: culture cells


title: posterior Fp_rep1


title: PE-1

description: Biological replicate 1 of 7 of PE cells of healthy human ciliary body tissue, same donor as for NPE-1

source_name: healthy human donor eye

tag: tissue

value: ciliary body

value: PE

value: laser dissection microscopy

source_name: Total RNA from pooled healty human RPE/choroid cells labeled with Cy3

value: RPE/chodoid [common reference]


title: ULL-MU-079

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43897.gif

tag: reference

value: Stratagene Reference, amplified total RNA

source_name: ULL-MU-079, ampl. totRNA

value: primary breast carcinoma


title: anterior Fa_rep3

source_name: Immortalized E10.5 anterior limb cell line

value: Anterior limb derived mesenchyme cells that express a temperature sensitive SV40 T antigen

value: immortalized murine E10.5 anterior limb cell line


title: A1555G 2

description: culture cells

value: hyper-methylation


title: IMR90_rep1

description: biological replicate 1 of 2

source_name: IMR90 fetal lung fibroblasts

value: IMR90 fetal lung fibroblasts


title: IMR90_rep2

description: biological replicate 2 of 2


title: HKCa_rep1

description: biological replicate 1 of 2


title: hiPS_K633IPS1_p44_633.1773.1.2

description: SAMPLE 8

source_name: Keratinocyte-derived human induced pluripotent cells

value: UNKNOWN


title: A1555G 1

description: culture cells

source_name: 143B cybrids


title: H1_rep2

description: biological replicate 2 of 2

source_name: H1 embryonic stem cells

value: H1 embryonic stem cells


title: HeLa + mtTFB1 2

description: culture cells


title: ULL-D-074

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43896.gif

source_name: ULL-D-074, ampl. totRNA

tag: ID


title: HeLa + mtTFB1 1

description: culture cells

tag: cell line


title: anterior Fa_rep1


title: PMBL3

status: Public on Sep 17 2012

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description: 1000-2000 microdissected tumor cells

hyb_protocol: Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Most bioinformatics analyses were performed using GeneSpring 7.3.1 software (Agilent Technologies) with GC-RMA preprocessing of the raw expression data (CEL files). Further statistical analysis was done with the computing environment R. Additional software packages (affy, geneplotter) were taken from the Bioconductor project.

label_protocol: The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).

growth_protocol:
PRIMARY TUMOR SAMPLES: Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
CELL LINE SAMPLES: In vitro growing cell cultures were cooled at 4°C and 500-1000 living cells were immediately subjected to fluorescence-activated cell sorting directly into Purescript lysis buffer (Gentra).

extract_protocol: The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.

tag: sample origin

value: Primary mediastinal B-cell lymphoma case 3

value: primary lymphoma cells

tag: isolated by

value: laser-microdissection from a patient's biopsy involved by primary mediastinal B-cell lymphoma


title: H1_rep1

description: biological replicate 1 of 2


title: ULL-D-083

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43899.gif

source_name: ULL-D-083, ampl. totRNA


title: PMBL5

description: 1000-2000 microdissected tumor cells

value: Primary mediastinal B-cell lymphoma case 5


title: anterior Fa_rep2


title: trans.diff_4F_HFF637.1_p5_Smooth.Muscle_630.1767.1.2

description: SAMPLE 7

source_name: transdifferentiated fibroblast to Smooth Muscle with Yamanaka Transcription Factors (OSKM)

value: MALE


title: PMBL4

description: 1000-2000 microdissected tumor cells

value: Primary mediastinal B-cell lymphoma case 4


title: PMBL1

description: 1000-2000 microdissected tumor cells

value: Primary mediastinal B-cell lymphoma case 1


title: PMBL2

description: 1000-2000 microdissected tumor cells

value: Primary mediastinal B-cell lymphoma case 2


title: trans.diff_4F.mIR_HFF637.1_p4_Smooth.Muscle_630.1766.1.2

description: SAMPLE 6

source_name: transdifferentiated fibroblast to Smooth Muscle with Yamanaka Transcription Factors (OSKM) and miR302-368


title: trans.diff_4F.mIR_HFF637.1_p4_endothelial_630.1765.1.2

description: SAMPLE 5

source_name: transdifferentiated fibroblast to endothelia with Yamanaka Transcription Factors (OSKM) and miR302-367


title: HDLM2

description: 500-1000 FACS-sorted living cells

source_name: classical Hodgkin lymphoma (cHL) cell line sample

value: Cultured classical Hodgkin lymphoma (cHL) cells

value: fluorescence-activated cell sorting


title: KMH2

description: 500-1000 FACS-sorted living cells


title: L428

description: 500-1000 FACS-sorted living cells


title: L1236

description: 500-1000 FACS-sorted living cells


title: trans.diff_4F.MIM_HFF637.1_p5_endothelial_630.1764.1.2

description: SAMPLE 4

source_name: Transdifferentiated fibroblast to endothelia with Yamanaka transcription factors (OSKM) and MIM media

value: transdifferentiated fibroblast to endothelia with Yamanaka transcription factors (OSKM) and MIM media


title: embryo MC-RR rep4

city: Wuhan

first: Yanyan

last: Zhao

address: Donghu South Road 7

institute: Institute of Hydrobiology

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

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

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

organism: Danio rerio

source_name: MC-RR treated embryos, 72hpf

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: To extract total RNA by miRNeasy Mini kit(Qiagen)

value: embryo

tag: age

value: 72 hpf

value: MC-RR


title: embryo MC-RR rep3


title: Vector, biological rep 1

city: Nishigo

first: Mayumi

last: Sugimoto

state: Fukushima

address: Odakurahara 1 Odakura

country: Japan

institute: National Livestock Breeding Center

description: Gene expression data from HeLa cells transfected with an empty vector control.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with R using RMA as normalization method.

source_name: Vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: HeLa cells were grown at at 37C in an atmosphere of 5 % CO2 and 95 % air.

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

treatment_protocol: HeLa cells were transfected with Lipofectamine RNAiMAX (Invitrogen) or Lipofectamine 2000 (Invitrogen).

value: HeLa

tag: genotype/variation


title: SLC44A5, biological rep 2

description: Gene expression data from HeLa cells transfected with bovine SLC44A5 expression plasmid.


title: Vector, biological rep 2

value: transfected with an empty vector control


title: embryo control rep2

source_name: saline solution treated embryos, 72hpf

value: control


title: Primary_Fibroblast_p5_608.1708.2.1

description: SAMPLE 2

source_name: Primary fibroblast

value: primary fibroblast


title: embryo MC-RR rep2


title: SLC44A5, biological rep 1

value: transfected with bovine SLC44A5 expression plasmid


title: embryo control rep4


title: embryo MC-RR rep1


title: siSLC44A5, biological rep 3

description: Gene expression data from HeLa cells transfected with siRNA against SLC44A5.

value: transfected with siRNA against SLC44A5


title: siSLC44A5, biological rep 2


title: Negative control, biological rep 3

description: Gene expression data from HeLa cells transfected with negative control.

source_name: Negative control

value: transfected with negative control


title: SLC44A5, biological rep 3


title: Primary_Fibroblast_p14_621.1709.2.1

description: SAMPLE 3

value: MALE


title: Primary_Fibroblast_p4_631.1768.1.2

description: SAMPLE 1


title: Vector, biological rep 3


title: embryo control rep3


title: Negative control, biological rep 2


title: Negative control, biological rep 1


title: embryo control rep1


title: Flank wound at D7, biological rep1

city: Gainesville

first: James

middle: R

last: Monaghan

state: FL

address: 2033 Mowry Road

department: Biology

institute: University of Florida

description: Gene expression data from injured flank wound

hyb_protocol: Following fragmentation, cRNA were hybridized for on 32 GeneChip Axolotl Microarrays (AMBY_002a520748F) in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner.

data_processing: Microarray data was analyzed in the software system R using the Bioconductor package and oneChannelGUI. Microarray data was preprocessed and normalized using RMA and a linear model testing the effect of time for each morph type was fit for each gene across all 32 GeneChips using limma.

organism: Ambystoma mexicanum

source_name: Flank wound at 7 days post injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Affymetrix GeneChip Expression Analysis Manual)

growth_protocol: Animals were housed individually at 21-23˚C in 40% Holtfreter’s Solution.

extract_protocol: RNA was isolated using Trizol Reagent followed by Qiagen RNeasy Clean-up columns

treatment_protocol: Sterile 4mm biopsy punches were used to create flank wounds on the side of the animal. Forelimbs were amputated just proximal to the elbow and the humerus trimmed to make the amputation plane flush. Denervation was performed by transecting the brachial nerves entering the limb.

value: Flank epidermis

tag: animal type

value: aquatic axolotl

tag: time

value: 7 days post injury


title: Innervated limb at D7, biological rep4

description: Gene expression data from amputated innervated limb

source_name: Innervated limb at 7 days post injury

value: Innervated limb epidermis


title: Flank wound at D7, biological rep3


title: siSLC44A5, biological rep 1


title: Innervated limb at D7, biological rep2


title: Flank wound at D7, biological rep4


title: Denervated limb at D7, biological rep2

description: Gene expression data from amputated denervated limb

source_name: Denervated limb at 7 days post injury

value: Denervated limb epidermis


title: Flank wound at D7, biological rep2


title: Innervated limb at D7, biological rep1


title: Denervated limb at D7, biological rep1


title: Denervated limb at D7, biological rep3


title: Innervated limb at D3, biological rep3

source_name: Innervated limb at 3 days post injury

value: 3 days post injury


title: Flank wound at D3, biological rep2

source_name: Flank wound at 3 days post injury


title: Flank wound at D3, biological rep1


title: Denervated limb at D3, biological rep2

source_name: Denervated limb at 3 days post injury


title: Denervated limb at D3, biological rep3


title: Innervated limb at D1, biological rep4

source_name: Innervated limb at 1 day post injury

value: 1 day post injury


title: Denervated limb at D3, biological rep4


title: Denervated limb at D3, biological rep1


title: Innervated limb at D3, biological rep1


title: Denervated limb at D7, biological rep4


title: Innervated limb at D3, biological rep2


title: Flank wound at D1, biological rep3

source_name: Flank wound at 1 day post injury


title: Flank wound at D3, biological rep4


title: Flank wound at D1, biological rep1


title: Innervated limb at D3, biological rep4


title: Flank wound at D3, biological rep3


title: Flank wound at D1, biological rep4


title: Flank wound at D1, biological rep2


title: Denervated limb at D1, biological rep3

source_name: Denervated limb at 1 day post injury


title: Innervated limb at D1, biological rep2


title: Innervated limb at D1, biological rep1


title: Innervated limb at D1, biological rep3


title: Denervated limb at D1, biological rep4


title: Denervated limb at D1, biological rep1


title: Innervated limb at D0, biological rep3

source_name: Innervated limb at time 0

value: day 0


title: Innervated limb at D0, biological rep4


title: CD4T_Cxcr5+Bcl6-_1

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

hyb_protocol: The samples were hybridized according to Affymetrix protocol. The chips were washed and stained using fluidics protocol FS450_0007.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 7G Scanner.

data_processing: Images were processed into CEL files with the Affymetrix GCOS v1.1 software. Raw intensity data was RMA normalized using Expression Console from Affymetrix.

source_name: Peripheral CD4+ T cells from lymph nodes

label_protocol: The samples were fragmented and biotin labeled using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) according to the manufacture protocol.

treatment_protocol: Cxcr5+Bcl6-RFP+, Cxcr5-Bcl6-RFP-, or Cxcr5+Bcl6-RFP- CD4+ CD44+T cells were isolated using Flow Cytometry Cell Sorter from draining lymph node tissues of Bcl6_RFP reporter mice (8-10 weeks, male) immunized with KLH/CFA

value: Bcl6_RFP reporter mice

value: 8-10 weeks

tag: gender

value: male


title: Flank wound at D0, biological rep3

source_name: Flank wound at time 0


title: Denervated limb at D1, biological rep2


title: CD4T_Cxcr5+Bcl6-_2


title: Innervated limb at D0, biological rep1


title: amiloride 0.5mM-rep4

city: kaohsiung

first: wen-hsin

last: chang

address: 100,Shih-Chuan 1st Road,Kaohsiung

country: Taiwan

institute: Kaohsiung Medical University

description:
exon-970506-A4
Gene expression data from K562 cells

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were normalized and analyzed for gene expression using Partek software.
The GeneChip Human Exon 1.0 ST microarray system has only perfect match probes, but no mismatch (MM) probes available to perform data normalization. Instead of the MM probes, we inferred and removed the existing systematic biases based on the observed intensities of the background probes (BGP) that were pre-designed by Affymetrix.
probe group file: HuEx-1_0-st-v2.r2.pgf

source_name: K562 leukemic cells, amiloride 0.5mM-rep4

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

extract_protocol: We used the RNeasy Mini kit (Qiagen Inc., USA) to isolate total RNA according to the manufacturer’s instructions and verified the RNA quality by analysis in 2100 Bioanalyzer (Agilent).

treatment_protocol: amiloride 0.5mM

value: K562 leukemia cell line

tag: agent

value: amiloride


title: Flank wound at D0, biological rep2


title: Innervated limb at D0, biological rep2


title: CD4T_Cxcr5+Bcl6+_2

tag: cell type


title: Flank wound at D0, biological rep1


title: CD4T_Cxcr5+Bcl6+_1


title: amiloride 0.5mM-rep3

description:
exon-970506-A3
Gene expression data from K562 cells

source_name: K562 leukemic cells, amiloride 0.5mM-rep3


title: CD4T_Cxcr5-Bcl6-_2


title: control-rep2

description:
exon-970506-C2
Gene expression data from K562 cells

source_name: K562 leukemic cells, control-rep2

value: control


title: Flank wound at D0, biological rep4


title: amiloride 0.5mM-rep2

description:
exon-970506-A2
Gene expression data from K562 cells

source_name: K562 leukemic cells, amiloride 0.5mM-rep2


title: control-rep3

description:
exon-970506-C3
Gene expression data from K562 cells

source_name: K562 leukemic cells, control-rep3


title: amiloride 0.5mM-rep1

description:
exon-970506-A1
Gene expression data from K562 cells

source_name: K562 leukemic cells, amiloride 0.5mM-rep1


title: CD4T_Cxcr5-Bcl6-_1


title: control-rep4

description:
exon-970506-C4
Gene expression data from K562 cells

source_name: K562 leukemic cells, control-rep4


title: control-rep1

description:
exon-970506-C1
Gene expression data from K562 cells

source_name: K562 leukemic cells, control-rep1


title: adjacent normal tissue 6

status: Public on Sep 16 2012

city: Zhoushan

first: lina

last: ma

address: Renmin North Road No.238

institute: Zhoushan Hospital

description:
SAMPLE 12
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalisation with Illumina Genomestudio software

source_name: lung

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

extract_protocol: RNA was extracted with Trizol reagent, followed by QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with 1% agrose electrophoresis   .

tag: disease state

value: NSCLC

tag: nsclc type

value: adenocarcinoma

value: adjacent normal

tag: tnm


title: adjacent normal tissue 4

description:
SAMPLE 8
replicate 1


title: NSCLC 5

description:
SAMPLE 9
replicate 1

value: cancer


title: NSCLC 6

description:
SAMPLE 11
replicate 1


title: adjacent normal tissue 3

description:
SAMPLE 6
replicate 1

value: squamous


title: NSCLC 2

description:
SAMPLE 3
replicate 1


title: adjacent normal tissue 5

description:
SAMPLE 10
replicate 1


title: adjacent normal tissue 2

description:
SAMPLE 4
replicate 1


title: NSCLC 4

description:
SAMPLE 7
replicate 1


title: NSCLC 3

description:
SAMPLE 5
replicate 1


title: Human PBMC total RNA in treatment c9 [QPCR]

status: Public on Sep 15 2012

city: Kuopio

first: Otto

middle: Taavetti

last: Mykkänen

address: Yliopistonranta 1

department: Public Health and Clinical Nutrition

country: Finland

institute: University of Eastern Finland

data_processing:
Raw Ct values (non-normalized data) were quantified with a standard curve on each plate per transcript and the quantities were corrected by a calibrator (0.3 ng/µL cDNA). The last 12 columns of the non_normalized data contains calibration control sample data from plate specific calibrator used with the data normalization process.
Data was normalized to the endogenous control, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene to gain an average of the total RNA equivalents per sample and then log-transformed (ln). The equation in short from the amount of mRNA (ng) quantified: (target (ng)/calibrator(ng)) /(GADPH(ng) /calibrator(ng)) = relative expression to GADPH

label: FAM

source_name: Human PBMCs

label_protocol: FAM™ with ABI Prism 7500 SDS software (TaqMan Gene Expression Assays; Foster City, CA, USA)

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). The RNA concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA was reverse transcribed into cDNA for microarrays and quantitative PCR (QPCR) using the High-Capacity cDNA Archive Kit (Applied Biosystems, Foster City, CA).

treatment_protocol: PBMCs were available from all study participants at 0 and 8 weeks. The total RNA for microarrays were selected from 3 subject PBMCs isolated from overnight fasting blood samples collected in a BD Vacutainer CPT Cell Preparation Tube with Sodium Citrate (BD, Franklin Lakes, NJ) according to the manufacturer’s instructions.

value: female

tag: age (years)

tag: time point

value: 8 wk

tag: group

tag: acute inflammation during the interventio (plasma hscrp >10mg/mlyes/no)

value: no


title: Human PBMC total RNA in treatment c12 [QPCR]


title: Innervated limb at D7, biological rep3

source_name: Innervated limb at 7 days post injury

tag: tissue

value: Innervated limb epidermis

value: aquatic axolotl

value: 7 days post injury


title: Human PBMC total RNA in treatment c11 [QPCR]


title: Human PBMC total RNA in treatment c7 [QPCR]


title: Human PBMC total RNA in treatment c10 [QPCR]

value: yes


title: Human PBMC total RNA in treatment c6 [QPCR]


title: adjacent normal tissue 1

description:
SAMPLE 2
replicate 1


title: Human PBMC total RNA in treatment c5 [QPCR]


title: Human PBMC total RNA in treatment c2 [QPCR]


title: Human PBMC total RNA in baseline c12 [QPCR]

value: 0 wk


title: Human PBMC total RNA in treatment c1 [QPCR]


title: Human PBMC total RNA in baseline c10 [QPCR]


title: Human PBMC total RNA in baseline c9 [QPCR]


title: Human PBMC total RNA in baseline c11 [QPCR]


title: Human PBMC total RNA in treatment c4 [QPCR]

value: male


title: Human PBMC total RNA in treatment c8 [QPCR]


title: NSCLC 1

description:
SAMPLE 1
replicate 1


title: Human PBMC total RNA in baseline c8 [QPCR]


title: Human PBMC total RNA in treatment c3 [QPCR]


title: Cont_Forager_1

city: Baltimore

first: Brian

last: Herb

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: JHU

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.

organism: Apis mellifera

source_name: Input fraction from Cont_Forager_1

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using Epicentre Mastepure DNA purification kit according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

value: Pooled Brains of adult continuous foragers

source_name: Methyl-depleted fraction from Cont_Forager_1


title: Human PBMC total RNA in baseline c7 [QPCR]


title: Human PBMC total RNA in baseline c6 [QPCR]


title: Human PBMC total RNA in baseline c5 [QPCR]


title: Human PBMC total RNA in baseline c4 [QPCR]


title: Human PBMC total RNA in baseline c2 [QPCR]


title: Human PBMC total RNA in baseline c3 [QPCR]


title: Rev_Nurse_2

source_name: Input fraction from Rev_Nurse_2

value: Pooled Brains of adult reverted nurses

source_name: Methyl-depleted fraction from Rev_Nurse_2


title: Human PBMC total RNA in baseline c1 [QPCR]

value: control


title: Human PBMC total RNA in treatment s15 [QPCR]

value: intervention (test)


title: Human PBMC total RNA in treatment s14 [QPCR]


title: Cont_Forager_2

source_name: Input fraction from Cont_Forager_2

source_name: Methyl-depleted fraction from Cont_Forager_2


title: Worker_5

source_name: Input fraction from Worker_5

value: Pooled Brains of newly emerged workers

source_name: Methyl-depleted fraction from Worker_5


title: Human PBMC total RNA in treatment s12 [QPCR]


title: Human PBMC total RNA in treatment s13 [QPCR]


title: Rev_Nurse_1

source_name: Input fraction from Rev_Nurse_1

source_name: Methyl-depleted fraction from Rev_Nurse_1


title: Human PBMC total RNA in treatment s9 [QPCR]


title: Control transfected sample 3

city: Iowa City

first: Christopher

last: Adams

state: IA

address: 540G EMRB, 200 Hawkins Drive

institute: University of Iowa

description: skeletal muscle RNA

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Mouse Exon 1.0 ST arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.  Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
Data were collected using the using the GeneChip operating software (GCOS) v1.4. The data were RMA normalized
probe group file: MoEx-1_0.st-v1.r2.pgf
meta-probeset file: MoEx-1_0.st-v1.r2.dt1.mm9.core.mps

source_name: tibialis anterior

label_protocol: 50 ng total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN.  Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: ATF4 mKO TA muscles were transfected with either pcDNA3 (left TA) or pCMV-FLAG-Gadd45a (right TA) and harvested 7 days later

value: tibialis anterior

tag: treatment

value: transfected with pcDNA3 (left TA)

value: 8 weeks

tag: Sex


title: Gadd45a sample 4

description: skeletal muscle RNA

value: transfected with pCMV-FLAG-Gadd45a (right TA)

tag: age


title: Gadd45a sample 2

description: skeletal muscle RNA


title: Control transfected sample 4

description: skeletal muscle RNA


title: Gadd45a sample 3

description: skeletal muscle RNA


title: Control transfected sample 2

description: skeletal muscle RNA


title: Gadd45a sample 1

description: skeletal muscle RNA


title: Control transfected sample 1

description: skeletal muscle RNA


title: Human PBMC total RNA in treatment s8 [QPCR]

value: 8 wk


title: Human PBMC total RNA in treatment s11 [QPCR]

value: no


title: Denervated sample 1

description: skeletal muscle RNA

treatment_protocol: Left sciatic nerves of C57BL/6 mice were transected and then bilateral tibialis anterior muscles were harvested 7 days later.

tag: strain

value: denervated


title: Cont_Nurse_3

source_name: Input fraction from Cont_Nurse_3

value: Pooled Brains of adult continuous nurses

source_name: Methyl-depleted fraction from Cont_Nurse_3


title: Human PBMC total RNA in treatment s2 [QPCR]

value: female


title: Denervated sample 2

description: skeletal muscle RNA


title: Denervated sample 4

description: skeletal muscle RNA


title: Human PBMC total RNA in treatment s7 [QPCR]


title: Human PBMC total RNA in treatment s10 [QPCR]


title: Human PBMC total RNA in treatment s6 [QPCR]


title: Human PBMC total RNA in treatment s5 [QPCR]


title: Queen_4

source_name: Input fraction from Queen_4

value: Pooled Brains of newly emerged queens

source_name: Methyl-depleted fraction from Queen_4


title: Worker_2

source_name: Input fraction from Worker_2

source_name: Methyl-depleted fraction from Worker_2


title: Innervated sample 3

description: skeletal muscle RNA

value: innervated


title: Cont_Nurse_1

source_name: Input fraction from Cont_Nurse_1

source_name: Methyl-depleted fraction from Cont_Nurse_1


title: Innervated sample 2

description: skeletal muscle RNA

value: male


title: Cont_Nurse_2

source_name: Input fraction from Cont_Nurse_2

source_name: Methyl-depleted fraction from Cont_Nurse_2


title: Human PBMC total RNA in treatment s1 [QPCR]

source_name: Human PBMCs


title: Human PBMC total RNA in baseline s15 [QPCR]

value: 0 wk


title: Human PBMC total RNA in baseline s14 [QPCR]


title: Innervated sample 4

description: skeletal muscle RNA


title: Worker_1

source_name: Input fraction from Worker_1

source_name: Methyl-depleted fraction from Worker_1


title: Human PBMC total RNA in baseline s13 [QPCR]

value: yes


title: Queen_2

source_name: Input fraction from Queen_2

source_name: Methyl-depleted fraction from Queen_2


title: Cont_Forager_3

source_name: Input fraction from Cont_Forager_3

value: Pooled Brains of adult continuous foragers

source_name: Methyl-depleted fraction from Cont_Forager_3


title: Innervated sample 1

description: skeletal muscle RNA

source_name: tibialis anterior


title: ATF4 sample 3

description: C2C12 Myotube RNA

source_name: C2C12 myotube

treatment_protocol: C2C12 myotubes were infected with adenovirus co-expressing either eGFP + ATF4∆bZIP-FLAG or eGFP + ATF4-FLAG.  Myotubes were harvested 48h later.

value: C2C12 myotube

value: eGFP + ATF4-FLAG


title: Human PBMC total RNA in baseline s11 [QPCR]

value: intervention (test)


title: Worker_3

source_name: Input fraction from Worker_3

value: Pooled Brains of newly emerged workers

source_name: Methyl-depleted fraction from Worker_3


title: Human PBMC total RNA in treatment s3 [QPCR]


title: Human PBMC total RNA in baseline s10 [QPCR]


title: Control sample 3

description: C2C12 Myotube RNA

value: eGFP + ATF4deltabZIP-FLAG


title: Worker_4

source_name: Input fraction from Worker_4

source_name: Methyl-depleted fraction from Worker_4


title: Control sample 2

description: C2C12 Myotube RNA


title: ATF4 sample 1

description: C2C12 Myotube RNA


title: Rev_Nurse_3

source_name: Input fraction from Rev_Nurse_3

value: Pooled Brains of adult reverted nurses

source_name: Methyl-depleted fraction from Rev_Nurse_3


title: Queen_1

source_name: Input fraction from Queen_1

source_name: Methyl-depleted fraction from Queen_1


title: Human PBMC total RNA in baseline s9 [QPCR]

source_name: Human PBMCs


title: Human PBMC total RNA in baseline s8 [QPCR]


title: Human PBMC total RNA in baseline s7 [QPCR]


title: Queen_5

source_name: Input fraction from Queen_5

source_name: Methyl-depleted fraction from Queen_5


title: Control sample 1

description: C2C12 Myotube RNA


title: Human PBMC total RNA in baseline s6 [QPCR]


title: Human PBMC total RNA in baseline s4 [QPCR]


title: Queen_3

source_name: Input fraction from Queen_3

source_name: Methyl-depleted fraction from Queen_3


title: ATF4 mKO mouse 2

description: skeletal muscle RNA

treatment_protocol: ATF4 mKO and littermate controls were fasted for 24 hours and then tibialis anterior muscles were harvested.

value: tibialis anterior

tag: genotype/variation

value: ATF4 mKO

value: 8 weeks


title: Human PBMC total RNA in baseline s3 [QPCR]

value: no


title: Human PBMC total RNA in baseline s2 [QPCR]

value: female


title: Control mouse 3

description: skeletal muscle RNA

value: littermate controls


title: ATF4 mKO mouse 1

description: skeletal muscle RNA


title: Denervated sample 3

description: skeletal muscle RNA

value: denervated


title: ATF4 sample 2

description: C2C12 Myotube RNA


title: Human PBMC total RNA in baseline s1 [QPCR]


title: Control mouse 1

description: skeletal muscle RNA

value: male


title: Human PBMC total RNA in baseline s5 [QPCR]

value: 0 wk


title: Control mouse 2

description: skeletal muscle RNA


title: DIO-SS-7

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Gene expression data from diet induced obese mice exposed to sidestream smoke (SS)

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep7

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Control, i.e., nonobese or regular weight (RW) and diet-induced obese (DIO) male C57BL/6 mice at 13 weeks of age were purchased from the Jackson Laboratories (Bar Harbor, ME).  For this study, RW mice are defined as those mice fed a regular diet consisting of pelleted PMI® 5002 Certified Rodent Diet (PMI 5002 Rodent Diet®, Richmond, IN; ~5kcal% fat) throughout the study.  DIO mice were fed a high calorie/high fat diet consisting of pelleted D12492 Rodent Diet (Research Diets Inc., New Brunswick, NJ; 60kal% fat) throughout the study starting at six weeks of age for a total of nine weeks prior to the start of the 4-day LPS exposure study.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Groups (N=8 biological replicates) of RW and DIO C57BL/6 mice (15-weeks old at start of exposures) were exposed to either filtered air (sham controls, SC), mainstream (MS) or sidestream (SS) cigarette smoke by nose-only inhalation exposure for 5 hr/day for a total of eight exposures over two weeks as follows: 5 consecutive days of exposure, followed by 2 days with no exposure, then three days of exposure, with necropsies occurring the day following the last exposure.

value: lung

tag: body weight

value: obese

value: Sidestream smoke (SS)


title: DIO-SS-8

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep8


title: DIO-SS-6

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep6


title: DIO-SS-5

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep5


title: DIO-SS-4

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep4


title: DIO-SS-1

source_name: Diet induced obese mice exposed to sidestream smoke (SS), biological rep1


title: Human PBMC total RNA in treatment s4 [QPCR]

tag: gender

value: 8 wk

value: yes


title: ATF4 mKO mouse 3

description: skeletal muscle RNA

source_name: tibialis anterior