title: 568R1

description: copy number profile

source_name: Human glioblastoma tissue 568R1

value: female


title: 437I

status: Public on Oct 06 2015

type: genomic

city: Seoul

first: Jinkuk

last: Kim

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: copy number profile

hyb_protocol: Conducted according  to manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  All 36 FE files were loaded simultaneously into Agilent Genomic Workbench v7 for normalization (using default parameters).

molecule: genomic DNA

organism: Homo sapiens

source_name: Human glioblastoma tissue 437I

growth_protocol: Not applicable.

extract_protocol: gDNA extraction was done using DNeasy kit (QIAgen), according to manufacturer's instructions.

tag: gender

tag: age

tag: tumor histology

value: GBM

tag: treatment

source_name: Random normal human tissue

value: male


title: Whole larvae_RAdiet_fish7

type: RNA

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: Arrays were prehybridized at 42°C in Nexterion Oligo Prehyb Buffer (Schott Nexterion) for at least 2 hours. Arrays were washed at room temperature for with 0.1% SDS for 5 minutes, followed by 3 5-minute washes with water. Slides were dried by spinning them for 5 minutes at 200x g and kept at 42°C. LifterSlips were prepared by washing them sequentially with water, water, 70% ethanol and 100% ethanol and drying them using compressed air.   For each array, 3 μg Cy5-labeled aRNA from an individual larva was combined with 3 μg Cy3-labeled aRNA from the common reference. Labeled aRNA was then fragmented using Ambion Fragmentation Reagents (Ambion). Fragmented aRNA and 2 μL of LNA blocker (Genisphere, Hatfield, Pennsylvania, USA) were combined in formamide-based hybridization buffer (Genisphere), applied to the array and hybridized overnight (∼16 h) at 42°C.  After hybridization, arrays were washed at room temperature for 15 minutes with 2xSSC/0.2% SDS which was pre-warmed at 42°C. Next slides were washed  at room temperature for 15 minutes with 2xSSC, followed by 2 15-minute washes with 0.2xSSC. Slides were dried by spinning them for 5 minutes at 200x g.

scan_protocol: Arrays were scanned at a resolution of 5 μm using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer).

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 3 * SD) for each channel on each array.  Logratios of duplicate spots were averaged.

molecule: total RNA

organism: Gadus morhua

source_name: Whole larvae, RA diet, individual fish

label_protocol: Individual DNAse-treated, column-purified total RNA samples from 8 fish per group (9 mm RA, 9 mm RA-PH and 9 mm RA-Zoo larvae) were used for microarray analysis using the Atlantic cod 20K oligonucleotide microarray platform (Booman et al. 2011) and a common reference experimental design.  On each array, RNA from an individual fish was hybridized together with a common reference RNA.  For each larva, 1 μg of RNA was amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion/Life Technologies) according to the manufacturer's protocol.  To generate the common reference pool, 10 μg of aRNA from each of the twenty-four 9 mm individuals was pooled.  Twenty μg of each individual sample aRNA was labeled with Cy5, and 20 μg aliquots of the common reference aRNA were labeled with Cy3 (CyDye Post-Labeling Reactive Dye Packs, GE Healthcare Life Sciences) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion/Life Technologies) according to the manufacturer's protocol.

growth_protocol: Eggs for this study were collected from communally spawning broodstock, disinfected with ozone and distributed into two 0.3 m^3 cone-shaped incubators with flow-through seawater (32 ppt) at 6.0-7.0°C until 100% hatch. The eggs had an average diameter of 1.6 mm, a 95% fertilization rate and 91% symmetrical cleavage. At 100% hatch (93.4 degree days) the larvae were transferred to 16, 400 L flow-through tanks at a density of 50 larvae L^-1. These tanks were then divided randomly into 3 different treatments based on feeding regime/diet. The experiment consisted of three different feeding regimes/diets as follows: Treatment 1 (RA), Treatment 2 (RA-Zoo), and Treatment 3 (RA-PH).  Potters clay (400 ml) was added to all the larval rearing tanks, twice a day, to increase tank turbidity and to reduce bacterial numbers within the tanks.  Rearing temperature was increased from 6.0-7.0°C (incubation temperature) to 10.5°C over a period of 10 days, and water flow rate was gradually increased from 0.8 l min^-1 (at 0 dph) to 4.5 l min^-1 at 35 dph. Dissolved oxygen levels in the tanks were measured daily (YSI, ProODO, OH, USA) and kept at an average value of 117% saturation to alleviate any possible issues with nitrogen super-saturation. Whole larvae from each feeding regimes/diets were sampled when fish in particular treatment reached an average length of   ~ 9 mm. The sampled larvae were anaesthetized in MS-222, rinsed in UV-treated filtered seawater on a mesh strainer, patted dry on a Kimwipe, transferred to RNase/DNase-free 1.5 mL microcentrifuge tubes, flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

extract_protocol: Larval samples were homogenized in 300 µL of TRIzol Reagent (Invitrogen/Life Technologies) using a motorized Kontes RNase-Free Pellet Pestle Grinder (Kimble Chase, Vineland, NJ).  An additional 450 µL of TRIzol Reagent (Invitrogen/Life Technologies) was added, mixed by pipetting, and the homogenates frozen on dry ice and stored at -80°C.  Frozen homogenates were further processed by slowly thawing on ice and then passing through a QIAshredder (QIAGEN, Mississauga, ON) spin column following the manufacturer’s instructions.  Two-hundred and fifty µL of TRIzol (Invitrogen/Life Technologies) was then added to each sample to make a total homogenate volume of approximately 1 mL, and the TRIzol total RNA extractions were then completed following the manufacturer’s instructions.  Individual total RNA samples were treated with 6.8 Kunitz units of DNaseI (RNase-Free DNase Set, QIAGEN) with the manufacturer’s buffer (1X final concentration) at room temperature for 10 min to degrade any residual genomic DNA.  DNase-treated RNA samples were column purified using the RNeasy MinElute Cleanup Kit (QIAGEN) following the manufacturer’s methods.

tag: tissue

value: Whole larvae

tag: life stage

value: Larvae

source_name: pool of RNAs from whole larvae, all three dietary treatments (RA, RA-Zoo, RA-PH).


title: Whole larvae_RA-Zoodiet_fish3

source_name: Whole larvae, RA-Zoo diet, individual fish


title: sample_03-CV-002 [copy number]

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

hyb_protocol: Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 (manufacturer's protocol).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G (manufacturer's protocol).

data_processing: Affymetrix® Genotyping Console.

label: Biotin

source_name: Breast cancer, CHER-LOB Arm C, pre-treated

label_protocol: Affymetrix (manufacturer's protocol).

extract_protocol: Qiagen DNeasy Blood & Tissue Kit (manufacturer's protocol).

treatment_protocol: CHER-LOB is a phase II, randomized, multicenter, trial in which 121 patients with primary HER2-positive breast cancer were randomized to receive preoperative chemotherapy with weekly paclitaxel times 12 followed by 4 courses of 3-weekly FEC (fluorouracil, epirubicin and cyclophosphamide) plus either trastuzumab (Arm A), lapatinib (Arm B) or the combination of trastuzumab and lapatinib (Arm C). The trial design, eligibility criteria, statistical analysis, and clinical results including response, surgery outcomes and treatment safety are described in details elsewhere.

tag: disease state

value: HER2-positive breast cancer

value: breast cancer

tag: cher-lob arm

value: C

tag: arm description

value: chemotherapy+trastuzumab+lapatinib

tag: pcr (1=yes)


title: Whole larvae_RAdiet_fish6


title: Whole larvae_RAdiet_fish5


title: sample_02-FML-002 [copy number]


title: sample_02-MS-003 [copy number]

source_name: Breast cancer, CHER-LOB Arm A, pre-treated

value: A

value: chemotherapy+trastuzumab


title: 642R1

description: copy number profile

scan_protocol: Conducted according  to manufacturer's instructions.

source_name: Human glioblastoma tissue 642R1

value: TMZ, radiation


title: 559R1

description: copy number profile

source_name: Human glioblastoma tissue 559R1

label_protocol: Conducted according  to manufacturer's instructions.


title: B6J, Liver, 21 days HFD, rep4

city: Munich

first: Barbara

last: Fridrich

address: Ingolstädter Landstraße 1

country: Germany

institute: Hemholtz Center Munich

description: Gene expression data from liver of random fed B6J mice, 21 days HFD

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.1) including median polish and Sketch-Quantile normalisation

label: biotin

organism: Mus musculus

source_name: B6J, Liver, 21 days HFD

label_protocol: GeneChip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix)

growth_protocol: Single housed animals

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: As described in the paper. Briefly, mice were fed with a HFD (21 days) or LFD (≤ 21 days) and gene transcription analyses in liver was performed.

tag: strain

value: 17 weeks

tag: genotype

value: WT

value: 21 days HFD


title: Whole larvae_RAdiet_fish4


title: B6J, Liver, 21 days HFD, rep2

scan_protocol: According to the Affymetrix expression protocol


title: sample_02-CS-010 [copy number]


title: B6J, Liver, 21 days HFD, rep3


title: 428I

description: copy number profile

source_name: Human glioblastoma tissue 428I


title: B6J, Liver, 21 days HFD, rep5


title: sample_02-BG-006 [copy number]


title: sample_01-VT-018 [copy number]


title: B6J, Liver, 21 days HFD, rep1


title: 594R1

description: copy number profile

source_name: Human glioblastoma tissue 594R1


title: 460I

description: copy number profile

source_name: Human glioblastoma tissue 460I


title: Whole larvae_RAdiet_fish2


title: Whole larvae_RAdiet_fish3


title: 458I

description: copy number profile

source_name: Human glioblastoma tissue 458I


title: Whole larvae_RAdiet_fish1


title: sample_01-VV-027 [copy number]


title: B6J, Liver, control, rep7

description: Gene expression data from liver of random fed B6J mice, control

source_name: B6J, Liver, control

value: 15-17 weeks


title: sample_01-ST-008 [copy number]


title: 608R1

description: copy number profile

source_name: Human glioblastoma tissue 608R1


title: B6J, Liver, control, rep8


title: P08

city: Taoyuan

first: Ji-Dung

last: Luo

address: No. 259, Wen-Hua 1st road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: Chang Gung University

description: circulating RNA from non-small cell lung cancer patient P08

hyb_protocol: Hybridization according to Illumina protocols on Illumina HumanHT-12 v4 Expression BeadChip. Arrays are hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with the BeadArray Reader.  Protocols can be found on the illumina web page.

data_processing: Data were normalized to average signal. Background was subtracted using GenomeStudio v2009.1.

source_name: circulating cell-free RNA

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit. Two rounds of amplification

growth_protocol: 10-mL peripheral blood samples were obtained from three non-small cell lung cancer patients and three age-matched healthy volunteers

extract_protocol: Plasma RNAs were extracted by TRIzol-LS protocol.

treatment_protocol: Plasma was collected after 1600 x g centrifugation.

tag: subject id

tag: subject status

value: non-small cell lung cancer patient

tag: age (yrs)

value: peripheral blood


title: B6J, Liver, control, rep5


title: P07

description: circulating RNA from non-small cell lung cancer patient P07


title: B6J, Liver, control, rep6


title: sample_01-PK-019 [copy number]


title: B6J, Liver, control, rep4


title: P04

description: circulating RNA from non-small cell lung cancer patient P04


title: 421R1

description: copy number profile

source_name: Human glioblastoma tissue 421R1

value: GBM


title: sample_01-SB-026 [copy number]

source_name: Breast cancer, CHER-LOB Arm B, pre-treated

value: B

value: chemotherapy+lapatinib


title: B6J, Liver, control, rep3

value: male


title: sample_01-PD-016 [copy number]

value: HER2-positive breast cancer


title: N12

description: circulating RNA from healthy volunteer N12

value: healthy volunteer


title: 386I

description: copy number profile

source_name: Human glioblastoma tissue 386I

source_name: Random normal human tissue


title: 372I

description: copy number profile

source_name: Human glioblastoma tissue 372I

value: female

value: AGA


title: B6J, Liver, control, rep2


title: I-023I

description: copy number profile

source_name: Human glioblastoma tissue I-023I


title: sample_01-TT-001 [copy number]

source_name: Breast cancer, CHER-LOB Arm C, pre-treated

value: breast cancer

value: C

value: chemotherapy+trastuzumab+lapatinib


title: sample_01-PDG-017 [copy number]


title: N11

description: circulating RNA from healthy volunteer N11


title: sample_01-NF-029 [copy number]


title: 773R1

description: copy number profile

source_name: Human glioblastoma tissue 773R1

value: TMZ, radiation


title: I-140R1

description: copy number profile

source_name: Human glioblastoma tissue I-140R1


title: sample_01-NB-020 [copy number]


title: N10

description: circulating RNA from healthy volunteer N10


title: sample_01-PJL-014 [copy number]


title: 129, Liver, 21 days HFD, rep7

description: Gene expression data from liver of random fed 129 mice, 21 days HFD

source_name: 129, Liver, 21 days HFD

value: 17 weeks

value: WT


title: B6J, Liver, control, rep1

value: 15-17 weeks


title: 129, Liver, 21 days HFD, rep6

value: 21 days HFD


title: 129, Liver, 21 days HFD, rep5


title: 129, Liver, 21 days HFD, rep4


title: 129, Liver, 21 days HFD, rep1


title: 129, Liver, 21 days HFD, rep3


title: mouse_macrophage_cell_R264.7_Dex_rep2

city: Grand Rapids

first: Eric

last: Xu

state: MICHIGAN

address: 333 Bostwick Ave

country: USA

institute: Van Andel Institute

description:
Dex-SAMPLE
Gene expression after Dex treatment

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions.  On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarrays (G4852A) for 17 hours at 10 rpm 65 °C in a rotating Agilent hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) followed by 1 minute with elevated temperature of 37 °C GE Wash buffer 2 (Agilent).  Microarrays were scanned immediately on the Agilent DNA Microarray Scanner (G2305C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: data procsessed by R limma package

source_name: mouse macrophage cell R264.7, Dex treatment, rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng total RNA using the One-Color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini kit (Qiagen) to purify the labeled, amplified RNA.  Dye incorporation and cRNA yield were evaluated with the NanoDrop 2000c Spectrophotometer (Thermo Fisher Scientific)

growth_protocol: RAW264.7 were grow in DMEM medium plus 10% FBS at 37C tissue cultrure incubator with 5% CO2 supply. Cells were splitted in 6 well plate at 0.25 million per well one day before induction.

extract_protocol: Then total RNA were extracted via Qiagen mini RNA extraction kit according to the manuel.

treatment_protocol: When RAW264.7 cells in 6 well plate reach 60% confluence, cells were   pretreated with various glucocorticoids (Dexamethasone, VSG22, VSGC12 and fluticasone furoate) at 100nM one hour before the onset of inflammation response via LPS at 1 ug/ml for 16 hours.

tag: cell line


title: 697I

description: copy number profile

source_name: Human glioblastoma tissue 697I


title: sample_01-OR-011 [copy number]

source_name: Breast cancer, CHER-LOB Arm A, pre-treated

value: A

value: chemotherapy+trastuzumab


title: 647R3

description: copy number profile

source_name: Human glioblastoma tissue 647R3

value: GBM


title: I-179R1

description: copy number profile

source_name: Human glioblastoma tissue I-179R1


title: 129, Liver, 21 days HFD, rep2


title: 586R1

description: copy number profile

source_name: Human glioblastoma tissue 586R1


title: 129, Liver, control, rep8

description: Gene expression data from liver of random fed 129 mice, control

source_name: 129, Liver, control


title: 453R1

description: copy number profile

source_name: Human glioblastoma tissue 453R1


title: 129, Liver, control, rep7


title: mouse_macrophage_cell_R264.7_Dex_rep1

source_name: mouse macrophage cell R264.7, Dex treatment, rep1


title: sample_01-MPC-024 [copy number]

source_name: Breast cancer, CHER-LOB Arm B, pre-treated

value: B

value: chemotherapy+lapatinib


title: 129, Liver, control, rep6

value: male


title: 538I

description: copy number profile

source_name: Human glioblastoma tissue 538I

source_name: Random normal human tissue


title: mouse_macrophage_cell_R264.7_FF_rep1

description:
FF-SAMPLE
Gene expression after FF treatment

source_name: mouse macrophage cell R264.7, FF treatment, rep1


title: 129, Liver, control, rep4


title: mouse_macrophage_cell_R264.7_C12_rep2

description:
VSGC12-SAMPLE
Gene expression after VSGC12 treatment

source_name: mouse macrophage cell R264.7, VSGC12 treatment, rep2


title: mouse_macrophage_cell_R264.7_C12_rep1

source_name: mouse macrophage cell R264.7, VSGC12 treatment, rep1


title: mouse_macrophage_cell_R264.7_FF_rep2

source_name: mouse macrophage cell R264.7, FF treatment, rep2


title: 129, Liver, control, rep5


title: 129, Liver, control, rep2


title: mouse_macrophage_cell_R264.7_VSG22_rep2

description:
VSG22-SAMPLE
Gene expression after VSG22 treatment

source_name: mouse macrophage cell R264.7, VSG22 treatment, rep2


title: sample_01-MR-006 [copy number]

value: HER2-positive breast cancer


title: mouse_macrophage_cell_R264.7_VSG22_rep1

source_name: mouse macrophage cell R264.7, VSG22 treatment, rep1


title: mouse_macrophage_cell_R264.7_EtoH_rep2

description:
EtoH-SAMPLE
Gene expression after EtoH treatment

source_name: mouse macrophage cell R264.7, EtoH treatment, rep2


title: 129, Liver, control, rep3


title: 775R2

description: copy number profile

source_name: Human glioblastoma tissue 775R2


title: 129, Liver, control, rep1


title: 122LD1MY

status: Public on Oct 05 2015

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona

scan_protocol: GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)

data_processing: The raw data from CEL ﬁles were normalized and summarized using RMA algorithm as implemented in R package oligo (ref: Carvalho B, Bengtsson H, Speed TP, Irizarry RA. 2007. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8(2): 485-499.)

source_name: D1  Immortalized HMEC

label_protocol: RNA was processed according to The Ambion WT Expression kit (PN 4425209C) and the WT Terminal Labeling and Hybridization User Manual (PN702880) to generate labeled target

growth_protocol: M87A medium supplemented with oxytocin and cholera toxin at 0.5 ng/ml

extract_protocol: Total RNA was harvested using Trizol and purified using the Qiagen miRNeasy Kit according to manufacturer's recomendation

tag: specimen id

value: mammary gland

tag: cell type

value: Immortal human mammary epithelial cells

tag: cell stage/status

value: ccnd1/CDK2 and MYC transduced Immortalized HMEC


title: 122Lp16sMY

hyb_protocol: WT Terminal Labeling and Hybridization User Manual (PN702880)

source_name: p16sh Immortalized HMEC

value: p16sh and MYC transduced Immortalized HMEC


title: 805Pp16sMY


title: 184Dp16sMY


title: 240LD1MY


title: mouse_macrophage_cell_R264.7_EtoH_rep1

source_name: mouse macrophage cell R264.7, EtoH treatment, rep1


title: sample_01-ESA-021 [copy number]

source_name: Breast cancer, CHER-LOB Arm A, pre-treated

value: breast cancer


title: sample_01-MGC-023 [copy number]


title: sample_01-GL-032 [copy number]


title: sample_01-MB-022 [copy number]


title: sample_01-EG-009 [copy number]


title: 240L-D1

source_name: D1  Post-Stasis HMEC

value: Post-Stasis human mammary epithelial cells

value: ccnd1/CDK2 transduced Post-Stasis HMEC


title: 805P

source_name: Pre-Stasis HMEC

value: Pre-Stasis human mammary epithelial cells

value: Pre-Stasis HMEC


title: 805P-p16sh

source_name: p16sh Post-Stasis HMEC

value: p16sh transduced Post-Stasis HMEC


title: Mouse lung fibroblasts, non-invading, 96h, biological replicate 5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from mouse lung fibroblast line MLg 2908, non-invading, 96h

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation

source_name: Mouse lung fibroblast line MLg 2908, non-invading, 96h

label_protocol: Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cell culture as described in the publication

treatment_protocol: 3D collagen invasion assay and TGFB1 treatment as described in the paper

value: ddY

tag: age

value: newborn

tag: gender

value: not determined

value: WT


title: 122L-p16sh

tag: tissue


title: 240L-p16sh


title: sample_01-FF-030 [copy number]

value: A

value: chemotherapy+trastuzumab


title: 240L


title: Mouse lung fibroblasts, non-invading, 96h, biological replicate 4


title: Mouse lung fibroblasts, non-invading, 96h, biological replicate 2


title: Mouse lung fibroblasts, invading, 96h, biological replicate 3

description: Gene expression data from mouse lung fibroblast line MLg 2908, invading, 96h

source_name: Mouse lung fibroblast line MLg 2908, invading, 96h


title: sample_01-LF-025 [copy number]

value: HER2-positive breast cancer


title: Mouse lung fibroblasts, invading, 96h, biological replicate 5


title: Mouse lung fibroblasts, non-invading, 96h, biological replicate 1


title: Mouse lung fibroblasts, invading, 96h, biological replicate 2


title: Mouse lung fibroblasts, non-invading, 96h, biological replicate 3


title: Mouse lung fibroblasts, invading, 96h, biological replicate 1


title: Mouse lung fibroblasts, non-invading, 72h, biological replicate 3

description: Gene expression data from mouse lung fibroblast line MLg 2908, non-invading, 72h

source_name: Mouse lung fibroblast line MLg 2908, non-invading, 72h


title: Mouse lung fibroblasts, non-invading, 72h, biological replicate 4


title: sample_01-ES-005 [copy number]

source_name: Breast cancer, CHER-LOB Arm C, pre-treated

value: C

value: chemotherapy+trastuzumab+lapatinib


title: Mouse lung fibroblasts, non-invading, 72h, biological replicate 1


title: 122L

value: mammary gland


title: Mouse lung fibroblasts, non-invading, 72h, biological replicate 2


title: sample_01-CB-007 [copy number]


title: Mouse lung fibroblasts, invading, 72h, biological replicate 4

description: Gene expression data from mouse lung fibroblast line MLg 2908, invading, 72h

source_name: Mouse lung fibroblast line MLg 2908, invading, 72h


title: Cell line 928, biological replicate 2

description:
Gene expression data from cell line 928, biological replicate 2
CL928_2

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3.0.187) including median polish and Sketch-Quantile normalisation

source_name: Cell line 928

label_protocol: WT Expression kit (Ambion) and WT Terminal Labeling and Fragmentation Kit (Affymetrix)

growth_protocol: Cell lines were generated and maintained as outlined in the publication

extract_protocol: RNeasy Mini or Micro Kit (Qiagen) including DNase treatment

value: P48Cre/+; Ptenfl/fl; Tsc1fl/+

tag: pathway

tag: histology

value: Cystic lesions

tag: background strain

value: mixed


title: Mouse lung fibroblasts, invading, 72h, biological replicate 2


title: Cell line 952, biological replicate 2

description:
Gene expression data from cell line 952, biological replicate 2
CL952_2

source_name: Cell line 952


title: Mouse lung fibroblasts, invading, 72h, biological replicate 3


title: sample_01-AV-013 [copy number]

tag: disease state

value: breast cancer

tag: cher-lob arm

tag: arm description


title: 184D

value: Pre-Stasis human mammary epithelial cells


title: Cell line 907, biological replicate 2

description:
Gene expression data from cell line 907, biological replicate 2
CL907_2

source_name: Cell line 907

tag: genotype

value: P48Cre/+; KrasG12D; Tsc1fl/+

value: Kras/Erk-mTOR

value: PDAC


title: Cell line 952, biological replicate 1

description:
Gene expression data from cell line 952, biological replicate 1
CL952_1


title: Mouse lung fibroblasts, invading, 72h, biological replicate 1

tag: strain

value: ddY

value: newborn


title: Cell line 926, biological replicate 2

description:
Gene expression data from cell line 926, biological replicate 2
CL926_2

source_name: Cell line 926


title: Mouse lung fibroblasts, invading, 96h, biological replicate 4

value: not determined

value: WT


title: Cell line 928, biological replicate 1

description:
Gene expression data from cell line 928, biological replicate 1
CL928_1


title: Cell line 926, biological replicate 1

description:
Gene expression data from cell line 926, biological replicate 1
CL926_1


title: Cell line 399, biological replicate 2

description:
Gene expression data from cell line 399, biological replicate 2
CL399_2

source_name: Cell line 399


title: Cell line 403, biological replicate 1

description:
Gene expression data from cell line 403, biological replicate 1
CL403_1

source_name: Cell line 403


title: Cell line 403, biological replicate 2

description:
Gene expression data from cell line 403, biological replicate 2
CL403_2


title: Cell line 897, biological replicate 2

description:
Gene expression data from cell line 897, biological replicate 2
CL897_2

source_name: Cell line 897


title: Cell line 907, biological replicate 1

description:
Gene expression data from cell line 907, biological replicate 1
CL907_1


title: Cell line 897, biological replicate 1

description:
Gene expression data from cell line 897, biological replicate 1
CL897_1


title: Cell line 399, biological replicate 1

description:
Gene expression data from cell line 399, biological replicate 1
CL399_1


title: Cell line 961, biological replicate 2

description:
Gene expression data from cell line 961, biological replicate 2
CL961_2

source_name: Cell line 961

value: P48Cre/+; P53fl/fl; Tsc1fl/+

value: Normal* (macroscopically)


title: Cell line 946F, biological replicate 2

description:
Gene expression data from cell line 946F, biological replicate 2
CL946F_2

source_name: Cell line 946F

value: P48Cre/+; P53fl/fl; Tsc1fl/fl

value: Acinar carcinoma


title: Cell line 946F, biological replicate 1

description:
Gene expression data from cell line 946F, biological replicate 1
CL946F_1


title: sample_01-AG-015 [copy number]

value: HER2-positive breast cancer

value: C

value: chemotherapy+trastuzumab+lapatinib

tag: pcr (1=yes)


title: Cell line 946, biological replicate 2

description:
Gene expression data from cell line 946, biological replicate 2
CL946_2

source_name: Cell line 946

value: mixed


title: Cell line 911, biological replicate 2

description:
Gene expression data from cell line 911, biological replicate 2
CL911_2

source_name: Cell line 911

value: Normal


title: Cell line 911, biological replicate 1

description:
Gene expression data from cell line 911, biological replicate 1
CL911_1


title: Cell line 946, biological replicate 1

description:
Gene expression data from cell line 946, biological replicate 1
CL946_1


title: 240Lp16sMY

source_name: p16sh Immortalized HMEC

value: mammary gland

value: Immortal human mammary epithelial cells

value: p16sh and MYC transduced Immortalized HMEC


title: T47D Starved Rep2

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol using an Illumina BeadArray reader.

data_processing: Raw image files were processed and analysed using the BeadArray R package. The data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: detection p-values are not available.

source_name: T47D cell line treated with vehicle

label_protocol: Standard Illumina label protocol.

growth_protocol: MCF-7 human breast cancer cells were cultured in DMEM (Invitrogen) supplemented with 10% FBS and antibiotics. ZR751 and T47D human breast cancer cells were cultured in RPMI (Invitrogen) supplemented with 10% FBS and antibiotics. All cells were maintained at 37°C, 5% CO2. Cell synchronisation via estrogen deprivation was carried out for three consecutive days in phenol red-free media supplemented with 5% charcoal dextran-treated FBS and antibiotics, with media changed every 24 h.

extract_protocol: RNA was extracted using the miRNeasy spin column kit (QIAGEN) and quality checked using an RNA 6000 Nano chip on a 2100 Bioanalyser (Agilent). 250ng RNA (RIN>7) was used for cRNA amplification and labelling using the Illumina TotalPrep-96 kit (Ambion 4397949).

treatment_protocol: Estrogen-deprived cells were stimulated with 1 nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen) for a period of 6 h.

value: estrogen receptor-positive breast cancer cell line

tag: treatment

value: vehicle

tag: tme point

value: 6 h


title: T47D E2 Rep1

source_name: T47D cell line treated with estrogen

tag: cell line

value: estrogen


title: 122L-D1

source_name: D1  Post-Stasis HMEC

tag: specimen id

tag: cell type

value: Post-Stasis human mammary epithelial cells

value: ccnd1/CDK2 transduced Post-Stasis HMEC


title: ZR751 FGF10 Rep3

source_name: ZR751 cell line treated with estrogen and FGF10

value: estrogen and FGF10


title: ZR751 Starved Rep2

source_name: ZR751 cell line treated with vehicle


title: 184D-p16sh

source_name: p16sh Post-Stasis HMEC

tag: cell stage/status

value: p16sh transduced Post-Stasis HMEC


title: ZR751 Starved Rep3


title: T47D FGF10 Rep2

source_name: T47D cell line treated with estrogen and FGF10


title: MCF7 Starved Rep3

source_name: MCF-7 cell line treated with vehicle


title: MCF7 E2 Rep1

source_name: MCF-7 cell line treated with estrogen


title: Cell line 961, biological replicate 1

description:
Gene expression data from cell line 961, biological replicate 1
CL961_1

value: P48Cre/+; P53fl/fl; Tsc1fl/+

value: Normal* (macroscopically)


title: MCF7 Starved Rep2


title: ZR751 FGF10 Rep1


title: MCF7 FGF10 Rep1

source_name: MCF-7 cell line treated with estrogen and FGF10


title: T47D Starved Rep3


title: MCF7 E2 Rep2


title: MCF7 FGF10 Rep3


title: ZR751 E2 Rep2

source_name: ZR751 cell line treated with estrogen


title: ZR751 FGF10 Rep2


title: ZR751 E2 Rep3


title: MCF7 FGF10 Rep2


title: T47D FGF10 Rep1


title: T47D E2 Rep3


title: ZR751 E2 Rep1


title: T47D E2 Rep2


title: ZR751 Starved Rep1


title: T47D Starved Rep1


title: MCF7 Starved Rep1


title: T47D FGF10 Rep3


title: MCF7 E2 Rep3


title: Non-IRIS_4041_baseline

city: London

first: Rachel

last: Lai

address: The Ridgeway

department: Mycobacterial Research

institute: National Institute for Medical Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using 75 Percentile Shift using GeneSpring GX 12.6.1 software.  For normalization, week 0 samples were baseline transformed to the median of all samples. For all other weeks, samples were baseline transformed either to the median of all samples or to the corresponding week 0 values. Samples 5411298027_F and 5412485008_F do not have a corresponding baseline and were therefore excluded in the analysis for the latter.  The data tables on each sample record represents the normalization to the median of all samples.  Data normalized to the corresponding week 0 values can be found on the series level.

source_name: Whole Blood Baseline

label_protocol: Biotinylated cRNA were prepared with Life Technologies' Illumina TotalPrep-96 RNA Amplification kit

growth_protocol: Whole blood from patients were drawn into Tempus Blood Tubes directly and stored at -20C until RNA extraction

extract_protocol: RNA from whole blood (in Tempus) was extracted using 5Prime PerfectPure RNA Blood kit according the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

tag: group

value: Non-IRIS

value: blood


title: TB-IRIS_4039_wkhalf

source_name: Whole Blood wkhalf

treatment_protocol: Whole blood from patients were drawn into Tempus Blood Tubes directly and stored at -20C until RNA extraction

value: TB-IRIS

tag: tissue


title: Non-IRIS_4037_wk2

source_name: Whole Blood wk2


title: Non-IRIS_4037_baseline


title: Non-IRIS_4041_wk1

source_name: Whole Blood wk1


title: Non-IRIS_4041_wk2


title: TB-IRIS_4036_wk2


title: TB-IRIS_4036_wkhalf


title: TB-IRIS_4036_baseline


title: TB-IRIS_4036_wk1


title: TB-IRIS_4039_wk1


title: Non-IRIS_4034_wk1


title: TB-IRIS_4035_wk1


title: Non-IRIS_4034_baseline


title: Non-IRIS_4033_wkhalf


title: Non-IRIS_4041_wkhalf


title: TB-IRIS_4032_wk1


title: TB-IRIS_4032_baseline


title: Non-IRIS_4031_wk1


title: Non-IRIS_4033_baseline


title: TB-IRIS_4039_baseline


title: TB-IRIS_4035_baseline


title: Non-IRIS_4034_wk2


title: Non-IRIS_4031_baseline


title: TB-IRIS_4032_wk2


title: Non-IRIS_4033_wk1


title: TB-IRIS_4035_wkhalf


title: Non-IRIS_4033_wk2


title: Non-IRIS_4037_wk1


title: Non-IRIS_4031_wk2


title: Non-IRIS_4024_wk2


title: TB-IRIS_4025_wk1


title: TB-IRIS_4030_wk1

description:
4030-C
This sample does not have a corresponding baseline sample


title: TB-IRIS_4030_wk2

description:
4030-D
This sample does not have a corresponding baseline sample


title: Non-IRIS_4024_wk1


title: Non-IRIS_4023_wk1


title: Non-IRIS_4023_baseline


title: TB-IRIS_4025_wkhalf


title: Non-IRIS_4022_wk2


title: Non-IRIS_4024_wkhalf


title: Non-IRIS_4029_wk2


title: TB-IRIS_4025_baseline


title: Non-IRIS_4029_wkhalf


title: TB-IRIS_4021_wk2


title: TB-IRIS_4020_wkhalf


title: TB-IRIS_4021_baseline


title: Non-IRIS_4023_wk2


title: Non-IRIS_4023_wkhalf


title: TB-IRIS_4019_wk2


title: TB-IRIS_4019_wkhalf


title: TB-IRIS_4020_baseline


title: Non-IRIS_4022_baseline


title: Non-IRIS_4029_baseline


title: TB-IRIS_4021_wk1


title: Non-IRIS_4022_wk1


title: Non-IRIS_4022_wkhalf


title: TB-IRIS_4020_wk1


title: TB-IRIS_4020_wk2


title: Non-IRIS_4024_baseline


title: TB-IRIS_4019_wk1


title: Non-IRIS_4016_baseline


title: Non-IRIS_4016_wk2


title: TB-IRIS_4015_wkhalf


title: TB-IRIS_4015_wk1


title: TB-IRIS_4017_wk2


title: TB-IRIS_4015_wk2


title: TB-IRIS_4018_baseline


title: TB-IRIS_4019_baseline


title: TB-IRIS_4017_wk1


title: TB-IRIS_4017_baseline


title: TB-IRIS_4018_wk1


title: TB-IRIS_4018_wk2


title: Non-IRIS_4016_wkhalf


title: Non-IRIS_4013_wk1


title: TB-IRIS_4018_wkhalf


title: Leaf_Wounding_Systemic_24h_rep4

city: Vancouver

first: Juergen

last: Ehlting

state: BC

address: 321 - 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

hyb_protocol: We pre-hybridized microarray slides for 45 min at 48°C in 5x SSC, 0.1% SDS, 0.2% BSA. Slides were washed twice with water for 1 min, dipped five times in isopropanol, and spun dry in Falcon tubes at 100 g for 3 min. The hybridization solution was applied to the microarray slides and covered with untreated glass cover slips (Fisher Scientific, Nepean, ON, Canada). Arrays were incubated over night in CMT hybridization chambers (Corning, Corning, NY, USA) submerged in a water bath at 42°C with moderate vertical shaking. Hybridization chambers were disassembled and slides were washed for 15 min at 42°C in 2x SSC, 0.5% SDS, and for two times 15 min in 0.5x SSC, 0.5% SDS. Subsequently, arrays were dipped five times in 0.1x SSC and spun dry as described above.

scan_protocol: Microarrays were scanned with a ScanArray Express (Perkin-Elmer, Woodbridge, ON, Canada) scanner with laser power set to 95% and photo-multiplier tube set to 64–77%. We identified and quantified spots using the ImaGene software (BioDiscovery, Marina Del Rey, CA, USA). Grids were manually placed and spot finding was performed using the ‘Auto adjust’ spot function repeated for three times. Spot finding was subsequently verified by visual inspection and manually adjusted when necessary. Poor spots were manually flagged (flag 1) and were not used in further data analyses.

data_processing: The median pixel intensities for each spot were used. Background was defined per subgrid as the mean signal intensities of the lowest 10% of all gene specific spots. This background was subtracted from the raw signal intensities of all spots in a given subgrid. All signal intensities that did not exceed background plus 3 standard deviations of the calculated background were excluded from further analysis (flooring).  On average 19% of all spots (ranging from 12% to 27%) were thus excluded from further analyses as non-detectable. Background corrected signal intensities were used for Loess normalization (Yang et al., 2002), thereby generating normalized log2expression ratios comparing each treatment with the corresponding control sample.

organism: Arabidopsis thaliana

source_name: mature rosette leaf, Wounding, systemic, 24h

label_protocol: Total RNA (80 μg) was incubated with 0.27 μm T17VN primer, 0.15 mm dATP, dCTP, and dGTP, 0.05 mm dTTP (Invitrogen), 0.025 mm Cyanidin3- or Cyanidin5-conjugated dUTP (Amersham, Piscataway, NJ, USA), 40 U RNAseInh (Promega, San Luis Obispo, CA, USA), and 400 U SuperscriptII (Invitrogen) in 10 mm DTT and 1x first strand buffer in a total volume of 40 μl. In addition, 0.3 fmol human cRNAs complementary to the human negative control oligonucleotides were used in labeling reactions (HsD17B1, KRT1, and MB). Prior to the addition of enzymes the solution was heated to 65°C for 5 min and for primer annealing cooled to 42°C. Following an incubation at 42°C for 2.5 h, the RNA was degraded with 8 μl 1 M sodium hydroxide for 15 min at 65°C, neutralized with 8 μl 1 m hydrochloric acid and buffered with 4 μl 1 m Tris, pH 7.5. Subsequently, the labeled cDNA was purified using a PCR purification kit according to the manufacturer's protocol (Qiagen, Mississauga, ON, Canada). DNA was eluted in 100 μl 10 mm Tris, pH 8.5, the two labeling reactions were combined, and 1 μl Cyanidin5-labeled GFP was added. Following an ethanol/sodium acetate precipitation the air-dried cDNA pellet was resuspended in 3 μl water, denatured at 95°C for 3 min, added to 50 μl pre-warmed array hybridization buffer no. 1 (Ambion, Austin, TX, USA), and kept at 65°C until further use.

growth_protocol:
Insect material:   The dietary specialist aphid Brevicoryne brassicae (L.) and the dietary generalist aphid Myzus persicae (Sulzer) were maintained as plant virus free clones on pak-choi plants. For chewing insects we selected the dietary specialist caterpillar Pieris rapae L. and the dietary generalist caterpillar Spodoptera exigua Hübner. Eggs of S. exigua were obtained from Benzon Research (Carlisle, PA) and larvae were kept on commercially available artificial Spodoptera diet (Bioserv, Frenchtown, NJ, USA). Eggs of P. rapae were purchased form the Carolina Biological Supply Service (North Carolina) and reared on pak-choi. Both caterpillar species were transferred to Col-0 WT plants one day before the experiments.
Plant material:   Ecotype Columbia (Col-0) seeds were vernalized and sown into 6 x 5 cm pots filled with sterile Metromix 200 (Scotts company, Marysville, Ohio, USA; contains sphagnum, peat moss, and horticultural perlite). Plants were kept in growth chambers at 22 ± 1 °C, 65 ± 5 % relative humidity, at 250 µmol m-2 s-1 light intensity, and on a 10:14 (L:D) photoperiod. Approximately twice a week the plants were watered as needed and fertilized every two weeks (21-7-7, Miracle Gro).

extract_protocol: Total RNA was isolated using a modified TRIZOL extraction method as follows. Approximately 1 g of plant material was ground in liquid nitrogen using a mortar and pestle, resuspended in 15 ml TRIZOL reagent (Invitrogen, Carlsbad CA, USA), vortexed and incubated at 65°C for 5 min with regular mixing. Cell debris was pelleted by centrifugation for 30 min at 12 000 g and 4°C and the supernatant was extracted with 3 ml chloroform twice. After centrifugation for 20 min at 12 000 g, the aqueous phase was recovered and RNA was precipitated at room temperature for 5 min with 0.5 volumes of 0.8 m sodium citrate and 0.5 volumes of isopropanol. After centrifugation for 30 min at 12 000 g, the pellet was washed with 70% ethanol and re-centrifuged. The RNA pellet was air dried for 5 min and resuspended in 200 μl RNAse free water.

treatment_protocol: Treatment of plants with caterpillars and aphids was conducted in separate experiments. Sampling of plants occurred several hours after removal of insect herbivores so that plant gene expression results were not confounded by insect rna or by plant gene expression elicited by the physical movement of insect removal. The caterpillar treatment scheme was designed to capture early gene expression events and minimize variation due to leaf age and amount of insect damage. Six to 10 second and third instar S. exigua and P. rapae caterpillars were allowed to feed for 2-4 hours to generate 3 'middle-aged' leaves with 10-30% leaf area removed. Caterpillars were wrangled as needed with camel hair brushes (size 0) to concentrate their feeding on 3 leaves, and leaves of control plants were jiggled with a camel-hair brush to simulate the leaf movement caused by wrangling. Once sufficient damage was achieved, caterpillars were removed and the plants were returned to the growth chamber. The mechanical wounding treatment was designed to mimic insect damage to tissues. Mechanical damage was inflicted by running a sterile pattern wheel across either side of the midrib of 6 leaves on each plant, once at the beginning of the caterpillar wrangling and once half way through the caterpillar wrangling period. Control plants were jiggled with a camel-hair brush to simulate the leaf movement caused by mechanical wounding. Leaves were harvested for gene expression at 6 and 24 hr, with damaged (i.e. local) leaves harvested separately from size-matched undamaged (i.e. systemic) leaves. All leaves selected for treatment and harvest came from the fully-expanded 'middle-aged' leaf and leaves from 2-3 plants were pooled for each of the four bioreplicates. Aphids have much smaller effects on plants than caterpillars (Mewis et al 2005, 2006) and cannot be readily contained on individual leaves. Twenty sub-adult (final instar) and adult aphids were caged on plants and allowed to feed for 1 week. Controls were caged plants without aphids. All aphids were removed and caged controls were jiggled with a camel-hair brush to simulate the leaf movement caused by caterpillar removal. Whole plants were harvested for gene expression at 6 and 24 hr after aphid removal.

tag: ecotype

tag: growth stage

tag: stress

value: Wounding, systemic

tag: time

value: mature rosette leaf

source_name: mature rosette leaf, control (Wo, systemic), 24h

value: control (Wo, systemic)


title: Leaf_Wounding_Systemic_24h_rep1


title: Leaf_Wounding_Systemic_6h_rep2

source_name: mature rosette leaf, Wounding, systemic, 6h

source_name: mature rosette leaf, control (Wo, systemic), 6h


title: Non-IRIS_4016_wk1


title: Non-IRIS_4013_wk2


title: TB-IRIS_4017_wkhalf


title: TB-IRIS_4015_baseline


title: Leaf_Wounding_Systemic_6h_rep4


title: Leaf_Wounding_Systemic_24h_rep2


title: Non-IRIS_4013_wkhalf


title: TB-IRIS_4011_wk2


title: Leaf_Wounding_Systemic_24h_rep3


title: Non-IRIS_4014_baseline


title: Non-IRIS_4013_baseline


title: TB-IRIS_4011_wk1


title: Leaf_Wounding_Local_24h_rep1

source_name: mature rosette leaf, control (Wo, local), 24h

value: control (Wo, local)

source_name: mature rosette leaf, Wounding, local, 24h

value: Wounding, local


title: Leaf_Wounding_Systemic_6h_rep1


title: TB-IRIS_4011_baseline


title: Leaf_Wounding_Local_24h_rep2


title: Leaf_Wounding_Local_24h_rep4


title: TB-IRIS_4010_baseline


title: TB-IRIS_4010_wk1


title: Leaf_Wounding_Local_24h_rep3


title: TB-IRIS_4010_wk2


title: TB-IRIS_4008_wk1


title: Leaf_Wounding_Local_6h_rep2

source_name: mature rosette leaf, Wounding, local, 6h

source_name: mature rosette leaf, control (Wo, local), 6h


title: Leaf_Myzus_persicae_6h_rep4

source_name: mature rosette leaf, Myzus persicae, 6h

value: Myzus persicae

source_name: mature rosette leaf, control (My), 6h

value: control (My)


title: TB-IRIS_4011_wkhalf


title: Leaf_Myzus_persicae_24h_rep4

source_name: mature rosette leaf, Myzus persicae, 24h

source_name: mature rosette leaf, control (My), 24h


title: Leaf_Myzus_persicae_6h_rep3


title: TB-IRIS_4008_baseline


title: Leaf_Wounding_Local_6h_rep1


title: Leaf_Myzus_persicae_24h_rep1


title: Leaf_Wounding_Local_6h_rep3


title: Leaf_Myzus_persicae_24h_rep3


title: TB-IRIS_4008_wk2


title: Leaf_Myzus_persicae_6h_rep2


title: Leaf_Myzus_persicae_6h_rep1


title: Non-IRIS_4006_wk2


title: Leaf_Myzus_persicae_24h_rep2


title: Non-IRIS_4006_baseline


title: TB-IRIS_4007_baseline


title: Non-IRIS_4006_wk1


title: TB-IRIS_4008_wkhalf


title: Non-IRIS_4006_wkhalf


title: Leaf_Brevicoryne_brassicae_24h_rep4

source_name: mature rosette leaf, Brevicoryne brassicae, 24h

value: Brevicoryne brassicae

source_name: mature rosette leaf, control (Br), 24h

value: control (Br)


title: TB-IRIS_4007_wkhalf

source_name: Whole Blood wkhalf


title: Leaf_Brevicoryne_brassicae_24h_rep2


title: Non-IRIS_4003_wk1


title: Leaf_Brevicoryne_brassicae_24h_rep3


title: Leaf_Brevicoryne_brassicae_6h_rep2

source_name: mature rosette leaf, Brevicoryne brassicae, 6h

source_name: mature rosette leaf, control (Br), 6h


title: Leaf_Brevicoryne_brassicae_24h_rep1


title: TB-IRIS_4004_wk2

source_name: Whole Blood wk2


title: TB-IRIS_4004_wk1

source_name: Whole Blood wk1


title: TB-IRIS_4004_wkhalf


title: Leaf_Brevicoryne_brassicae_6h_rep3


title: Leaf_Brevicoryne_brassicae_6h_rep4


title: Leaf_Brevicoryne_brassicae_6h_rep1

source_name: mature rosette leaf, control (Sp, local), 6h

value: control (Sp, local)


title: Leaf_Spodoptera_exigua_Systemic_24h_rep3

source_name: mature rosette leaf, control (Sp, systemic), 24h

value: control (Sp, systemic)

source_name: mature rosette leaf, Spodoptera exigua, systemic, 24h

value: Spodoptera exigua, systemic


title: Leaf_Spodoptera_exigua_Systemic_24h_rep1


title: Leaf_Spodoptera_exigua_Systemic_6h_rep1

source_name: mature rosette leaf, control (Sp, systemic), 6h

source_name: mature rosette leaf, Spodoptera exigua, systemic, 6h


title: Leaf_Spodoptera_exigua_Local_24h_rep4

source_name: mature rosette leaf, Spodoptera exigua, local, 24h

value: Spodoptera exigua, local

source_name: mature rosette leaf, control (Sp, local), 24h


title: Astrocytes transfected with Ascl1Ert2, control 48h, biological replicate 2

hyb_protocol: According to the Affymetrix expression protocol

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including quantile normalisation

source_name: Cultured postnatal astrocytes from cerebral cortex

label_protocol: MessageAmp Premier RNA Amplification Kit (Ambion)

growth_protocol: Astrocytes were isolated from postnatal cerebral cortex and cultured as described in the paper

extract_protocol: RNeasy Plus Micro Kit (Qiagen) including removal of genomic DNA

treatment_protocol: Transduction with virus encoding for DsRed control, Neurog2ERT2-ires-DsRed and Ascl1ERT2-ires-DsRed and treated with OHT as described in the paper

value: transfected with Ascl1Ert2, control

tag: age

value: Postnatal day 6

tag: gender

value: not determined

value: wildtype


title: Leaf_Spodoptera_exigua_Systemic_6h_rep2


title: Leaf_Spodoptera_exigua_Systemic_24h_rep4


title: Leaf_Spodoptera_exigua_Local_24h_rep3


title: Non-IRIS_4002_baseline

source_name: Whole Blood Baseline

value: Non-IRIS

value: blood


title: TB-IRIS_4004_baseline

value: TB-IRIS


title: Leaf_Spodoptera_exigua_Systemic_6h_rep4

value: mature rosette leaf


title: Astrocytes transfected with Ascl1Ert2, control 48h, biological replicate 1

value: Cultured postnatal astrocytes from cerebral cortex

tag: genotype


title: Leaf_Spodoptera_exigua_Systemic_6h_rep3


title: Non-IRIS_4003_wk2


title: Leaf_Spodoptera_exigua_Local_6h_rep3

source_name: mature rosette leaf, Spodoptera exigua, local, 6h


title: Non-IRIS_4003_baseline


title: Leaf_Spodoptera_exigua_Local_24h_rep1


title: Leaf_Spodoptera_exigua_Local_6h_rep2


title: Leaf_Spodoptera_exigua_Local_6h_rep1


title: Leaf_Pieris_brassicae_Systemic_24h_rep4

source_name: mature rosette leaf, Pieris brassicae, systemic, 24h

value: Pieris brassicae, systemic

source_name: mature rosette leaf, control (Pi, systemic), 24h

value: control (Pi, systemic)


title: Astrocytes transfected with Ascl1Ert2, control 4h, biological replicate 3

tag: strain


title: Astrocytes transfected with Ascl1Ert2, control 24h, biological replicate 3


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 48h, biological replicate 1


title: Leaf_Pieris_brassicae_Systemic_24h_rep3


title: Astrocytes transfected with Ascl1Ert2, control 4h, biological replicate 2


title: Astrocytes transfected with Ascl1Ert2, control 4h, biological replicate 1


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 48h, biological replicate 2


title: Astrocytes transfected with Ascl1Ert2, control 24h, biological replicate 1


title: Astrocytes transfected with Ascl1Ert2, control 24h, biological replicate 2


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 24h, biological replicate 3


title: Leaf_Pieris_brassicae_Systemic_24h_rep1


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 24h, biological replicate 2


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 4h, biological replicate 2


title: Leaf_Pieris_brassicae_Systemic_24h_rep2


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 24h, biological replicate 1


title: Astrocytes transfected with Neurog2Ert2, control 24h, biological replicate 1

value: transfected with Neurog2Ert2, control


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 4h, biological replicate 3


title: Astrocytes transfected with Ascl1Ert2, induced with 4-hydroxytamoxifen for 4h, biological replicate 1


title: Leaf_Pieris_brassicae_Systemic_6h_rep2

source_name: mature rosette leaf, Pieris brassicae, systemic, 6h

source_name: mature rosette leaf, control (Pi, systemic), 6h


title: Leaf_Pieris_brassicae_Systemic_6h_rep3


title: Leaf_Pieris_brassicae_Systemic_6h_rep4


title: Astrocytes transfected with Neurog2Ert2, control 24h, biological replicate 3


title: Astrocytes transfected with Neurog2Ert2, control 48h, biological replicate 1


title: Astrocytes transfected with Neurog2Ert2, control 24h, biological replicate 2


title: Astrocytes transfected with Neurog2Ert2, control 4h, biological replicate 4


title: Astrocytes transfected with Neurog2Ert2, control 4h, biological replicate 3


title: Leaf_Pieris_brassicae_Local_24h_rep4

source_name: mature rosette leaf, Pieris brassicae, local, 24h

value: Pieris brassicae, local

source_name: mature rosette leaf, control (Pi, local), 24h

value: control (Pi, local)


title: Astrocytes transfected with Neurog2Ert2, control 4h, biological replicate 2


title: Leaf_Pieris_brassicae_Local_24h_rep2


title: Leaf_Pieris_brassicae_Local_24h_rep1


title: Leaf_Pieris_brassicae_Systemic_6h_rep1


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 24h, biological replicate 2


title: Leaf_Pieris_brassicae_Local_24h_rep3


title: Astrocytes transfected with Neurog2Ert2, control 4h, biological replicate 1


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 4h, biological replicate 3


title: Leaf_Pieris_brassicae_Local_6h_rep3

source_name: mature rosette leaf, control (Pi, local), 6h

source_name: mature rosette leaf, Pieris brassicae, local, 6h


title: Leaf_Pieris_brassicae_Local_6h_rep2


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 48h, biological replicate 1


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 48h, biological replicate 2


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 24h, biological replicate 1


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 4h, biological replicate 4


description: Gene expression data from Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 4h, biological replicate 1


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 4h, biological replicate 2


title: Leaf_Pieris_brassicae_Local_6h_rep1


title: Wild type rep2

status: Public on Oct 04 2015

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

country: Japan

institute: Akita Prefectural University

hyb_protocol: GeneChip® Hybridization Oven 640 (Affymetrix)

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix)

data_processing:
The perfect match data were normalized by using the SuperNORM data service (Skylight Biotech Inc., Akita, Japan) according to a three-parameter lognormal distribution model [details on PMID 18764774, 18958174, 22784577].
The log values are log10 (rawdata - gamma): z-score = (log10 (rawdata- gamma) - mu)/sigma.

source_name: Wild type_VC-deprived

label_protocol: GeneChip® WT Terminal Labeling Kit (Affymetrix), performed by Genetic Lab Inc., Sapporo, Japan

growth_protocol: WT mice were fed a VC-deprived diet and had free access to water without VC. Animals were maintained on a 12-h light/dark cycle in a controlled environment.

extract_protocol: Total RNA was extracted by using ISOGEN® (Wako Pure Chemical, Osaka, Japan). Briefly, liver was homogenized with a teflon-pestle homogenizer in ISOGEN, and total RNA was extracted according to the manufacturer’s protocol.

treatment_protocol: The concentration of AA in the drinking water was enough to maintain normal AA levels in all tissues. EDTA was added to stabilize AA in drinking water, which retained that stable state for at least for 4 days. Water bottles were changed every 3 or 4 days. Other than the water, all mice were fed an AA-deficient diet (CL-2, CLEA Japan, Tokyo, Japan) ad libitum.

tag: strain background

value: C57BL/6NCrSlc (Ishigami, A., Am. J. Pathol., 2002)

value: male

tag: genotype/variation

value: wild type

value: liver

tag: diet

value: Vitamin C (VC)-deprived


title: Wild type rep1


title: SMP30/GNL KO mice rep1

source_name: SMP30/GNL KO_AA-deficient

value: SMP30/GNL KO

value: ascorbic acid (AA)-deficient


title: ST55_F_C

status: Public on Oct 03 2015

city: Nagoya

first: Kazumi

last: Taguchi

address: Kawasumi-1, Mizuho-cho, Mizuho-ku

department: Nephro-urology

institute: Nagoya City University Graduate School of Medical Sciences

description: Renal papillary biopsy during intrarenal surgery

hyb_protocol: Cy3 labbeled cRNA was hybridyzed for 17 hours on SurePrint G3 Human 8x60K v2 slides using Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Softwarev.10.7.3.1 (Agilent) using default parameters.

source_name: control, normal tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the SureTag DNA Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Micro kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. Then cDNA was synthesized using Ovation® PicoSL WTA System V2 (NuGEN, San Carlos, CA) .RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Human renal papillary tip tissues were biopsied during endoscopic kidney stone surgery. Samples were reserved in RNAlater.

value: female

tag: lesion

value: Normal mucosa

tag: tissue type

value: normal papillary tissue from control patients without any kidney stone


title: SMP30/GNL KO mice rep2


title: ST56_M_P

source_name: CaOx>CaP, plaque tissue

value: Plaque mucosa

value: Randall's Plaque from calcium stone


title: ST56_M_N

source_name: CaOx>CaP, normal tissue

value: normal papillary tissue from calcium stone


title: SMP30/GNL KO mice, AA supplemented rep2

source_name: SMP30/GNL KO_AA suplemented

value: ascorbic acid (AA)-supplemented


title: ST53_F_P


title: ST54_F_P


title: ST40_F_P

source_name: CaP plaque tissue


title: ST54_F_N


title: ST45_M_P


title: ST45_M_N

source_name: CaP, normal tissue


title: ST44_M_P


title: SMP30/GNL KO mice, AA supplemented rep1


title: ST53_F_N


title: ST43_F_N

source_name: CaOx, normal tissue


title: ST50_F_N


title: ST52_M_N


title: ST48_F_P

source_name: CaOx plaque tissue


title: ST52_M_P


title: ST44_M_N


title: ST48_F_N


title: ST43_F_P


title: ST50_F_P


title: ST40_F_N


title: Leaf_Spodoptera_exigua_Systemic_24h_rep2

source_name: mature rosette leaf, Spodoptera exigua, systemic, 24h

value: Spodoptera exigua, systemic

value: mature rosette leaf

source_name: mature rosette leaf, control (Sp, systemic), 24h

value: control (Sp, systemic)


title: ST36_M_N


title: ST49_M_N


title: ST29_M_N


title: ST27_M_N


title: ST47_M_N


title: ST46_M_N


title: ST35_M_N


title: ST32_M_P


title: ST49_M_P


title: ST31_F_N


title: ST38_M_N


title: ST47_M_P


title: ST46_M_P


title: ST29_M_P


title: ST42_M_P


title: ST24_F_C


title: ST41_M_P


title: ST38_M_P


title: ST27_M_P


title: ST34_M_P


title: ST34_M_N


title: ST41_M_N


title: ST36_M_P


title: ST35_M_P


title: ST42_M_N


title: ST33_F_P


title: ST31_F_P


title: ST33_F_N


title: Baf60a LKO liver, biological rep2

city: Ann Arbor

first: Zhuoxian

last: Meng

state: Michigan

address: 210 Washtenaw Ave

institute: University of Michigan

description:
Gene expression data from Baf60a LKO liver, pool 2
Lin_034

hyb_protocol: According to standard Affymetrix protocol.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.15.1. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Baf60a LKO mouse liver

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

treatment_protocol:
Wild type and Baf60a liver specific knockout mice were fed with high-fat diet starting at six weeks of age for ten weeks.
Liver tissues were harvested after overnight starvation.

value: Baf60a LKO

value: high-fat diet


title: Astrocytes transfected with Neurog2Ert2, induced with 4-hydroxytamoxifen for 24h, biological replicate 3

source_name: Cultured postnatal astrocytes from cerebral cortex

tag: cell type

tag: treatment

value: Postnatal day 6

value: not determined

value: wildtype


title: DPBQ, biological rep1

city: Madison

first: Mark

last: Burkard

state: WI

address: 1111 Highland Ave.

department: Medicine

institute: UW-Madison

description: Gene expression data from MCF7 cells, DPBQ treatment

hyb_protocol: 6.5 ug of fragmented labeled aRNA applied to AFX HG U133A 2.0 array & hybridized at 45°C for 16 hours in AFX 640 Hyb oven

scan_protocol: All GC’s scanned on AFX GC3000 G7 scanner (S/N 50208130)

data_processing:
Data extracted from GC3000 G7 scanned images using the AFX Expression Console v 1.2.0.20 software.
Array data was normalized by RMA method and the data exported to GSEA for analysis

source_name: MCF7 cells, DPBQ treatment

label_protocol: Hybridization cocktail prepared according to protocols & procedures in the AFX Expression Analysis Technical Manual (P/N 702232 Rev. 3) for the U133A 2.0 array

growth_protocol: Cells were incubated at 37°C, 5% CO2

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

treatment_protocol: Cells were treated with DPBQ for six hours, collected using trypsin, washed with PBS, and placed in Trizol

tag: cell line

tag: agent

value: DPBQ


title: WT liver, biological rep2

description:
Gene expression data from wild type liver, pool 2
Lin_032

scan_protocol: According to standard Affymetrix protocol.

source_name: Wild type mouse liver

value: wild type

tag: tissue

value: liver


title: ST9_F_C

value: female

value: Normal mucosa


title: No treament, biological rep 2

description: Gene expression data from MCF7 cells, no treatment

source_name: MCF7 cells, no treatment

value: control


title: DPBQ, biological rep2


title: ST28_M_C

value: male

value: normal papillary tissue from control patients without any kidney stone


title: DPBQ, biological rep3


title: No treament, biological rep 3


title: ST21_M_P

value: Plaque mucosa

value: Randall's Plaque from calcium stone


title: No treament, biological rep 1


title: Baf60a LKO liver, biological rep1

description:
Gene expression data from Baf60a LKO liver, pool 1
Lin_033

label_protocol: According to standard Affymetrix protocol.


title: ST19_M_N

value: normal papillary tissue from calcium stone


title: ST20_M_N


title: ST19_M_P


title: ST22_M_N


title: ST20_M_P

source_name: CaOx, plaque tissue


title: MLL D 34+38-93-

status: Public on Oct 02 2015

city: Stanford

first: Masayuki

last: Iwasaki

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University School of Medicine

hyb_protocol: The array was placed in 45°C hybridization oven, at 60 rpm, and incubated for 17 hours ± 1 hour.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used for scanning. It takes approximately 10 minutes to scan each Gene Array.

data_processing: RMA using Custom CDF chip definition files

source_name: human MLLr leukemia cells

label_protocol: The Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay is  designed to generate amplified and biotinylated sense-strand DNA targets

extract_protocol: Total RNA was extracted from prospectively isolated cells using Trizol reagent followed by RNeasy MinElute Cleanup Kit

value: human leukemia cells

tag: cell subtype

value: CD34+CD38-CD93- sorted cells


title: WT liver, biological rep1

description:
Gene expression data from wild type liver, pool 1
Lin_031

value: high-fat diet


title: MLL E 34+38-93+

value: CD34+CD38-CD93+ sorted cells


title: MLL E 34+38-93-


title: MLL D 34+38-93+


title: ST22_M_P


title: ST18_F_N


title: ST16_F_C

source_name: control, normal tissue


title: ST17_M_C


title: ST18_F_P

source_name: CaOx>CaP, plaque tissue


title: MLL C 34+38-93+


title: MLL B 34+38-93+


title: MLL C 34+38-93-


title: FLS_Mock_#2

city: Gwangju

first: Jang-Soo

last: Chun

department: School of Life Science

institute: Gwangju institute of science and technology

description: Gene expression data from murin fibroblast-like synoviocytes infected with empty adenovirus

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: FLS, Mock infected

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Murine synovial tissues were minced and digested in collagenase for 4 h at 37℃. The fibroblast-like synoviocytes (FLS) were plated on coverslips in RPMI-1640 medium and incubated for 4 d. FLS between passage 4 and 8 were used for further analysis. Pure FLS (>90% CD90+/<1% CD14+) were identified by flow cytometry using antibodies against the fibroblast marker CD90 and the macrophage marker CD14 (Abcam).

treatment_protocol: FLS were infected with empty adenovirus or Ad-Epas1 at a multiplicity of infection (MOI) of 800 for 2 h and incubated for 24 hr on 35-mm culture dishes containing 1 ml of RPMI-1640 medium.

tag: passage

value: Passage 4~8

value: Knee synovium


title: Hdac3-Isl1KO hearts, rep1

city: Worcester

first: Chinmay

middle: M

last: Trivedi

state: MA

address: 368 Plantation St AS7-1047

department: Cardiovascular Medicine

institute: University of Massachusetts Medical School

description: Gene expression data from Hdac3-Isl1KO E9.5 hearts

hyb_protocol: 3ug of cDNA were hybridized for 16 hours at 45ºC on GeneChip Mouse Gene 2.0 ST arrays. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were processed using Bioconductor biocLite oligo package in R software with the mogene20sttranscriptcluster library. RMA correction was applied to probe intensities.

source_name: Pooled Hdac3-Isl1KO mouse embryonic hearts at E9.5

label_protocol: Fragmented and biotinylated cDNA were prepared using the GeneChip WT PLUS Reagent Kit according to the Affymetrix protocol from 100ng total RNA.

extract_protocol: Total RNA was extracted from pooled embryonic heart samples using Qiagen Rneasy Kit according to the manufacturer's instructions.

value: embryonic heart

value: Hdac3-flox/flox; Isl1-Cre


title: non_reactive_ac_rep1

description:
Gene expression data from FACS-sorted, eGFP-positive cortical cells from somatosensory GM of non-injured Aldh1L1-eGFP mice, biological replicate 1.
Pooled cells from about 15 animals.

hyb_protocol: Affymetrix Mouse Genome 430 2.0 Array according to the Affymetrix expression protocol.

scan_protocol: Array Scanner 3000 7G, according to the Affymetrix expression protocol.

data_processing: RMA probeset summary with standard settings in CARMAweb (https://carmaweb.genome.tugraz.at/carma/).

source_name: non-reactive astrocytes

label_protocol: MessageAmp (1. round) and MessageAmp II-Biotin Enhanced (2.round) 2-cycle protocol (Ambion).

growth_protocol: Animals were housed under standard conditions.

extract_protocol: RNeasy Micro Kit (Qiagen).

treatment_protocol:
Stab wound in the grey matter of the somatosensory cerebral cortex was performed as previously described (Buffo et al., 2008). Briefly, animals were anaesthetized, and using a stereotactic apparatus, subjected to 0.7 mm deep and 1-1.2 mm long stab wound on the right cortical hemisphere. Proliferating cells were labeled with BrdU (Sigma) added to the drinking water (1 mg per ml water containing 1% sucrose) for 5 consecutive days or by single intraperitoneal injection of BrdU (10 mg BrdU/100 g body weight) 2 h prior to analysis on 1, 3, 5 and 7 dpi.
Tissue dissociation and purification of cells using FACS: Cortical cells from a tissue volume (diameter 0.35 cm) punched from the lesioned somatosensory GM of GFAP-eGFP mice at 5 dpi or the corresponding region of  non-injured Aldh1L1-eGFP mice were dissociated as described previously (Buffo et al., 2008) and  sorted by a FACS Aria (BD), as described by Beckervordersandforth et al. (2010). Briefly, dead cells labelled by propidium iodide (1:1000; Sigma) and cell debris were gated out. Duplets and cell clusters were gated out in a plot of FSC-height and FSC-width, and non- or auto-fluorescent cells by setting the gate for GFP in comparison to non-fluorescent cells prepared from the intact somatosensory GM of C57BL/6 mice. The sorted GFP+ cells were either directly subjected to RNA isolation or resuspended in Dulbecco’s Modified Eagle Medium (DMEM/F-12 Mixture, 1% B27 Supplement, 2 mM L-Glutamine, 1% penicillin-streptomycin liquid (all from Gibco)) and plated on poly-D-Lysin coated coverslips for immunocytochemistry.

tag: strain/background

value: FVB/N

value: 2-3 months

value: not determined

value: astrocytes from cerebral cortex

value: no injury


title: Hdac3-Isl1KO hearts, rep3

tag: age


title: FLS_Mock_#1


title: FLS_Mock_#3


title: FLS_Ad-Epas1_#2

description: Gene expression data from murin fibroblast-like synoviocytes infected with Epas1 adenovirus

source_name: FLS, Ad-Epas1 infected


title: MLL A 34+38-93+


title: Hdac3-flox/flox hearts, rep1

description: Gene expression data from Hdac3-flox/flox E9.5 hearts

source_name: Pooled Hdac3-flox/flox mouse embryonic hearts at E9.5


title: Hdac3-flox/flox hearts, rep3


title: Hdac3-Isl1KO hearts, rep2


title: Hdac3-flox/flox hearts, rep2


title: reactive_ac_rep3

description:
Gene expression data from FACS-sorted, eGFP-positive cortical cells from lesioned somatosensory GM of GFAP-eGFP mice at 5 dpi, biological replicate 3.
Pooled cells from about 15 animals.

source_name: reactive astrocytes

value: TgN(hGFAP-EGFP) GFEA

tag: gender

value: stab wound injury

tag: time point

value: 5 days post-injury


title: FLS_Ad-Epas1_#3

tag: strain


title: non_reactive_ac_rep3

description:
Gene expression data from FACS-sorted, eGFP-positive cortical cells from somatosensory GM of non-injured Aldh1L1-eGFP mice, biological replicate 3.
Pooled cells from about 15 animals.


title: FLS_Ad-Epas1_#1


title: non_reactive_ac_rep2

description:
Gene expression data from FACS-sorted, eGFP-positive cortical cells from somatosensory GM of non-injured Aldh1L1-eGFP mice, biological replicate 2.
Pooled cells from about 15 animals.


title: reactive_ac_rep1

description:
Gene expression data from FACS-sorted, eGFP-positive cortical cells from lesioned somatosensory GM of GFAP-eGFP mice at 5 dpi, biological replicate 1.
Pooled cells from about 15 animals.


title: reactive_ac_rep2

description:
Gene expression data from FACS-sorted, eGFP-positive cortical cells from lesioned somatosensory GM of GFAP-eGFP mice at 5 dpi, biological replicate 2.
Pooled cells from about 15 animals.


title: MLL A 34+38-93-


title: GMP A

description: GMPs fractionated by FACS

data_processing: RMA

source_name: BM cells

value: Normal


title: GMP C

description: GMPs fractionated by FACS


title: L-GMP C

description: GMPs fractionated by FACS

value: HoxA9+Meis1 AML


title: 1806Q3

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: Biological replicate 2 BCG vaccination group

hyb_protocol: Microarray analyses were performed as previously described (Mehra S et al, AJRCCM, 2015) by assessing the relative expression of transcripts in the Cy5 (experimental)-labeled samples relative to the Cy3(control)-labeled samples, using Agilent 4x44k Rhesus Monkey microarrays (Mehra S et al, AJRCCM, 2015).  Arrays were hybridized overnight at 55 C and washed using Agilent reagents prescribed for the 4x44k arrays

scan_protocol: Arrays were scanned using a GenePix 4000B dual laser scanner using GenePix Pro 6.3 software.

data_processing: The resulting .gpr files were uploaded to Spotfire DecisionSite for Microarray Analysis running the Splus suite, and normalization performed using the LOWESS method.  The resulting log2 fold changes were calculated and used for uploading to Database for Annotation, Visualization and Integrated Discovery (DAVID) (NCBI).Two-fold up or down regulated genes were uploaded to DAVID. Pathways/terms which were enriched in a statistically significant manner (P <0.05; FDR corrected) were used for further analysis and display.

organism: Macaca mulatta

source_name: unvaccinated naïve_BAL

label_protocol: The cDNA derived from the amplified RNA samples from pre-vaccination time points were labeled with Cy3, and samples from the 3-week post-vaccination time point were labeled with Cy5 (Agilent Technologies).

extract_protocol: For transcriptomics, RNA was isolated from total BAL obtained at the pre-vaccination and the 3 week post-vaccination time points as previously described (Mehra S et al, AJRCCM, 2015) using an RNAEasy kit (Qiagen), followed by RNA amplification (Ambion MessageAmp).

treatment_protocol: BAL samples were obtained from animals prior to vaccination (-2 weeks) and post-vaccination (weeks 3) previously described (Mehra S et al, AJRCCM, 2015).  For stabilization, 8 mL of 100% fetal bovine serum (Invitrogen, Life Sciences) was immediately added to 80 mL of the BAL sample collected. The sample was centrifuged at 400 rpm for 10 min at 4°C in an Allegra benchtop centrifuge. The pelleted cells were washed with cold RPMI media (Invitrogen, Life Sciences) and stored at -80°C until analysis.

value: Bronchoalveolar lavage cells

value: prior to infection (-2 wks)

tag: sample type

value: Prevaccination sample from BCG-vaccinated macaque

tag: vaccinated with

value: aerosols with BCG

value: Week 3 post-vaccination


title: GMP B

description: GMPs fractionated by FACS

tag: genotype/variation


title: 1805Q3

description: Biological replicate 3 MtbDsigH vaccination group

value: Prevaccination sample from MtbDsigH-vaccinated macaque

value: aerosols with attenuated MtbDsigH mutant


title: 1806Q4

description: Biological replicate 3 BCG vaccination group


title: NR8383_CNT-2

city: Tsukuba

first: Makiko

last: Fukuda

state: Ibaraki

address: West,16-1 onogawa, Tsukuba, Ibaraki,305-8569,JAPAN

institute: Technology Research Association for Single Wall Carbon Nanotubes

description: Gene expression after 24hr in CNT-2-exposed rat alveolar macrophages

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data is the average of n=4.

organism: Rattus norvegicus

source_name: Rat alveolar macrophages, 24hr, CNT-2, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Rat alveolar macrophages NR8383 were seeded into each well of a 96-well plate and grown in the F-12K with 10% heat-inactivated fetal bovine serum medium for 24 hours.

extract_protocol: Total RNA was extracted from the cells using the RNeasy mini (Qiagen, Tokyo, Japan) following the manufactures instructions. Total RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Each medium were replaced by two kinds of the impurity-free single-wall carbon nanotubes (SWCNTs) working solutions, CNT-1 or CNT-2. These working solutions were dissolved in 1mg/mL bovine serum albumin (BSA). Cell concentrations at this point were approximately 2.0 x 10^5 cells/mL. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: alveolar macrophages

tag: time


title: L-GMP A

description: GMPs fractionated by FACS


title: 1805Q1

description: Biological replicate 1 MtbDsigH vaccination group


title: L-GMP D

description: GMPs fractionated by FACS


title: L-GMP B

description: GMPs fractionated by FACS


title: GMP D

description: GMPs fractionated by FACS


title: NR8383_CNT-1

description: Gene expression after 24hr in CNT-1-exposed rat alveolar macrophages

source_name: Rat alveolar macrophages, 24hr, CNT-1, replicate 4


title: 1805Q4

description: Biological replicate 1 BCG vaccination group


title: vessel_hypertensive_5months_rep2

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Labeled test samples and common reference were combined and hybridized on SurePrint G3 Rat GE 8x60K microarrays (G4858A-028279, Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: After washing, the arrays were scanned in an ozone-free room with an Agilent DNA microarray scanner (G2565CA, Agilent Technologies). Data was extracted with Feature Extraction software v10.7.3.1 (Agilent Technologies)

data_processing: Data processing was carried out with Bioconductor packages in the statistical software package R (Version 3.0.0). Background correction was performed using the “normexp” method with an offset of 15 to adjust the foreground signal without introducing negative values (limma package). The resulting log ratios were transformed using intensity-dependent loess normalization (limma package). Control probes were down-weighted to zero in the normalization step. Normalized log-ratios for replicate probes were averaged.

source_name: vessel, hypertensive, 5months

label_protocol: 100 ng total RNA per test sample was combined with Spike A and amplified incorporating Cy3 according to the “Agilent Two-Color Microarray-Based Gene Expression  Analysis Guide” version 6.6 using the Quick Amp Labeling Kit (Agilent Technologies). As common reference an equimolar pool of all test samples was made of which 100 ng was amplified as described  above with the exception that Spike B was included and Cy5 was used for labeling. Synthesized cyanine-dye labeled antisense RNA (aRNA) was purified using the RNeasy MinElute Cleanup Kit (Qiagen) before measuring yield and dye incorporation on a NanoDrop ND-1000.

extract_protocol: Total RNA including microRNAs was isolated using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. Integrity of the isolated RNA was evaluated using the RNA 6000 Pico kit and Small RNA kit on a BioAnalyzer system (Agilent Technologies).

value: artery

value: 5 months

tag: condition

value: hypertensive

tag: subline

value: SHR/SP

source_name: reference pool

value: reference pool


title: DTC_Advanced_6

city: Seattle

first: Min

last: Fang

state: WA

address: 825 Eastlake Ave E, G7-500

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
2693
6066001119_R05C02
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on an iScan+ (Illumina).

data_processing: Using the normal female lymphocyte reference set and LNCaP cell aliquots, we established parameters for smoothing interprobe variation and segmentation of probes into regions with similar values of average log2 ratio. Furthermore, we determined log2 ratio thresholds that minimized background noise while allowing for accurate SCNA calls.   Nexus 6.0 was first used for data visualization and analysis.  Optimization of segmentation parameters for use on WGA samples was determined using 5-cell aliquots of normal female lymphocytes.  The SNP-FASST2 segmentation algorithm based on Hidden Markov Model was used. To normalize for genome-wide waviness due to changes in GC-content, samples were corrected using the quadratic correction algorithm with a custom file that accounts for GC probe intensity surrounding each probe.  Segmentation parameters required a minimum of ten probes and had a maximum segment size of 1 Mb, except for increasing the probe minimum to 25 for samples with an unusually high amount of interprobe variation.  Probe re-centering was based on the genomic median of all probes or using the ASCAT algorithm.  Thresholds for calling copy number alterations were as follows: high copy gain >=0.41, copy gain >= 0.13, copy loss <= -0.18, and high copy loss: <= -0.9. Manufacturer recommended settings were used for all other parameters.  Samples were manually curated to eliminate likely false-positive calls and to combine disjointed segments present in mosaic segments.  Calls were eliminated if they had an insignificant p-value (p=1.0), had log2 ratio values that were highly variable among probes or were not clearly different from surrounding normal regions, and did not have evidence of skewing in the B-allele frequency track.

source_name: prostate cancer

label_protocol: 4ul of WGA samples were additionally whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MSM) and primer/neutralization mixes (WG-MA1 and WG-MA2). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol:
For WGA of samples containing ≤ 40 cells, PCR tubes with cells were thawed in a 96-well rack prechilled on ice, and contents were briefly collected by centrifuging at 13,000 rpm for one minute.  Tubes were dried completely in a SpeedVac on low or medium setting, with monitoring to avoid over-drying samples.  To control for possible contamination throughout the WGA process, a water-only sample was also dried in the SpeedVac and was treated in the same manner as tubes containing cell aliquots.  The WGA were carried out using the PicoPLEX WGA kit (Rubicon Genomics, Ann Arbor, MI) according to the instructions. All steps involving WGA were done in a manner to minimize possible contamination and maintain good PCR practices. When possible, individual samples and reagents were handled by metal tweezers, opened only in a PCR workstation (AirClean Systems, Creedmoor, NC), and samples were kept on ice whenever possible.
Briefly, DTC samples that were originally collected in a 0.5 mL microfuge tube in 5-10 µL H2O. Following sample drying in a SpeedVac, Cell samples were resuspended in 5 µL of Cell Extraction Buffer. Then 5 µL of freshly prepared Extraction Cocktail was added to each tube. Samples were vortexed, centrifuged and incubated in a PTC-100 thermocycler (MJ Research Inc, St. Bruno, Canada) at 75ºC for ten minutes, and then at 95ºC for four minutes. Samples were collected by centrifugation, had 5 µL of freshly prepared Pre-Amp Cocktail added, and were vortexed and centrifuged. Samples were incubated in a thermocycler as follows: 1 cycle at 95ºC for 2 mins followed by 12 cycles of 95ºC for 15 s, 15ºC for 50 s, 25ºC for 40 s, 35ºC for 30 s, 65ºC for 40 s, 75ºC for 40 s. Samples were then placed immediately on ice, collected by centrifugation, and 60 µL of freshly prepared Amplification Cocktail were added. Samples were mixed well by vortexing, briefly centrifuged, then amplified in a thermocycler as follows: 95ºC for 2 min, followed by 14 cycles of 95ºC for 15 s, 65ºC for 1 min, 75ºC for 1 min.
Following WGA, samples were purified using Qiagen PCR purification columns according to manufacturer’s directions, with the following modifications: following initial wash with 0.75 mL Buffer PE, tubes were transferred to an empty 1.5 mL microfuge tube and completely dried by centrifuging at 13,000 rpm for three minutes; DNA was eluted in a room temperature 1 EB:1 water mixture by adding 30 µL to column, allowed to stand at room temp for up to three minutes, then centrifuged at 13,000 rpm for one minute, followed by a second elution with 25 µL, for a total of 55 µL per sample.

treatment_protocol:
The methods to isolate DTCs from bone marrow aspirates have been described previously.  Briefly, 10 mL of bone marrow were aspirated from the right iliac crest and combined with 10 mL of 6% sodium citrate.  Samples were processed as soon as possible.  Aspirates were placed over 15 mL of Ficoll-Isopaque 1.077 g/mL (Accurate Chemical, Westbury, NY) and centrifuged to yield a mononuclear cell layer.  Two rounds of immunomagnetic selection (Miltenyi Biotec, San Diego, CA) were used to enrich for DTCs.  First, negative selection of leukocytes, megakaryocytes and platelets was carried out using antibodies to CD45 and CD61.  Second, immunomagnetic beads coated with an anti-EpCAM antibody (clone HEA-125/CD326) were used to positively select cells expressing epithelial antigens.  The eluted fraction contained a cell mixture enriched for cells of epithelial origin.
To identify and isolate DTC, the enriched cell population was immunostained with FITC-labeled BerEP4 clone of the anti-EpCAM antibodies (Dako, Carpinteria, CA), which bind to a different epitope on human EpCAM than the antibody used for positive selection.  A phycoerythrin-conjugated anti-CD45 antibody was also used to counterstain leukocytes.  Cells were viewed under fluorescent light using an inverted microscope.  DTCs were defined as CD45-negative cells that have intermediate to high labeling with anti-EpCAM. EpCAM+/CD45- cells were kept on ice, viewed under fluorescent light, and intact cells with a clearly defined EpCAM labelled membrane were isolated using a micromanipulator and were dispensed into individual snap-top PCR tubes containing 10 µL of water.  Samples were frozen immediately on dry ice and stored at -80ºC until WGA. We were able to generate data of comparable quality from samples stored up to twelve years relative to DTCs acquired within the last two years.

tag: disease state

value: advanced stage of prostate cancer

tag: disease feature

value: metastatic CRPC

value: Male

value: bone marrow

tag: cell type

value: disseminated tumor cell (DTC)

tag: cell number


title: DTC_Advanced_8

description:
2346
5773627150_R02C01
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array

value: androgen-dependent metastases

tag: tissue


title: NR8383_Control for CNT-1 or CNT-2

description: Gene expression after 24hr in rat alveolar macrophages as control for CNT-1 or CNT-2

source_name: Rat alveolar macrophages, 24hr, solvent control (BSA) for CNT-1 or CNT-2, replicate 4

tag: cell line

tag: treatment

value: Control for CNT-1 or CNT-2


title: vessel_hypertensive_5months_rep1

description: Array did not pass quality control, and was excluded from further analysis

tag: age

value: SHR/NHsd


title: DTC_Advanced_3

description:
2373
6066001119_R04C01
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array

tag: gender


title: DTC_Advanced_1

description:
2451
6066001119_R01C02
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array


title: vessel_hypertensive_6weeks_rep3  (technical replicate)

source_name: vessel, hypertensive, 6weeks

value: 6 weeks


title: DTC_Advanced_2

description:
2380C1
6066001119_R05C01
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array


title: vessel_normotensive_5months_rep3

source_name: vessel, normotensive, 5months

value: normotensive

value: WKY/NTac


title: vessel_hypertensive_6weeks_rep2  (technical replicate)


title: vessel_normotensive_5months_rep1

value: WKY/NCrL


title: vessel_normotensive_6weeks_rep3

source_name: vessel, normotensive, 6weeks

value: artery

value: WKY/NHsd


title: vessel_hypertensive_5months_rep2 (technical replicate)

value: 5 months

value: hypertensive


title: vessel_hypertensive_6weeks_rep2

value: SHR/SP

value: reference pool


title: vessel_hypertensive_5months_rep3 (technical replicate)

value: SHR/NCrL


title: DTC_Advanced_5

description:
2439
6066001119_R06C01
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array

value: advanced stage of prostate cancer

value: metastatic CRPC

value: Male


title: DTC_Advanced_7

description:
2474
6066001119_R02C02
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array

value: bone marrow

value: disseminated tumor cell (DTC)


title: vessel_normotensive_6weeks_rep1


title: vessel_hypertensive_6weeks_rep1


title: vessel_normotensive_5months_rep2


title: DTC_Advanced_4

description:
2299
6066001119_R03C01
Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array


title: vessel_hypertensive_6weeks_rep3

value: SHR/NHsd


title: Astrocytes transfected with Neurog2Ert2, control 48h, biological replicate 2

scan_protocol: According to the Affymetrix expression protocol

source_name: Cultured postnatal astrocytes from cerebral cortex

value: transfected with Neurog2Ert2, control

value: Postnatal day 6

value: not determined

tag: genotype

value: wildtype


title: vessel_hypertensive_5months_rep3

value: artery


title: U87MG_Vec_rep1

city: shanghai

first: feng

last: li

address: 2005, songhu road

country: China

institute: fudan university

data_processing: The data were normalized using quantile normalization

label_protocol: Labeled with Flourolink Cy3

extract_protocol: RNA extraction was performed following the instruction of Trizol RNA Extraction Reagent


title: A549_CNT-2

description: Gene expression after 24hr in CNT-2-exposed human alveolar epithelial cell lines

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) or Agilent  Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven, respectively. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

source_name: Human alveolar epithelial cell lines, 24hr, CNT-2, replicate 4

growth_protocol: Rat alveolar macrophages NR8383 were seeded into each well of a 96-well plate and grown in the F-12K with 10% heat-inactivated fetal bovine serum medium for 24 hours. Human alveolar epithelial cell line A549 were seeded into each well of a 96-well plate (Becton, Dickinson and Company, Franklin Lakes, NJ) and grown in the DMEM with 10% heat-inactivated fetal bovine serum medium for 24 hours.

treatment_protocol: Each medium were replaced by two kinds of single-wall carbon nanotubes (SWCNTs) working solutions, CNT-1 or CNT-2. These working solutions were dissolved in 1mg/mL bovine serum albumin (BSA). Cell concentrations at this point were approximately 2.0 x 10^5 cells/mL. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: alveolar epithelial cell


title: Bt_B22M_27

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
27_Bt_B22M_567_3

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing:
Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software. Data from each matrix were analyzed and filtered separately to avoid any bias.
Normalized with quantile method; 'blank' (no value) corresponds to probes not considered for the normalization step; null corresponds to missing data from analysis and/or probes (genes) that didn't pass the filtering step.

organism: Bos taurus

source_name: Bull_treated TBA(200 mg)+BE2(40 mg)

label_protocol: Amplification and labelling was done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: RNA from liver and muscle tissues' aliquots was isolated using Trizol reagent according to manufacturer's instruction and purified according to Qiagen RNeasy Mini Kit protocol for tissue samples.

value: Muscle

tag: breed

value: Charolais

value: male

value: 10-14 months


title: Bt_B22M_29

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
29_Bt_B22M_568_1


title: A549_CNT-1

description: Gene expression after 24hr in CNT-1-exposed human alveolar epithelial cell lines

source_name: Human alveolar epithelial cell lines, 24hr, CNT-1, replicate 4


title: A549_Control for CNT-1 or CNT-2

description: Gene expression after 24hr in human alveolar epithelial cell lines as cotrol for CNT-1 or CNT-1

source_name: Human alveolar epithelial cell lines, 24hr, solvent control (BSA) for CNT-1 or CNT-2, replicate 4

value: Control for CNT-1 or CNT-2


title: Bt_B22M_24

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
24_Bt_B22M_566_4


title: Bt_B22M_25

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
25_Bt_B22M_567_1


title: U87MG_R132HSIRT5_rep1

hyb_protocol: Standard Illumina hybridization protocol


title: Bt_B22M_28

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
28_Bt_B22M_567_4


title: Bt_B22M_23

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
23_Bt_B22M_566_3


title: Bt_B22M_21

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
21_Bt_B22M_566_1


title: U87MG_R132H_rep1


title: Bt_B22M_30

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
30_Bt_B22M_568_2


title: 1805Q2

description: Biological replicate 2 MtbDsigH vaccination group

value: Bronchoalveolar lavage cells

tag: time point

value: prior to infection (-2 wks)

tag: sample type

value: Prevaccination sample from MtbDsigH-vaccinated macaque

value: aerosols with attenuated MtbDsigH mutant

value: Week 3 post-vaccination