title: LungTumorNodule_mouse631_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 631


title: LungTumorNodule_mouse788_Kras37bpMarkerGenotype_AB_heterozygous_rep1

status: Public on Mar 14 2016

type: RNA

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description: sample name: 788

hyb_protocol: Fluorescent dye-labeled cRNA was hybridized to SurePrint G3 Mouse Exon 4x180K arrays (Agilent); hybridization and washing were performed on Agilent’s microarray platform, according to standard protocols.

scan_protocol: Microarray images were acquired using an Agilent DNA microarray scanner.

data_processing: Raw data were generated using Agilent Feature Extraction software. Raw median probe intensities were pre-processed using the limma (Ritchie, 2015) package of the R/Bioconductor project. A batch effect was present as samples had been assayed in two different experiments (95 samples in batch 1 and 48 samples in batch 2). Thus, raw data from each batch of arrays were log2-transformed and normalized independently using quantile normalization. The ComBat method (Johnson, 2007), implemented in the sva R package (Leek, 2012), was then applied to remove the batch effect from normalized data. After ComBat correction expression data from replicated probes were summarized calculating the mean expression.

molecule: total RNA

organism: Mus musculus

label_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling kit, according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

growth_protocol: Mice were maintained at the animal facility of Fondazione IRCCS Istituto Nazionale dei Tumori. Animal experiments were authorized by the Institute Animal Experimentation Ethical Committee (CESA) in March 2012, according to the Italian law DL116/92), and performed in accordance to institutional guidelines

extract_protocol: Total RNA was extracted from lung tumor specimens using RNeasy Midi Kit (Qiagen), purified with RNeasy MinElute Cleanup (Qiagen), and quantified by spectrophotometry (ND-1000 spectrophotometer, NanoDrop, Wilmington, DE, USA). RNA integrity was verified using the RNA 6000 Nano Assay Kit (Agilent Technologies, Palo Alto, CA, USA); the mean RIN value was 8.9 (SD = 0.8; range, 6.7 to 9.9).

treatment_protocol: At 4 weeks of age, 143 male ABF4 mice were treated with a single intraperitoneal injection of urethane (1 g/kg body weight) according to a standard procedure for inducing the development of lung tumors (Shimkin, 1975).

tag: strain background

value: A/J X C57BL/6

tag: strain

value: offspring bred to the 4th generation (ABF4)

tag: gender

value: male

tag: age

value: 40 wks

tag: number of lung tumors

tag: kras37bp marker genotype

tag: tissue

value: lung tumor nodule

tag: batch


title: LungTumorNodule_mouse674_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 674


title: LungTumorNodule_mouse500_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 500


title: LungTumorNodule_mouse513_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 513


title: LungTumorNodule_mouse787_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 787


title: LungTumorNodule_mouse754_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 754


title: LungTumorNodule_mouse792_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 792


title: PBMC_s019_8hr

city: Bethesda

first: Yuri

last: Kotliarov

state: MD

address: 4 Memorial Dr., room 134

department: CHI

country: USA

institute: NHLBI

description: Gene expression data from PBMC extracted from individual s019 at 8 hours after 250 mg of steroid administration

hyb_protocol: Labeled cDNA were hybridized to Human 1.0 ST GeneChip arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the respective manufacturers' instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The raw intensities of gene probesets in the CEL files were processed using Affymetrix Power Tools. The apt-probeset_summarize script was used for background correction and normalization (RMA with sketch, quantile normalization). The Bioconductor package arrayQualityMetrics was used to assess the quality of the microarray data.

label: biotin

organism: Homo sapiens

source_name: Individual s019 at 8 hours

label_protocol: Fragmented single-stranded sense cDNA were terminally labeled with biotin according to the standard Affymetrix protocol.

growth_protocol: Blood specimens were collected in heparinized syringes and peripheral blood mononuclear cells (PBMC) were isolated using Leucosep tubes with Ficoll-Paque Plus density gradient media and centrifugation. Fresh isolated PBMC were directly lysed in 700ul of Qiazol and stored at -80oC till isolation.

extract_protocol: Total RNA was isolated from freshly isolated PBMC using miRNeasy kit (Qiagen) according to the manufacturer’s instructions and eluted in 40ul of elution buffer with the addition of 1ul of RNase inhibitor (Invitrogen).

treatment_protocol: Eligible subjects were admitted to the NIH Clinical Center, a heparin lock was placed in the arm, and a minimum of one hour elapsed before the first blood draw to minimize any effect of a cortisol response due to I.V. insertion. Immediately after baseline phlebotomy the subjects were administered a single dose of intravenous (IV) hydrocortisone at either 50 mg or 250 mg concentrations.

value: PBMC

tag: dose

value: 250 mg hydrocortisone

tag: time

tag: individual

tag: ethnicity

value: Caucasian


title: PBMC_s020_4hr

description: Gene expression data from PBMC extracted from individual s020 at 4 hours after 250 mg of steroid administration

source_name: Individual s020 at 4 hours

value: Hispanic


title: PBMC_s020_12hr

description: Gene expression data from PBMC extracted from individual s020 at 12 hours after 250 mg of steroid administration

source_name: Individual s020 at 12 hours


title: PBMC_s020_1hr

description: Gene expression data from PBMC extracted from individual s020 at 1 hour after 250 mg of steroid administration

source_name: Individual s020 at 1 hour


title: PBMC_s019_1hr

description: Gene expression data from PBMC extracted from individual s019 at 1 hour after 250 mg of steroid administration

source_name: Individual s019 at 1 hour


title: PBMC_s019_4hr

description: Gene expression data from PBMC extracted from individual s019 at 4 hours after 250 mg of steroid administration

source_name: Individual s019 at 4 hours


title: PBMC_s018_24hr

description: Gene expression data from PBMC extracted from individual s018 at 24 hours after 250 mg of steroid administration

source_name: Individual s018 at 24 hours

value: Asian


title: PBMC_s019_24hr

description: Gene expression data from PBMC extracted from individual s019 at 24 hours after 250 mg of steroid administration

source_name: Individual s019 at 24 hours


title: LungTumorNodule_mouse712_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 712


title: PBMC_s019_0hr

description: Gene expression data from PBMC extracted from individual s019 immediately prior steroid administration

source_name: Individual s019 at baseline


title: PBMC_s020_0hr

description: Gene expression data from PBMC extracted from individual s020 immediately prior steroid administration

source_name: Individual s020 at baseline


title: PBMC_s020_24hr

description: Gene expression data from PBMC extracted from individual s020 at 24 hours after 250 mg of steroid administration

source_name: Individual s020 at 24 hours


title: PBMC_s020_8hr

description: Gene expression data from PBMC extracted from individual s020 at 8 hours after 250 mg of steroid administration

source_name: Individual s020 at 8 hours


title: PBMC_s019_12hr

description: Gene expression data from PBMC extracted from individual s019 at 12 hours after 250 mg of steroid administration

source_name: Individual s019 at 12 hours


title: Medulloblastoma_tumor_QD_vehicle_treated_1h_rep1

city: Roma

first: Gessica

last: Filocamo

address: Via Savona 6

institute: Exiris s.r.l.

description:
gene expression data of medulloblastoma allografts following vehicle treatment at the indicated time
QD_vehicle_1h_1

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.

growth_protocol: Allograft of medulloblastoma into CD1 nude mice

extract_protocol: Total RNA was extracted in Eppendorf tubes using the Qiagen Rneasy mini kit.

treatment_protocol: subministration of the indicated amount of MK4101 or vehicle treatment

tag: host strain

value: nude CD1

tag: tissue type

value: allograft of medulloblastoma from Ptch1+/- mice

tag: treated with

value: vehicle for 1hr

value: single dose (QD)

value: Medulloblastoma


title: LungTumorNodule_mouse957_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 957


title: LungTumorNodule_mouse808_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 808


title: PBMC_s021_0hr

description: Gene expression data from PBMC extracted from individual s021 immediately prior steroid administration

source_name: Individual s021 at baseline

value: female


title: LungTumorNodule_mouse530_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 530


title: LungTumorNodule_mouse821_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 821


title: LungTumorNodule_mouse1103_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1103


title: LungTumorNodule_mouse742_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 742


title: LungTumorNodule_mouse586_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 586


title: LungTumorNodule_mouse512_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 512


title: LungTumorNodule_mouse748_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 748


title: LungTumorNodule_mouse780_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 780


title: LungTumorNodule_mouse516_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 516


title: LungTumorNodule_mouse546_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 546


title: LungTumorNodule_mouse527_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 527


title: LungTumorNodule_mouse544_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 544


title: PBMC_s018_12hr

description: Gene expression data from PBMC extracted from individual s018 at 12 hours after 250 mg of steroid administration

source_name: Individual s018 at 12 hours


title: PBMC_s018_8hr

description: Gene expression data from PBMC extracted from individual s018 at 8 hours after 250 mg of steroid administration

source_name: Individual s018 at 8 hours


title: PBMC_s016_12hr

description: Gene expression data from PBMC extracted from individual s016 at 12 hours after 50 mg of steroid administration

source_name: Individual s016 at 12 hours

value: 50 mg hydrocortisone


title: PBMC_s018_4hr

description: Gene expression data from PBMC extracted from individual s018 at 4 hours after 250 mg of steroid administration

source_name: Individual s018 at 4 hours


title: LungTumorNodule_mouse778_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 778

value: A/J X C57BL/6


title: LungTumorNodule_mouse529_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 529

value: offspring bred to the 4th generation (ABF4)


title: LungTumorNodule_mouse589_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 589

value: male


title: PBMC_s018_0hr

description: Gene expression data from PBMC extracted from individual s018 immediately prior steroid administration

source_name: Individual s018 at baseline


title: PBMC_s016_24hr

description: Gene expression data from PBMC extracted from individual s016 at 24 hours after 50 mg of steroid administration

source_name: Individual s016 at 24 hours


title: LungTumorNodule_mouse889_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 889

value: 40 wks


title: LungTumorNodule_mouse619_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 619

value: lung tumor nodule


title: PBMC_s016_0hr

description: Gene expression data from PBMC extracted from individual s016 immediately prior steroid administration

source_name: Individual s016 at baseline

value: PBMC


title: PBMC_s016_1hr

description: Gene expression data from PBMC extracted from individual s016 at 1 hour after 50 mg of steroid administration

source_name: Individual s016 at 1 hour


title: PBMC_s015_24hr

description: Gene expression data from PBMC extracted from individual s015 at 24 hours after 50 mg of steroid administration

source_name: Individual s015 at 24 hours

value: African American


title: PBMC_s016_8hr

description: Gene expression data from PBMC extracted from individual s016 at 8 hours after 50 mg of steroid administration

source_name: Individual s016 at 8 hours

value: Caucasian


title: LungTumorNodule_mouse679_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 679


title: LungTumorNodule_mouse501_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 501


title: PBMC_s016_4hr

description: Gene expression data from PBMC extracted from individual s016 at 4 hours after 50 mg of steroid administration

source_name: Individual s016 at 4 hours


title: LungTumorNodule_mouse636_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 636


title: LungTumorNodule_mouse489_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 489


title: PBMC_s015_12hr

description: Gene expression data from PBMC extracted from individual s015 at 12 hours after 50 mg of steroid administration

source_name: Individual s015 at 12 hours


title: LungTumorNodule_mouse1129_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 1129


title: PBMC_s015_4hr

description: Gene expression data from PBMC extracted from individual s015 at 4 hours after 50 mg of steroid administration

source_name: Individual s015 at 4 hours


title: PBMC_s015_1hr

description: Gene expression data from PBMC extracted from individual s015 at 1 hour after 50 mg of steroid administration

source_name: Individual s015 at 1 hour


title: LungTumorNodule_mouse1128_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1128


title: LungTumorNodule_mouse1126_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1126


title: PBMC_s018_1hr

description: Gene expression data from PBMC extracted from individual s018 at 1 hour after 250 mg of steroid administration

source_name: Individual s018 at 1 hour

value: 250 mg hydrocortisone


title: PBMC_s015_0hr

description: Gene expression data from PBMC extracted from individual s015 immediately prior steroid administration

source_name: Individual s015 at baseline


title: LungTumorNodule_mouse1117_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 1117


title: PBMC_s015_8hr

description: Gene expression data from PBMC extracted from individual s015 at 8 hours after 50 mg of steroid administration

source_name: Individual s015 at 8 hours


title: LungTumorNodule_mouse1101_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1101


title: PBMC_s014_4hr

description: Gene expression data from PBMC extracted from individual s014 at 4 hours after 50 mg of steroid administration

source_name: Individual s014 at 4 hours


title: PBMC_s014_8hr

description: Gene expression data from PBMC extracted from individual s014 at 8 hours after 50 mg of steroid administration

source_name: Individual s014 at 8 hours


title: LungTumorNodule_mouse1102_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1102


title: PBMC_s014_24hr

description: Gene expression data from PBMC extracted from individual s014 at 24 hours after 50 mg of steroid administration

source_name: Individual s014 at 24 hours


title: PBMC_s014_12hr

description: Gene expression data from PBMC extracted from individual s014 at 12 hours after 50 mg of steroid administration

source_name: Individual s014 at 12 hours


title: LungTumorNodule_mouse702_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 702


title: LungTumorNodule_mouse1099_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1099


title: LungTumorNodule_mouse1084_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1084


title: LungTumorNodule_mouse1090_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 1090


title: PBMC_s014_1hr

description: Gene expression data from PBMC extracted from individual s014 at 1 hour after 50 mg of steroid administration

source_name: Individual s014 at 1 hour


title: PBMC_s014_0hr

description: Gene expression data from PBMC extracted from individual s014 immediately prior steroid administration

source_name: Individual s014 at baseline


title: LungTumorNodule_mouse1091_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 1091


title: LungTumorNodule_mouse1072_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 1072


title: PBMC_s013_4hr

description: Gene expression data from PBMC extracted from individual s013 at 4 hours after 50 mg of steroid administration

source_name: Individual s013 at 4 hours


title: PBMC_s013_8hr

description: Gene expression data from PBMC extracted from individual s013 at 8 hours after 50 mg of steroid administration

source_name: Individual s013 at 8 hours


title: PBMC_s013_12hr

description: Gene expression data from PBMC extracted from individual s013 at 12 hours after 50 mg of steroid administration

source_name: Individual s013 at 12 hours


title: PBMC_s013_24hr

description: Gene expression data from PBMC extracted from individual s013 at 24 hours after 50 mg of steroid administration

source_name: Individual s013 at 24 hours


title: PBMC_s012_24hr

description: Gene expression data from PBMC extracted from individual s012 at 24 hours after 50 mg of steroid administration

source_name: Individual s012 at 24 hours


title: LungTumorNodule_mouse972_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 972


title: PBMC_s013_0hr

description: Gene expression data from PBMC extracted from individual s013 immediately prior steroid administration

source_name: Individual s013 at baseline


title: LungTumorNodule_mouse970_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 970


title: PBMC_s012_8hr

description: Gene expression data from PBMC extracted from individual s012 at 8 hours after 50 mg of steroid administration

source_name: Individual s012 at 8 hours


title: PBMC_s012_1hr

description: Gene expression data from PBMC extracted from individual s012 at 1 hour after 50 mg of steroid administration

source_name: Individual s012 at 1 hour


title: PBMC_s012_4hr

description: Gene expression data from PBMC extracted from individual s012 at 4 hours after 50 mg of steroid administration

source_name: Individual s012 at 4 hours


title: PBMC_s012_0hr

description: Gene expression data from PBMC extracted from individual s012 immediately prior steroid administration

source_name: Individual s012 at baseline


title: PBMC_s013_1hr

description: Gene expression data from PBMC extracted from individual s013 at 1 hour after 50 mg of steroid administration

source_name: Individual s013 at 1 hour


title: LungTumorNodule_mouse969_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 969


title: LungTumorNodule_mouse959_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 959


title: PBMC_s011_24hr

description: Gene expression data from PBMC extracted from individual s011 at 24 hours after 250 mg of steroid administration

source_name: Individual s011 at 24 hours

value: Asian


title: LungTumorNodule_mouse958_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 958


title: LungTumorNodule_mouse888_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 888


title: LungTumorNodule_mouse887_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 887


title: PBMC_s011_12hr

description: Gene expression data from PBMC extracted from individual s011 at 12 hours after 250 mg of steroid administration

source_name: Individual s011 at 12 hours


title: PBMC_s011_8hr

description: Gene expression data from PBMC extracted from individual s011 at 8 hours after 250 mg of steroid administration

source_name: Individual s011 at 8 hours


title: PBMC_s011_4hr

description: Gene expression data from PBMC extracted from individual s011 at 4 hours after 250 mg of steroid administration

source_name: Individual s011 at 4 hours


title: PBMC_s011_0hr

description: Gene expression data from PBMC extracted from individual s011 immediately prior steroid administration

source_name: Individual s011 at baseline


title: PBMC_s010_24hr

description: Gene expression data from PBMC extracted from individual s010 at 24 hours after 250 mg of steroid administration

source_name: Individual s010 at 24 hours


title: LungTumorNodule_mouse886_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 886


title: PBMC_s009_12hr

description: Gene expression data from PBMC extracted from individual s009 at 12 hours after 250 mg of steroid administration

source_name: Individual s009 at 12 hours


title: PBMC_s009_24hr

description: Gene expression data from PBMC extracted from individual s009 at 24 hours after 250 mg of steroid administration

source_name: Individual s009 at 24 hours


title: PBMC_s010_8hr

description: Gene expression data from PBMC extracted from individual s010 at 8 hours after 250 mg of steroid administration

source_name: Individual s010 at 8 hours


title: PBMC_s010_1hr

description: Gene expression data from PBMC extracted from individual s010 at 1 hour after 250 mg of steroid administration

source_name: Individual s010 at 1 hour


title: PBMC_s010_0hr

description: Gene expression data from PBMC extracted from individual s010 immediately prior steroid administration

source_name: Individual s010 at baseline


title: PBMC_s010_12hr

description: Gene expression data from PBMC extracted from individual s010 at 12 hours after 250 mg of steroid administration

source_name: Individual s010 at 12 hours


title: PBMC_s011_1hr

description: Gene expression data from PBMC extracted from individual s011 at 1 hour after 250 mg of steroid administration

source_name: Individual s011 at 1 hour


title: PBMC_s010_4hr

description: Gene expression data from PBMC extracted from individual s010 at 4 hours after 250 mg of steroid administration

source_name: Individual s010 at 4 hours


title: LungTumorNodule_mouse882_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 882


title: PBMC_s009_8hr

description: Gene expression data from PBMC extracted from individual s009 at 8 hours after 250 mg of steroid administration

source_name: Individual s009 at 8 hours


title: PBMC_s009_4hr

description: Gene expression data from PBMC extracted from individual s009 at 4 hours after 250 mg of steroid administration

source_name: Individual s009 at 4 hours


title: PBMC_s009_1hr

description: Gene expression data from PBMC extracted from individual s009 at 1 hour after 250 mg of steroid administration

source_name: Individual s009 at 1 hour


title: LungTumorNodule_mouse829_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 829


title: LungTumorNodule_mouse881_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 881


title: PBMC_s009_0hr

description: Gene expression data from PBMC extracted from individual s009 immediately prior steroid administration

source_name: Individual s009 at baseline


title: LungTumorNodule_mouse820_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 820


title: LungTumorNodule_mouse825_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 825


title: LungTumorNodule_mouse880_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 880


title: PBMC_s012_12hr

description: Gene expression data from PBMC extracted from individual s012 at 12 hours after 50 mg of steroid administration

source_name: Individual s012 at 12 hours


title: PBMC_s007_4hr

description: Gene expression data from PBMC extracted from individual s007 at 4 hours after 250 mg of steroid administration

source_name: Individual s007 at 4 hours


title: PBMC_s007_24hr

description: Gene expression data from PBMC extracted from individual s007 at 24 hours after 250 mg of steroid administration

source_name: Individual s007 at 24 hours


title: PBMC_s007_8hr

description: Gene expression data from PBMC extracted from individual s007 at 8 hours after 250 mg of steroid administration

source_name: Individual s007 at 8 hours


title: PBMC_s007_1hr

description: Gene expression data from PBMC extracted from individual s007 at 1 hour after 250 mg of steroid administration

source_name: Individual s007 at 1 hour


title: PBMC_s007_12hr

description: Gene expression data from PBMC extracted from individual s007 at 12 hours after 250 mg of steroid administration

source_name: Individual s007 at 12 hours


title: LungTumorNodule_mouse819_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 819


title: LungTumorNodule_mouse824_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 824


title: LungTumorNodule_mouse815_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 815


title: LungTumorNodule_mouse800_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 800


title: LungTumorNodule_mouse814_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 814


title: PBMC_s006_1hr

description: Gene expression data from PBMC extracted from individual s006 at 1 hour after 250 mg of steroid administration

source_name: Individual s006 at 1 hour


title: PBMC_s006_4hr

description: Gene expression data from PBMC extracted from individual s006 at 4 hours after 250 mg of steroid administration

source_name: Individual s006 at 4 hours


title: PBMC_s006_8hr

description: Gene expression data from PBMC extracted from individual s006 at 8 hours after 250 mg of steroid administration

source_name: Individual s006 at 8 hours


title: PBMC_s005_8hr

description: Gene expression data from PBMC extracted from individual s005 at 8 hours after 50 mg of steroid administration

source_name: Individual s005 at 8 hours


title: PBMC_s005_24hr

description: Gene expression data from PBMC extracted from individual s005 at 24 hours after 50 mg of steroid administration

source_name: Individual s005 at 24 hours


title: PBMC_s005_4hr

description: Gene expression data from PBMC extracted from individual s005 at 4 hours after 50 mg of steroid administration

source_name: Individual s005 at 4 hours


title: PBMC_s006_24hr

description: Gene expression data from PBMC extracted from individual s006 at 24 hours after 250 mg of steroid administration

source_name: Individual s006 at 24 hours


title: LungTumorNodule_mouse797_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 797


title: PBMC_s005_12hr

description: Gene expression data from PBMC extracted from individual s005 at 12 hours after 50 mg of steroid administration

source_name: Individual s005 at 12 hours


title: PBMC_s003_12hr

description: Gene expression data from PBMC extracted from individual s003 at 12 hours after 50 mg of steroid administration

source_name: Individual s003 at 12 hours


title: PBMC_s005_0hr

description: Gene expression data from PBMC extracted from individual s005 immediately prior steroid administration

source_name: Individual s005 at baseline


title: PBMC_s003_24hr

description: Gene expression data from PBMC extracted from individual s003 at 24 hours after 50 mg of steroid administration

source_name: Individual s003 at 24 hours


title: PBMC_s003_0hr

description: Gene expression data from PBMC extracted from individual s003 immediately prior steroid administration

source_name: Individual s003 at baseline


title: PBMC_s006_0hr

description: Gene expression data from PBMC extracted from individual s006 immediately prior steroid administration

source_name: Individual s006 at baseline


title: PBMC_s003_4hr

description: Gene expression data from PBMC extracted from individual s003 at 4 hours after 50 mg of steroid administration

source_name: Individual s003 at 4 hours


title: PBMC_s005_1hr

description: Gene expression data from PBMC extracted from individual s005 at 1 hour after 50 mg of steroid administration

source_name: Individual s005 at 1 hour


title: PBMC_s003_1hr

description: Gene expression data from PBMC extracted from individual s003 at 1 hour after 50 mg of steroid administration

source_name: Individual s003 at 1 hour


title: PBMC_s003_8hr

description: Gene expression data from PBMC extracted from individual s003 at 8 hours after 50 mg of steroid administration

source_name: Individual s003 at 8 hours


title: LungTumorNodule_mouse798_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 798


title: PBMC_s007_0hr

description: Gene expression data from PBMC extracted from individual s007 immediately prior steroid administration

source_name: Individual s007 at baseline


title: LungTumorNodule_mouse630_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 630


title: LungTumorNodule_mouse791_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 791


title: LungTumorNodule_mouse799_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 799


title: LungTumorNodule_mouse784_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 784


title: LungTumorNodule_mouse783_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 783


title: PBMC_s002_12hr

description: Gene expression data from PBMC extracted from individual s002 at 12 hours after 50 mg of steroid administration

source_name: Individual s002 at 12 hours


title: LungTumorNodule_mouse627_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 627


title: LungTumorNodule_mouse620_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 620


title: PBMC_s002_24hr

description: Gene expression data from PBMC extracted from individual s002 at 24 hours after 50 mg of steroid administration

source_name: Individual s002 at 24 hours


title: PBMC_s002_4hr

description: Gene expression data from PBMC extracted from individual s002 at 4 hours after 50 mg of steroid administration

source_name: Individual s002 at 4 hours


title: PBMC_s002_0hr

description: Gene expression data from PBMC extracted from individual s002 immediately prior steroid administration

source_name: Individual s002 at baseline


title: PBMC_s002_8hr

description: Gene expression data from PBMC extracted from individual s002 at 8 hours after 50 mg of steroid administration

source_name: Individual s002 at 8 hours


title: LungTumorNodule_mouse611_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 611


title: PBMC_s001_1hr

description: Gene expression data from PBMC extracted from individual s001 at 1 hour after 50 mg of steroid administration

source_name: Individual s001 at 1 hour


title: 18-H_Sor6 2%

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 1.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA (as implemented in the XPS v1.10.2 package of Bioconductor). Reported values are on log2-scale.

source_name: HepG2S1 cells

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: Cells were grown in Williams Medium E (WEM, Invitrogen) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 20 mU/ml insulin, 50 nM dexamethasone, 100 U/ml penicillin, 100 µg/ml streptomycin, 2.5 µg fungizone, 50 µg/ml gentamycin and 100 µg/ml vancomycin (=WEM-C). To develop the sorafenib resistant HepG2S1 cells from the HepG2 cell line, we first determined the IC50 of HepG2 for sorafenib. Next, we cultured HepG2 in 6-well plates at 75x103 cells per well and incubated the cells with sorafenib concentrations just below their IC50. During the following weeks, we slowly increased the sorafenib dose with 0.25 µM per time. Over several months we developed the HepG2S1 cell lines resistant to sorafenib. After establishment, these resistant cell lines were continuously cultured in the presence of sorafenib. Sorafenib (Bayer HealthCare, Leverkusen, Germany) was dissolved in 100% dimethylsulfoxid (DMSO).

extract_protocol: Cells were harvested with Trizol (Invitrogen, Merelbeke, Belgium) treatment and RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer's instructions. The RNA quality was assessed with the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA).

treatment_protocol: HepG2S1 cells were grown at 1x106 in 25 cm² tissue flasks in 2% O2/5% CO2/93% N2, in the presence of 6 µM sorafenib. After 72 hours, cells were harvested.

tag: cell line

value: HepG2S1 cells

tag: exposure

value: sorafenib and 2% O2 (72h)


title: PBMC_s002_1hr

description: Gene expression data from PBMC extracted from individual s002 at 1 hour after 50 mg of steroid administration

source_name: Individual s002 at 1 hour


title: PBMC_s001_8hr

description: Gene expression data from PBMC extracted from individual s001 at 8 hours after 50 mg of steroid administration

source_name: Individual s001 at 8 hours


title: 15-H_S6_onttr 20%

treatment_protocol: HepG2S1 cells were grown at 1x106 in 25 cm² tissue flasks in 20% O2/5% CO2/75% N2, withdrawn from sorafenib. After 72 hours, cells were harvested.

value: withdrawl sorafenib and 20% O2 (72h)


title: PBMC_s001_4hr

description: Gene expression data from PBMC extracted from individual s001 at 4 hours after 50 mg of steroid administration

source_name: Individual s001 at 4 hours


title: PBMC_s001_0hr

description: Gene expression data from PBMC extracted from individual s001 immediately prior steroid administration

source_name: Individual s001 at baseline


title: PBMC_s001_12hr

description: Gene expression data from PBMC extracted from individual s001 at 12 hours after 50 mg of steroid administration

source_name: Individual s001 at 12 hours


title: 10-H_Sor6 20%

treatment_protocol: HepG2S1 cells were grown at 1x106 in 25 cm² tissue flasks in 20% O2/5% CO2/75% N2, in the presence of 6 µM sorafenib. After 72 hours, cells were harvested.

value: sorafenib and 20% O2 (72h)


title: 9-H_Sor6 20%


title: 17-H_Sor6 2%


title: LungTumorNodule_mouse601_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 601

tag: strain background


title: LungTumorNodule_mouse610_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 610

tag: strain


title: 7-H_Sor6 20%

growth_protocol: Cells were grown in Williams Medium E (WEM, Invitrogen) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 20 mU/ml insulin, 50 nM dexamethasone, 100 U/ml penicillin, 100 µg/ml streptomycin, 2.5 µg fungizone, 50 µg/ml gentamycin and 100 µg/ml vancomycin (=WEM-C). To develop the sorafenib resistant HepG2S1 cells from the HepG2 cell line, we first determined the IC50 of HepG2 for sorafenib. Next, we cultured HepG2 in 6-well plates at 75x103 cells per well and incubated the cells with sorafenib concentrations just below their IC50. During the following weeks, we slowly increased the sorafenib dose with 0.25 <U+00B5>M per time. Over several months we developed the HepG2S1 cell lines resistant to sorafenib. After establishment, these resistant cell lines were continuously cultured in the presence of sorafenib. Sorafenib (Bayer HealthCare, Leverkusen, Germany) was dissolved in 100% dimethylsulfoxid (DMSO).


title: 14-H_S6_onttr 20%


title: 3-HepG2 20%

source_name: HepG2 human hepatoblastoma cells (HB-8065)

growth_protocol: Cells were grown in Williams Medium E (WEM, Invitrogen) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 20 mU/ml insulin, 50 nM dexamethasone, 100 U/ml penicillin, 100 µg/ml streptomycin, 2.5 µg fungizone, 50 µg/ml gentamycin and 100 µg/ml vancomycin (=WEM-C).

treatment_protocol: HepG2 cells were grown at 1x106 in 25 cm² tissue flasks in 20% O2/5% CO2/75% N2, without sorafenib exposure. After 72 hours, cells were harvested.

value: HepG2 cells

value: no sorafenib and 20% O2 (72h)


title: 2-HepG2 20%


title: LungTumorNodule_mouse608_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 608

tag: gender


title: LungTumorNodule_mouse651_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 651

tag: age


title: LungTumorNodule_mouse650_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 650

tag: number of lung tumors


title: LungTumorNodule_mouse652_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 652

tag: kras37bp marker genotype


title: LungTumorNodule_mouse602_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 602

tag: tissue


title: LungTumorNodule_mouse653_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 653

tag: batch


title: LungTumorNodule_mouse599_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 599


title: 16-H_Sor6 2%


title: 6-H_Sor6 20%


title: 13-H_S6_onttr 20%


title: PBMC_s001_24hr

description: Gene expression data from PBMC extracted from individual s001 at 24 hours after 50 mg of steroid administration

source_name: Individual s001 at 24 hours

tag: dose

value: 50 mg hydrocortisone

value: female


title: LungTumorNodule_mouse596_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 596

value: A/J X C57BL/6

value: offspring bred to the 4th generation (ABF4)


title: PBMC_s006_12hr

description: Gene expression data from PBMC extracted from individual s006 at 12 hours after 250 mg of steroid administration

source_name: Individual s006 at 12 hours

tag: time


title: Saline-mouse2-2-rep1

city: Stanford

first: Rosemarie

last: DeKruyff

state: CA

address: Stanford University

institute: Department of Medicine

hyb_protocol: Affymetrix standard protocol for Mouse Gene 1.0 ST array, performed by the microarray core facility at the Dana Farber Cancer Institute (DFCI)

data_processing: CEL files processed using RMA algorithm in ExpressionFileCreator module in GenePattern; statistical analyses performed using Multiplot Suite in GenePattern

source_name: Lung, sensitized and challenged with saline

extract_protocol: Total RNA was isolated from lung tissues using RNeasy mini kit (QIAGEN),

value: Balb/c

value: lung


title: Isotype-mouse2-2-rep1

scan_protocol: Affymetrix standard protocol for Mouse Gene 1.0 ST array, performed by the microarray core facility at the Dana Farber Cancer Institute (DFCI)

source_name: Lung, sensitized and challenged with OVA, treated with isotype


title: aRGMB treated-mouse1-2-rep1

source_name: Lung, sensitized and challenged with OVA, treated with aRGMB mAb

label_protocol: Affymetrix standard protocol for Mouse Gene 1.0 ST array, performed by the microarray core facility at the Dana Farber Cancer Institute (DFCI)


title: aRGMB treated-mouse3-2-rep1


title: LungTumorNodule_mouse588_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 588

value: male

value: 40 wks

value: lung tumor nodule


title: 1-HepG2 20%


title: Saline-mouse3-2rep1


title: aRGMB treated-mouse2-2-rep1


title: Saline-mouse1-2-rep1


title: LungTumorNodule_mouse772_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 772


title: Isotype-mouse1-2-rep1


title: Isotype-mouse1-rep1


title: aRGMB treated-mouse2-rep1


title: LungTumorNodule_mouse773_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 773


title: LungTumorNodule_mouse782_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 782


title: Isotype-mouse3-rep1


title: Isotype-mouse2-rep1


title: aRGMB treated-mouse1-rep1


title: LungTumorNodule_mouse781_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 781


title: Saline-mouse3-rep1


title: LungTumorNodule_mouse766_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 766


title: LungTumorNodule_mouse771_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 771


title: aRGMB treated-mouse3-rep1


title: Saline-mouse1-rep1


title: Saline-mouse2-rep1


title: LungTumorNodule_mouse763_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 763


title: LungTumorNodule_mouse760_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 760


title: E5

city: Boston

first: Lois

last: Smith

state: MA

address: 300 Longwood Avenue

department: Ophthalmology

institute: Harvard Medical School

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Background Correction with Illumina Genome Studio

source_name: Vldlr KO

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit

extract_protocol: RNA extreated with Rneasy Mini Kit (Qiagen, cat 74104)

tag: background strain

value: JAX

tag: genotype/variation

value: Vldlr KO

value: retina


title: C4

source_name: Jax WT

value: wild-type


title: E2


title: E4


title: d6TG-null-5

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: Prdm1 null d6 TG replicate 5

data_processing: Rank invariant normalization using Gene Expression Module V1.9.0 of Illumina GenomeStudio

source_name: TG cell cultures

label_protocol: Total RNA was labeled according to the standard Illumina protocol

growth_protocol: Trophoblast stem cells differentiated to trophoblast giant cells by withdrawal of FGF4, TGFbeta1 and heparin sulfate.

extract_protocol: RNA was extracted with QIAGEN Rneasy mini kit and DNase I treatment on-column in accordance with the prescribed protocol provided with the kit.

tag: genotype

tag: cell type

value: trophoblast cells


title: LungTumorNodule_mouse756_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 756


title: d6TG-null-3

description: Prdm1 null d6 TG replicate 3


title: LungTumorNodule_mouse759_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 759


title: d6TG-null-2

description: Prdm1 null d6 TG replicate 2


title: LungTumorNodule_mouse752_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 752


title: C6


title: d6TG-null-4

description: Prdm1 null d6 TG replicate 4


title: d6TG-null-1

description: Prdm1 null d6 TG replicate 1


title: LungTumorNodule_mouse725_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 725


title: d6TG-cont-5

description: Control d6 TG replicate 5


title: d6TG-cont-8

description: Control d6 TG replicate 8


title: d6TG-cont-6

description: Control d6 TG replicate 6


title: d6TG-null-6

description: Prdm1 null d6 TG replicate 6


title: d6TG-cont-7

description: Control d6 TG replicate 7


title: LungTumorNodule_mouse731_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 731


title: LungTumorNodule_mouse721_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 721


title: d6TG-cont-4

description: Control d6 TG replicate 4


title: C5


title: LungTumorNodule_mouse765_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 765


title: LungTumorNodule_mouse719_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 719


title: LungTumorNodule_mouse713_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 713


title: d6TG-cont-1

description: Control d6 TG replicate 1


title: d4TG-null-3

description: Prdm1 null d4 TG replicate 3


title: d4TG-null-6

description: Prdm1 null d4 TG replicate 6


title: d6TG-cont-3

description: Control d6 TG replicate 3


title: d4TG-null-2

description: Prdm1 null d4 TG replicate 2


title: d4TG-cont-6

description: Control d4 TG replicate 6


title: LungTumorNodule_mouse711_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 711


title: d4TG-null-5

description: Prdm1 null d4 TG replicate 5


title: d4TG-null-4

description: Prdm1 null d4 TG replicate 4


title: d4TG-null-1

description: Prdm1 null d4 TG replicate 1


title: d4TG-cont-8

description: Control d4 TG replicate 8


title: d4TG-cont-4

description: Control d4 TG replicate 4


title: d4TG-cont-2

description: Control d4 TG replicate 2


title: d6TG-cont-2

description: Control d6 TG replicate 2


title: d4TG-cont-7

description: Control d4 TG replicate 7


title: d2TG-null-10

description: Prdm1 null d2 TG replicate 10


title: LungTumorNodule_mouse703_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 703


title: LungTumorNodule_mouse706_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 706


title: LungTumorNodule_mouse701_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 701


title: LungTumorNodule_mouse687_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 687


title: d4TG-cont-5

description: Control d4 TG replicate 5


title: LungTumorNodule_mouse673_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 673


title: LungTumorNodule_mouse705_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 705


title: LungTumorNodule_mouse675_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 675


title: LungTumorNodule_mouse699_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 699


title: LungTumorNodule_mouse672_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 672


title: d2TG-null-5

description: Prdm1 null d2 TG replicate 5


title: d2TG-null-3

description: Prdm1 null d2 TG replicate 3


title: d2TG-null-6

description: Prdm1 null d2 TG replicate 6


title: d2TG-cont-10

description: Control d2 TG replicate 10


title: d2TG-null-1

description: Prdm1 null d2 TG replicate 1


title: d2TG-null-8

description: Prdm1 null d2 TG replicate 8


title: d2TG-null-2

description: Prdm1 null d2 TG replicate 2


title: d2TG-null-7

description: Prdm1 null d2 TG replicate 7


title: LungTumorNodule_mouse664_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 664


title: d2TG-cont-9

description: Control d2 TG replicate 9


title: LungTumorNodule_mouse642_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 642


title: LungTumorNodule_mouse645_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 645


title: d2TG-cont-8

description: Control d2 TG replicate 8


title: d2TG-cont-6

description: Control d2 TG replicate 6


title: d2TG-cont-4

description: Control d2 TG replicate 4


title: d2TG-cont-7

description: Control d2 TG replicate 7


title: d2TG-null-4

description: Prdm1 null d2 TG replicate 4


title: d2TG-cont-2

description: Control d2 TG replicate 2


title: d2TG-cont-5

description: Control d2 TG replicate 5


title: d0TS-null-8

description: Prdm1 null d0 TS replicate 8

source_name: TS cell cultures


title: LungTumorNodule_mouse558_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 558


title: d0TS-null-6

description: Prdm1 null d0 TS replicate 6


title: d0TS-null-7

description: Prdm1 null d0 TS replicate 7


title: d0TS-null-1

description: Prdm1 null d0 TS replicate 1


title: d2TG-cont-1

description: Control d2 TG replicate 1


title: LungTumorNodule_mouse641_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 641


title: d0TS-null-4

description: Prdm1 null d0 TS replicate 4


title: LungTumorNodule_mouse639_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 639


title: LungTumorNodule_mouse555_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 555


title: d2TG-cont-3

description: Control d2 TG replicate 3


title: d0TS-null-2

description: Prdm1 null d0 TS replicate 2


title: d0TS-null-5

description: Prdm1 null d0 TS replicate 5


title: LungTumorNodule_mouse540_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 540


title: d0TS-cont-9

description: Control d0 TS replicate 9


title: LungTumorNodule_mouse554_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 554


title: LungTumorNodule_mouse549_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 549


title: d0TS-cont-6

description: Control d0 TS replicate 6


title: d2TG-null-9

description: Prdm1 null d2 TG replicate 9


title: LungTumorNodule_mouse514_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 514


title: d0TS-cont-7

description: Control d0 TS replicate 7


title: LungTumorNodule_mouse507_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 507


title: d4TG-cont-1

description: Control d4 TG replicate 1


title: LungTumorNodule_mouse532_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 532


title: I-3D C. perfringens Caco-2 in S/D/DMEM(-) 3 h

status: Public on Mar 13 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: Arrays were scanned using Agilent Scan software A8.3.1.

data_processing: Data were extracted using Feature Extraction 10.7.3.1. Microarray data were normalized with the bacterial control genes, log2 transformed.

organism: Clostridium perfringens

label_protocol: Total RNA prepared was labeled with the Agilent Low Input Quick-Amp WT Labeling Kit according to the manufacturer’s instructions.

growth_protocol: Bacterial strains and growth conditions. C. perfringens food poisoning (FP) type A strain NCTC8239 was purchased from the National Collection of Type Cultures. To achieve the sporulation, bacteria were inoculated into fluid thioglycollate (FTG; BD, Franklin Lakes, NJ) medium and incubated anaerobically for 18 h at 37ºC. One milliliter of the bacterial culture was passaged into 10 ml Duncan-Strong (DS) medium [31] and cultured for 24 h at 37ºC. One milliliter of the culture was then heated at 75ºC for 20 min and passaged into 10 ml of fresh DS medium. The heat treatment and passage were repeated until the amount of spores observed by phase contrast microscopy was greater than half of the total number of bacteria. These bacterial cells were heated and stored at -80°C with glycerol for future use.

extract_protocol: Total RNA was extracted with slight modifications. Bacterial cultures containing 2 × 107 CFU of C. perfringens were treated with RNAprotect Bacteria Reagent (Qiagen) according to the manufacturer’s instructions. After centrifugation at 5,000 × g for 10 min, the pellets were washed with SET buffer (25% sucrose, 50 mM EDTA (pH 8.0) and 50 mM Tris-HCl (pH 8.0)) at 5,000 × g for 10 min. The pellets, which were suspended in GTC buffer (4 M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate (pH 7.0) and 0.1 M β-mercaptoethanol), were homogenized by passing 3 times through a 21-gauge needle to disrupt Caco-2 cell membranes. After being centrifuged at 5,000 × g for 10 min, the pellets were washed with SET buffer once. The bacterial cells were lysed by suspending in 100 µl SET buffer with 20 mg/ml lysozyme (Sigma) and 100 μg/ml proteinase K (Roche Applied Science) at 37ºC for 30 min. Following incubation, they were transferred to a tube containing zirconia beads (AMR, Gifu, Japan), vortexed for 5 min, and centrifuged at 21,130 × g for 5 min. Total RNA was extracted from the supernatants using TRI reagent LS (Sigma), and then purified with RNeasy MinElute Cleanup (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Bacteria were co-cultured with human intestinal epithelial Caco-2 cells but with slight modifications. Briefly, Caco-2 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM; Sigma, St. Louis, MO) supplemented with 10% fetal bovine serum. The cells were plated in a 24-well plate (1.3x105 cells per well) and incubated for 4 days. Just before the inoculation of bacteria, the cells were washed using phosphate buffered saline (PBS) three times and incubated in 1 ml glucose-negative DMEM (DMEM(-); Life Science Technologies, Carlsbad, CA) supplemented with 0.4% starch and 50 uM DCA (Wako, Osaka, Japan). Strain NCTC8239 was pre-cultured in FTG anaerobically for 18 h at 37ºC. The cultures were washed with PBS twice and 100 ul of bacterial culture (1-5 x 107 colony-forming units (CFU) per ml) were inoculated into Caco-2 cells and incubated in the CO2 incubator at 37ºC. The number of viable vegetative cells was determined by plating serially diluted samples onto Brain Heart Infusion (BHI) agar, incubating at 37°C for 24 h in anaerobic conditions, and calculating CFU. The number of heat-resistant spores was counted by plating heat-treated cultures onto BHI agar. The detection threshold was 200 CFU/ml.

tag: time (h)

tag: s/dmem(s) or s/d/dmem(d)

value: D

tag: biological replicate

value: I


title: LungTumorNodule_mouse502_Kras37bpMarkerGenotype_B_homozygous_rep1

description: sample name: 502

tag: strain background


title: H-3D C. perfringens Caco-2 in S/D/DMEM(-) 3 h

value: H

tag: strain


title: d0TS-cont-5

description: Control d0 TS replicate 5


title: E-3D (2) C. perfringens Caco-2 in S/D/DMEM(-) 3 h

value: E


title: E-3S C. perfringens Caco-2 in S/DMEM(-) 3 h

description: C. perfringens Caco-2 in S/DMEM(-) 3 h

value: S


title: I-3S C. perfringens Caco-2 in S/DMEM(-) 3 h

description: C. perfringens Caco-2 in S/DMEM(-) 3 h


title: d0TS-cont-4

description: Control d0 TS replicate 4


title: E-3D C. perfringens Caco-2 in S/D/DMEM(-) 3 h


title: d0TS-cont-3

description: Control d0 TS replicate 3


title: H-2D C. perfringens Caco-2 in S/D/DMEM(-) 2 h


title: I-2D C. perfringens Caco-2 in S/D/DMEM(-) 2 h


title: d0TS-cont-8

description: Control d0 TS replicate 8


title: H-3S C. perfringens Caco-2 in S/DMEM(-) 3 h

description: C. perfringens Caco-2 in S/DMEM(-) 3 h


title: d0TS-cont-2

description: Control d0 TS replicate 2


title: d0TS-cont-1

description: Control d0 TS replicate 1


title: LungTumorNodule_mouse492_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 492

value: A/J X C57BL/6

tag: gender


title: LungTumorNodule_mouse491_Kras37bpMarkerGenotype_A_homozygous_rep1

description: sample name: 491

value: offspring bred to the 4th generation (ABF4)

tag: age


title: H-2S C. perfringens Caco-2 in S/DMEM(-) 2 h

description: C. perfringens Caco-2 in S/DMEM(-) 2 h


title: E-2D C. perfringens Caco-2 in S/D/DMEM(-) 2 h


title: d4TG-cont-3

description: Control d4 TG replicate 3


title: I-2S C. perfringens Caco-2 in S/DMEM(-) 2 h

description: C. perfringens Caco-2 in S/DMEM(-) 2 h


title: I-0.5D C. perfringens Caco-2 in S/D/DMEM(-) 0.5 h


title: E-1S C. perfringens Caco-2 in S/DMEM(-) 1 h

description: C. perfringens Caco-2 in S/DMEM(-) 1 h


title: E-2S C. perfringens Caco-2 in S/DMEM(-) 2 h

description: C. perfringens Caco-2 in S/DMEM(-) 2 h


title: I-1D C. perfringens Caco-2 in S/D/DMEM(-) 1 h


title: E-1D C. perfringens Caco-2 in S/D/DMEM(-) 1 h


title: I-1S C. perfringens Caco-2 in S/DMEM(-) 1 h

description: C. perfringens Caco-2 in S/DMEM(-) 1 h


title: I-0S (2) C. perfringens Caco-2 in S/DMEM(-) 2 h

description: C. perfringens Caco-2 in S/DMEM(-) 2 h


title: H-0S C. perfringens Caco-2 in S/DMEM(-) 3 h

description: C. perfringens Caco-2 in S/DMEM(-) 3 h


title: G-12D C. perfringens Caco-2 in S/D/DMEM(-) 12 h

value: G


title: E-0.5S C. perfringens Caco-2 in S/DMEM(-) 0.5 h


title: D-12D C. perfringens Caco-2 in S/D/DMEM(-) 12 h


title: LungTumorNodule_mouse490_Kras37bpMarkerGenotype_AB_heterozygous_rep1

description: sample name: 490

tag: number of lung tumors


title: E-0S C. perfringens Caco-2 in S/DMEM(-) 0 h

description: C. perfringens Caco-2 in S/DMEM(-) 0 h


title: A-12D C. perfringens Caco-2 in S/D/DMEM(-) 12 h

value: A


title: E-0.5D C. perfringens Caco-2 in S/D/DMEM(-) 0.5 h


title: E-0S (2) C. perfringens Caco-2 in S/DMEM(-) 1 h

description: C. perfringens Caco-2 in S/DMEM(-) 1 h


title: G-12S C. perfringens Caco-2 in S/DMEM(-) 12 h

description: C. perfringens Caco-2 in S/DMEM(-) 12 h


title: VS_LPS_TS

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

hyb_protocol: The hybridization was carried out for 17 hours at 65°C using the QIamp labeling kit.

scan_protocol: The microarray slides were scanned with the DNA Microarray scanner G2505C at resolution of 5 µm. The scanned images were analyzed with Feature Extraction Software 10.5.1.

data_processing: The analysis of microarray data was performed and the figures were created using the R (v.2.13) and the Bioconductor software suite. The raw data were filtered and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were carried out using hierarchical clustering, principal component analysis (made4 library) and the Linear Models for Microarray Analysis (limma library).

label_protocol: In brief, 400 ng of RNA were labeled with cyanine-3 CTP using a Low RNA Input Fluorescent Amplification kit.

growth_protocol: In short, venous blood was drawn from the cubital vein of all participants into 10 ml EDTA tubes. PBMCs were isolated from whole blood using density gradient centrifugation on Ficoll-Hypaque (GE Healthcare, Uppsala, Sweden). The cells from the interphase were aspirated and washed twice in sterile PBS and resuspended in Roswell Park Memorial Institute (RPMI) 1640 Dutch modification culture medium (Sigma-Alderich, St Louis, MO, USA) supplemented with 1% L-glutamine, 1% pyruvate and 1% gentamicin.

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen) and DNAse treatment.  The quality of the RNA preparation was assessed using the 2100 Bioanalyzer and the RNA 6000 Nano LabChip kit (Agilent Technologies), and its quantity was assessed using a Nanodrop.

treatment_protocol: To assess gene expression, PBMCs were incubated for 8 hours in a flat-bottom 24-wells plate (volume 1 ml/well) at a concentration of [10^7 cells/ml] at 37°C and 5% CO2 with heat-killed C. burnetii NM [10^7/ml], E. coli LPS [10 ng/ml] or culture medium alone.

tag: patient id

tag: diagnosis

value: healthy

value: F

tag: stimulated

value: Y

value: LPS


title: VS_Cb_TS

value: Cb


title: d0TS-null-3

description: Prdm1 null d0 TS replicate 3


title: VS_NS_MC

value: N

value: NS


title: VS_Cb_MC


title: VS_LPS_MC


title: A-12S C. perfringens Caco-2 in S/DMEM(-) 12 h

description: C. perfringens Caco-2 in S/DMEM(-) 12 h


title: G-8D C. perfringens Caco-2 in S/D/DMEM(-) 8 h


title: D-12S C. perfringens Caco-2 in S/DMEM(-) 12 h

description: C. perfringens Caco-2 in S/DMEM(-) 12 h


title: VS_Cb_Trj


title: G-6D C. perfringens Caco-2 in S/D/DMEM(-) 6 h


title: A-8D C. perfringens Caco-2 in S/D/DMEM(-) 8 h


title: D-6D C. perfringens Caco-2 in S/D/DMEM(-) 6 h


title: A-6D C. perfringens Caco-2 in S/D/DMEM(-) 6 h


title: VS_NS_MJ

value: M


title: VS_NS_TS


title: A-6S C. perfringens Caco-2 in S/DMEM(-) 6 h

description: C. perfringens Caco-2 in S/DMEM(-) 6 h


title: VS_LPS_Trj


title: D-6S (2) C. perfringens Caco-2 in S/DMEM(-) 6 h

description: C. perfringens Caco-2 in S/DMEM(-) 6 h

value: D


title: G-4D C. perfringens Caco-2 in S/D/DMEM(-) 4 h


title: D-8D C. perfringens Caco-2 in S/D/DMEM(-) 8 h


title: P_NS_0076

value: Q fever


title: VS_LPS_MJ


title: VS_NS_Trj


title: P_Cb_0016


title: G-4S C. perfringens Caco-2 in S/DMEM(-) 4 h

description: C. perfringens Caco-2 in S/DMEM(-) 4 h


title: A-4D C. perfringens Caco-2 in S/D/DMEM(-) 4 h


title: P_Cb_0094


title: P_Cb_0076


title: P_LPS_0094


title: D-4D C. perfringens Caco-2 in S/D/DMEM(-) 4 h


title: P_LPS_0016


title: VS_Cb_MJ


title: P_NS_0094


title: 5-8F-R1-OFF

city: Guangzhou

first: Mei-Yin

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

country: China

institute: Sun Yat-sen University Cancer Center

description: microRNA profile of 5-8F-R1-OFF

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels,EXPression Analyzer and DisplayER (EXPANDER) version 4.1 was used.

source_name: nasopharyngeal carcinoma

label_protocol: 2.5 μg of total RNA of intrahepatic cholangiocarcinoma/normal intrahepatic bile duct tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

value: nasopharyngeal carcinoma


title: P_LPS_0076


title: G-6S (2) C. perfringens Caco-2 in S/DMEM(-) 6 h

description: C. perfringens Caco-2 in S/DMEM(-) 6 h


title: D-4S C. perfringens Caco-2 in S/DMEM(-) 4 h

description: C. perfringens Caco-2 in S/DMEM(-) 4 h


title: CNE-2-R1-OFF

description: microRNA profile of CNE-2-R1-OFF


title: CNE-2-R1-ON

description: microRNA profile of CNE-2-R1-ON


title: 5-8F-R1-ON

description: microRNA profile of 5-8F-R1-ON


title: A-4S C. perfringens Caco-2 in S/DMEM(-) 4 h

description: C. perfringens Caco-2 in S/DMEM(-) 4 h


title: G-0S C. perfringens Caco-2 in S/DMEM(-) 0 h

description: C. perfringens Caco-2 in S/DMEM(-) 0 h


title: HONE-1-R1-OFF

description: microRNA profile of HONE-1-R1-OFF


title: HONE-1-R1-ON

description: microRNA profile of HONE-1-R1-ON


title: P_NS_0016


title: P_LPS_0074


title: A-0S C. perfringens Caco-2 in S/DMEM(-) 0 h

description: C. perfringens Caco-2 in S/DMEM(-) 0 h


title: 72h after KA-SE rep3

status: Public on Mar 12 2016

city: Amsterdam

first: Marijn

last: Schouten

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description:
treatment replicate 3
KA-SE3

data_processing:
Transcripts with raw cycle treshold (Ct) values >35 were excluded from further analysis (highlighted in italic red and striked through values)
Target gene signals were normalized to housekeeping gene RNU6; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Excel file with 3 worksheets:
[1] Matrix non-normalized: raw ct values
[2] Matrix normalized: target expression relative to RNU6 (deltaCt)
[3] Fold change: 2^-(deltadeltaCt)

label: Transcript specific taqman probes

source_name: Mus musculus dentate gyrus

label_protocol: 800ng of each total RNA sample was processed into cDNA using Taqman microRNA RT Kit and Megaplex RT primers (Applied Biosystems), according to the manufacturers’ protocol. Subsequently, cDNA samples were combined with a Taqman Universal Master Mix prior to loading onto Mouse microRNA fluidic v3.0 cards (Applied Biosystems).

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Animals received saline (control) or low dose status epilepticus inducing kainic acid (treatment) intraperitoneal injections 72h prior to microdissection of the dentate gyrus.

value: 6-8 weeks

tag: Sex

value: Male

tag: time after i.p. injections

value: 72 hours

tag: tissue

value: Microdissected Dentate gyrus


title: 72h after KA-SE rep2

description:
treatment replicate 2
KA-SE2


title: 72h after saline rep2

description:
control replicate 2
SAL2


title: 72h after KA-SE rep1

description:
treatment replicate 1
KA-SE1


title: 72h after saline rep3

description:
control replicate 3
SAL3


title: P_NS_0004


title: P_Cb_0074


title: P_NS_0023


title: P_Cb_0023


title: P_Cb_0004


title: P_LPS_0004


title: D-0S (2) C. perfringens Caco-2 in S/DMEM(-) 0 h

description: C. perfringens Caco-2 in S/DMEM(-) 0 h

value: S


title: P_NS_0074


title: P_LPS_0023


title: 72h after saline rep1

description:
control replicate 1
SAL1


title: Glioblastoma_DS05

type: genomic

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

hyb_protocol: Genomic DNA was bisulfite converted with the Zymo Research EZ DNA Methylation kit.  Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged with the Illumina HiScan scanner using standard settings

data_processing: GenomeStudio software V2011.1

molecule: genomic DNA

source_name: Glioblastoma

label_protocol: Standard Illumina protocol

extract_protocol: DNA extraction was done using QIAamp DNA mini kit (Quiagen, USA). Sodium bisulfite conversion of the genomic DNA was done with EZ DNA methylation Kit (ZymoReasearch, USA) following manufacturer’s guidelines. Briefly, purified genomic DNA (1µg) was mixed with 5 µL M-Dilution Buffer to a final volume of 45 µL and incubated at 37oC for 15 min. To this, 100 µL CT Conversion reagent (750 µL water and 210 µL M-Dilution buffer) and samples were incubated in thermocycler overnight (95oC for 30 sec; 50oC for 1hr; 16 cycles). Bisulfite converted DNA was column purified using a ZymoSpin IC column and eluted in 20 µL of nuclease-free water.

tag: age (yrs)

tag: p53 status

tag: mib

tag: egfr status

tag: gfap status

tag: site

value: Left parietal cystic lesion

value: Glioblastoma


title: Glioblastoma_DS11

value: Left temporal


title: Glioblastoma_DN59

value: Left posterior temporal


title: Glioblastoma_DN55

value: Low

value: Negative

value: Left posterior frontal


title: Glioblastoma_DS10

value: Right frontal


title: Glioblastoma_DN54

value: F

value: Left tempero parietal


title: Glioblastoma_DS02

value: M

value: Left posterior fronto parietal


title: Glioblastoma_DN33II

value: positive

value: Positive


title: Glioblastoma_DN53

value: Left parieto occipital lesion


title: Glioblastoma_DS04

value: Corpus callosum


title: Glioblastoma_DN50

value: Left tempero parietal occipital


title: Glioblastoma_DN35II

value: Left basifrontal


title: Glioblastoma_DN41II

value: Right tempero parietal

value: Glioblastoma


title: Glioblastoma_DN51

value: Right parietal


title: Glioblastoma_DN18

value: ND

value: Right temporal


title: Glioblastoma_DN46

value: Negative

value: Left fronto temporal


title: Glioblastoma_DN15

value: F


title: Glioblastoma_DN24

value: Left medial frontal


title: Glioblastoma_DN30II

value: M

value: Right frontal


title: Glioblastoma_DN48

value: positive

value: Left temporal


title: Glioblastoma_DN20

value: Positive

value: Left frontal


title: Glioblastoma_DN36II


title: Glioblastoma_DS03

value: Left Insular


title: Glioblastoma_DN12II


title: Glioblastoma_DN10


title: Glioblastoma_DN16II


title: Glioblastoma_DN13


title: Glioblastoma_DN39II

value: Left basifrontal


title: 72h after KA-SE rep2

description:
replicate 2
KA-SE2

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

label_protocol: Biotinylated cRNA were prepared with the TotalPrep RNA Amplification kit from Ambion, Life Technologies

value: 6-8 weeks

value: Male

value: 72 hours

value: Dentate gyrus


title: Glioblastoma_DN17

value: ND

value: Glioblastoma


title: Glioblastoma_DN14II

value: Negative


title: 72h after KA-SE rep1

description:
replicate 1
KA-SE1


title: 72h after saline rep2

description:
replicate 2
SAL2


title: Hipp16_WT_ct18

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description: RNA from hippocampus wild-type mice at circadian time point 18.

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis- Low Input Quick Amp Labeling (version 6.5, May 2010). Complementary RNA (cRNA) samples were linearly amplified and labeled with Cyanine3 starting from 50ng of total RNA. Following fragmentation, labeled cRNA were hybridized on Agilent-028005 SurePrint G3 Mouse Gene Expression 8x60K Microarray, for 17hrs at 65°C under 10rpm.

scan_protocol: AgilentG3_GX_1Color (scan resolution : 3 µm, Tiff : 20 bit). After washes, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3μM resolution in a 20-bit scan mode, according to the AgilentG3_GX_1Color protocol. Raw .tif images were then extracted using Agilent Feature Extraction, version 10.10.1.1 following GE1_1010_Sep10 protocol.

data_processing:
The scanned images were analyzed with Feature Extraction software (Agilent) version 10.10.1.1 to obtain gprocessed signal data.
gprocessed signal data were quantile normalized and log2 transformed.

source_name: Hippocampus, CT18

extract_protocol: Total RNA was extracted.

treatment_protocol: Dark-dark conditions.

tag: genotype/variation

value: wild-type

value: hippocampus

tag: circadian time point

value: male

tag: developmental stage

value: adult


title: 72h after KA-SE rep3

description:
replicate 3
KA-SE3

tag: strain

tag: age


title: 72h after saline rep1

description:
replicate 1
SAL1


title: Hipp14_WT_ct18

label_protocol: One-Color Microarray-Based Gene Expression Analysis- Low Input Quick Amp Labeling (version 6.5, May 2010).

tag: gender


title: Hipp11_WT_ct12

description: RNA from hippocampus wild-type mice at circadian time point 12.

source_name: Hippocampus, CT12


title: Hipp10_WT_ct12


title: Glioblastoma_DN03

value: M

value: Left posterior frontal


title: 72h after saline rep3

description:
replicate 3
SAL3


title: Hipp6_WT_ct6

description: RNA from hippocampus wild-type mice at circadian time point 6.

source_name: Hippocampus, CT6


title: Glioblastoma_DN08

value: Positive

value: Left tempero parietal


title: Hipp12_WT_ct12


title: Hipp7_WT_ct6


title: Glioblastoma_DN07

value: positive

value: Right parietal


title: Glioblastoma_DN09

value: Right frontal


title: Hipp5_WT_ct6


title: Anaplastic Astrocytoma (grade III)_GS235II

source_name: Anaplastic Astrocytoma (grade III)

value: Right tempero parietal

value: Anaplastic Astrocytoma (grade III)


title: Hipp3_WT_ct0

description: RNA from hippocampus wild-type mice at circadian time point 0.

source_name: Hippocampus, CT0


title: Anaplastic Astrocytoma (grade III)_GS231II

value: Left fronto temporal


title: Anaplastic Astrocytoma (grade III)_GS291

value: Left insular with basifrontal extension


title: Hipp2_WT_ct0


title: Anaplastic Astrocytoma (grade III)_GN417

value: Left insular


title: Anaplastic Astrocytoma (grade III)_GN24

value: Right fronto parietal


title: Hipp1_WT_ct0

value: wild-type


title: Anaplastic Astrocytoma (grade III)_GN406

value: Left parieto occiptal


title: Hipp15_WT_ct18

value: hippocampus

value: male


title: Anaplastic Astrocytoma (grade III)_GN23

value: M


title: Anaplastic Astrocytoma (grade III)_GN331

value: F


title: Glioblastoma_DN05

value: Negative

value: Posterior frontal

value: Glioblastoma


title: Anaplastic Astrocytoma (grade III)_GN39

value: Positive

value: Left frontal lobe


title: Anaplastic Astrocytoma (grade III)_DNB65

value: Supramarginal/angular gyrus


title: Anaplastic Astrocytoma (grade III)_GN235II

value: Right frontal

value: Anaplastic Astrocytoma (grade III)


title: Anaplastic Astrocytoma (grade III)_GN09

value: Left temporal frontal


title: endogenous parvalbumin neurons

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: PV-GFP transgenic C57BL/6 mice

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

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

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console

source_name: mouse endogenous parvalbumin neurons

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

growth_protocol: Mouse embryonic fibroblasts were cultured in D10 medium in vitro.

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

treatment_protocol: Mouse embryonic fibroblasts were infected with adenovirus and induced into neurons in vitro.

value: PV-GFP transgenic

value: 13.5 day embryos

tag: cell type

value: endogenous PV neurons


title: 14dpi iPV neurons

description: PV-GFP transgenic C57BL/6 mice

source_name: mouse embryonic fibroblasts induced parvalbumin neurons for 14 days

value: 14dpi iPV neurons


title: sorted induced PV-GFP+ neurons

description: PV-GFP transgenic C57BL/6 mice

source_name: sorted induced parvalbumin-GFP+ neurons at 14 dpi

value: 14dpi iPV neurons, sorted, GFP+


title: 3dpi iPV neurons

description: PV-GFP transgenic C57BL/6 mice

source_name: mouse embryonic fibroblasts induced parvalbumin neurons for 3 days

value: 3dpi iPV neurons


title: 7dpi iPV neurons

description: PV-GFP transgenic C57BL/6 mice

source_name: mouse embryonic fibroblasts induced parvalbumin neurons for 7 days

value: 7dpi iPV neurons


title: mouse embryonic fibroblasts

description: PV-GFP transgenic C57BL/6 mice

source_name: mouse embryonic fibroblasts

value: embryonic fibroblasts


title: Diffuse Astrocytoma (grade II)_GS306

source_name: Diffuse Astrocytoma (grade II)

value: F

value: Left frontal

value: Diffuse Astrocytoma (grade II)


title: Anaplastic Astrocytoma (grade III)_DNB42

value: M


title: Anaplastic Astrocytoma (grade III)_GN416II


title: Diffuse Astrocytoma (grade II)_GS335

value: Negative


title: FO-R

city: Matsumoto City

first: Fuminori

last: Kawano

state: Nagano

address: Niimura 2095-1

department: Graduate School of Health Sciences

institute: Matsumoto University

description: Hypertrophied muscle of adult rat

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8×60K Microarrays 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), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Hypertrophied soleus muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was exracted from tissue segment of skeletal muscle using Isogen (NIPPON GENE) followed by isopropanol precipitation.

value: Muscle

value: male


title: Anaplastic Astrocytoma (grade III)_DNB18

value: Positive

value: Medial temporal

value: Anaplastic Astrocytoma (grade III)


title: FO-L

description: Regenerated muscle of adult rat after overloading

source_name: Regenerated soleus muscle after overloading


title: Diffuse Astrocytoma (grade II)_GS151

value: Left posterior frontal


title: Anaplastic Astrocytoma (grade III)_DNB32

value: Right temporal


title: Diffuse Astrocytoma (grade II)_GN555

value: Right frontal


title: Resveratrol-enriched rice DJ526 group_01

city: Jeonju

first: Seong-Tshool

last: Hong

state: Chonbuk

address: Gungi-ro 20

department: Biomedical Sciences and Institute for Medical Science

country: South Korea

institute: Chonbuk National University

description: Gene expression from the mice on resveratrol-enriched rice DJ526 (DJ526) diet after 6 month

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Mouse Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpringGX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

source_name: Resveratrol-enriched rice DJ526 liver tissue_6 mon_01

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

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

treatment_protocol: The control (Ctrl) mice fed a NFD in which the carbohydrate source was corn starch and sucrose; The resveratrol (RS) mice fed a NFD in which the carbohydrate source was corn starch and sucrose except containing resveratrol; Dongjin (DJ) mice fed a NFD in which the corn starch and sucrose were replaced with Dongjin rice; DJ526, mice fed a NFD in which the corn starch and sucrose were replaced with the resveratrol enriched rice DJ526.

value: Liver

value: Female


title: Diffuse Astrocytoma (grade II)_GS257


title: 8wk-R

description: Normal muscle of adult rat

source_name: Normal soleus muscle


title: Diffuse Astrocytoma (grade II)_GN345


title: Diffuse Astrocytoma (grade II)_GN495

value: Right insular


title: Diffuse Astrocytoma (grade II)_DNB50

value: Right thalamus


title: Diffuse Astrocytoma (grade II)_GNB37


title: Diffuse Astrocytoma (grade II)_DNB77


title: Glioblastoma_DN02

source_name: Glioblastoma

value: ND

value: Right parieto occipital

value: Glioblastoma


title: Diffuse Astrocytoma (grade II)_DNB207

value: F

value: Left temporal

value: Diffuse Astrocytoma (grade II)


title: Diffuse Astrocytoma (grade II)_DNB312

value: M

value: Negative

value: Left frontal


title: Diffuse Astrocytoma (grade II)_DNB48

value: Frontal


title: Diffuse Astrocytoma (grade II)_DNB75


title: Diffuse Astrocytoma (grade II)_GN419

value: Left fronto parietal


title: Diffuse Astrocytoma (grade II)_DNB62

value: Left temporal pole


title: Control group_01

description: Gene expression from the mice on control (Ctrl) diet after 6 month

source_name: Control liver tissue_6 mon_01


title: Dongjin rice group_03

description: Gene expression from the mice on Dongjin rice (DJ) diet after 6 month

source_name: Dongjin liver tissue_6 mon_03


title: Control group_02

source_name: Control liver tissue_6 mon_02


title: Resveratrol group_03

description: Gene expression from the mice on resveratrol (RS) diet after 6 month

source_name: Resveratrol liver tissue_6 mon_03


title: Dongjin rice group_01

source_name: Dongjin liver tissue_6 mon_01


title: 8wk-L

description: Regenerated muscle of adult rat

source_name: Regenerated soleus muscle 8 weeks after CTX injection

value: Muscle

value: male


title: Resveratrol group_01

source_name: Resveratrol liver tissue_6 mon_01

value: Liver

value: Female


title: Control brain_NN33

source_name: Control brain

value: Control brain


title: Resveratrol-enriched rice DJ526 group_02

source_name: Resveratrol-enriched rice DJ526 liver tissue_6 mon_02


title: Resveratrol group_02

source_name: Resveratrol liver tissue_6 mon_02


title: Dongjin rice group_02

source_name: Dongjin liver tissue_6 mon_02


title: Resveratrol-enriched rice DJ526 group_03

source_name: Resveratrol-enriched rice DJ526 liver tissue_6 mon_03


title: Control group_03


title: Diffuse Astrocytoma (grade II)_DNB212

source_name: Diffuse Astrocytoma (grade II)

value: Positive

value: Right frontal


title: Jurkat-shIKKE

status: Public on Mar 11 2016

city: Wuhan

first: Junjie

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Jurkat-shIKKE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis

growth_protocol: we grow Jurkat T cells under general protocol

extract_protocol: Total RNA was extracted by using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: PMA (10 ng/ml ) and ionomycin (0.5 uM) treatment for 3h

tag: cell line

value: Jurkat


title: Jurkat-Vector induce

source_name: Jurkat-Vector induce


title: Control brain_DNN09


title: Jurkat-shIKKE induce

source_name: Jurkat-shIKKE induce


title: Jurkat-Vector

source_name: Jurkat-Vector


title: Control brain_DNN04

value: F


title: Control brain_DNN01


title: Control brain_DNN03


title: Control brain_NN16


title: Control brain_DNN02


title: Control brain_DNN07


title: Control brain_DNN08


title: E19_Bl012_BRP012

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

institute: Maastricht University Medical Center

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified by REPLI-g Single Cell Kit (Qiagen).

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing: Image data was analyzed using Genomestudio with genotyping module (Illumina). The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0.75. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG). The data is provided as family stuctures, i.e. a BRP family for each cross.

organism: Bos taurus

source_name: Blastomere

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The zygotes were transferred to synthetic oviductal fluid (SOF) supplemented with essential and non-essential amino acids (SOFaa), 0.4% BSA and ITS (5 µg/ml insulin, 5 µg/ml transferrin and 5 ng/ml selenium). In vitro culture (IVC) occurred in 4-well dishes in 20 µL drops (1 per donor cow) covered with mineral oil. Embryos were incubated at 38.5°C in 5% CO2, 5% O2 and 90% N2.

extract_protocol: The isolated blastomeres were placed immediately on dry ice and stored in -20oC for 30 minutes prior to whole genome amplification (WGA). WGA was performed on the day of blastomere isolation. DNA from single blastomeres was whole-genome amplified using commercial MDA kits (REPLI-g Single Cell Kit, Qiagen and GenomiPhiV2, GE Healthcare Biosciences). MDA amplification with GenomiPhiV2 was performed as described previously (Spits et al. 2006, Nat Protoc). MDA amplification of single blastomeres with the single-cell Repli-g kit was performed according to the manufacturer’s instructions for the fast 3-hour protocol. WGA products were purified using SPRI-beads (AMPure) at 0.8x of total reaction volume.

treatment_protocol: The embryos were treated with pronase to dissolve the zona pellucida (0.1% protease from S. griseus, P88110, Sigma-Aldrich in TCM-199) and were subsequently washed in TCM-199 with 10% FBS followed by Ca+2/Mg+2 free PBS with 0.05% BSA to stimulate blastomere dissociation. Subsequently, the zona-free embryos were washed in Ca+2/ Mg+2 free PBS with 0.1% PVP (wash medium) and were transferred onto a petri dish for blastomere dissociation. Blastomere pick-up and tubing was performed with the use of a mouth-pipetting system using a 75μm capillary.

tag: dna sample

value: Single Cell

tag: wga

value: MDA (REPLI-g)


title: Mother_BRP012

description: DNA extracted from a large amount of cells derived from the cow's ovarian tissue using DNeasy Blood and Tissue kit (Qiagen).

source_name: Ovarian tissue

value: Multi cell


title: Father_BRP012

description: DNA extracted from a large amount of cells derived from the bull's semen using DNeasy Blood and Tissue kit (Qiagen).

source_name: Semen


title: E07_Bl004_BRP012

description: DNA extracted from single blastomere derived from cleavage stage day-2post-insemination, in vitro produced embryo and subsequently whole genome amplified by REPLI-g Single Cell Kit (Qiagen).


title: E19_Bl011_BRP012


title: E19_Bl005_BRP012


title: E19_Bl007_BRP012


title: E19_Bl008_BRP012


title: E19_Bl003_BRP012


title: E17_Bl007_BRP011


title: E17_Bl006_BRP011


title: E07_Bl002_BRP012


title: E07_Bl001_BRP012


title: E19_Bl004_BRP012


title: E19_Bl006_BRP012


title: Mother_BRP011


title: Father_BRP011


title: E19_Bl001_BRP012


title: E19_Bl002_BRP012


title: E19_Bl009_BRP012


title: ExpandedBlastocyst_BRP011

description: DNA extracted from the entire expanded blastocyst stage in vitro produced embryo and subsequently whole genome amplified by REPLI-g Single Cell Kit (Qiagen).

source_name: Entire embryo

value: Few cell


title: E07_Bl003_BRP012


title: E17_Bl002_BRP011


title: E17_Bl003_BRP011


title: E17_Bl005_BRP011


title: E19_Bl010_BRP012


title: E17_Bl004_BRP011


title: E17_Bl001_BRP011


title: E16_Bl006_BRP011


title: E16_Bl009_BRP011


title: E16_Bl007_BRP011


title: E16_Bl008_BRP011


title: E08_Bl003_BRP011


title: E16_Bl003_BRP011


title: E16_Bl005_BRP011


title: E16_Bl004_BRP011


title: E10_Bl002_BRP011


title: E10_Bl004_BRP011


title: E10_Bl008_BRP011


title: E08_Bl002_BRP011


title: E08_Bl001_BRP011


title: E10_Bl006_BRP011


title: E10_Bl003_BRP011


title: E16_Bl002_BRP011


title: E16_Bl010_BRP011


title: E10_Bl001_BRP011


title: E10_Bl007_BRP011


title: E16_Bl001_BRP011


title: E10_Bl005_BRP011


title: E04_Bl004_BRP010


title: E04_Bl006_BRP010


title: E08_Bl004_BRP011


title: Mother_BRP010


title: ExpandedBlastocyst_BRP010


title: E12_Bl010_BRP010


title: E04_Bl005_BRP010


title: E12_Bl007_BRP010


title: E04_Bl007_BRP010


title: E12_Bl009_BRP010


title: E12_Bl005_BRP010


title: E12_Bl011_BRP010


title: E12_Bl004_BRP010


title: E12_Bl006_BRP010


title: E04_Bl002_BRP010


title: E04_Bl003_BRP010


title: E11_Bl005_BRP010


title: E12_Bl002_BRP010


title: E11_Bl004_BRP010


title: E12_Bl003_BRP010


title: E04_Bl001_BRP010


title: E11_Bl007_BRP010


title: E11_Bl003_BRP010


title: E12_Bl008_BRP010


title: E11_Bl006_BRP010


title: Father_BRP010


title: E03_Bl003_BRP010


title: E11_Bl001_BRP010


title: E11_Bl002_BRP010


title: E12_Bl001_BRP010


title: E11_Bl008_BRP010


title: Grandmother_BRP009


title: E03_Bl001_BRP010


title: E03_Bl004_BRP010


title: E23_Bl006_BRP009

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).

value: MDA (GenomiPhiV2)


title: GFAP-EGC in vivo rep2

city: Würzburg

first: Corinna

last: Rosenbaum

address: Röntgenring 11

department: Department of Tissue Engineering and Regenerative Medicine

country: Germany

institute: University Hospital Wuerzburg

description: replicate 2

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan instrument

data_processing: The data were normalised using quantile normalization by Illumina GenomeStudio

source_name: small intestinal LMMP

label_protocol: 250ng RNA per sample were ethanol precipitated with GlycoBlue (Invitrogen) as carrier and dissolved at a concentration of 100-150 ng/µl prior to probe synthesis using the TargetAmp™- Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies).

growth_protocol: Cells were grown in Dulbecco’s modified Eagle medium (DMEM)/F-12 medium supplemented with Glutamax (Life Technologies, Darmstadt, Germany), penicillin (100 U mL-1; PAA, Coelbe, Germany), streptomycin (100 mg mL-1; PAA), B27 without vitamin A (1:50; Invitrogen), N2 (1:100; Invitrogen), sorted for GFP by flow cytometry and seeded onto culture dishes coated with poly-ornithine (0.01%), fibronectin and laminin (both 1 µg cm-2; Sigma-Aldrich). Epidermal growth factor (EGF; 40 ng mL-1; Peprotech, Hamburg, Germany) and basic fibroblast growth factor (bFGF; 40 ng mL-1; Peprotech) were added daily and cells cultured under hypoxic conditions (2% O2) in a humidified incubator at 37°C. Cell culture medium was changed by 50% every 2-3 days.

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit according to the manufacturer’s instructions (Qiagen). Before microarray analysis RNA integrity and concentration was examined on an Agilent 2100 Bioanalyzer (Agilent Technologies) using the RNA 6.000 LabChip Kit (Agilent Technologies) according to the manufacturer’s instructions.

treatment_protocol: For LPS-stimulation experiments, cells were passaged after 2 weeks and seeded on uncoated plastic dishes to promote spheroid formation. Cells from each animal preparation (n = 3) were split into two six well dishes, one stimulated with LPS (100 µg mL-1, from E. coli O26:B6, Sigma Aldrich, potency 3 EU/ng). After 48 h, cells processed for total RNA isolation.

tag: background strain

value: FVB

tag: genotype

value: hGFAP-eGFP

tag: tissue

value: small intestinal LMMP

value: postnatal day 7


title: E22_Bl007_BRP009


title: GFAP-EGC in vivo rep3

description: replicate 3


title: E23_Bl008_BRP009


title: GFAP-EGC in vivo rep1

description: replicate 1


title: E03_Bl002_BRP010


title: E23_Bl005_BRP009


title: E23_Bl001_BRP009


title: Grandfather_BRP009


title: GFAP-EGC in vitro LPS-treated rep3

description: replicate 3


title: Father_BRP009


title: E23_Bl003_BRP009


title: Mother_BRP009


title: E22_Bl005_BRP009


title: GFAP-EGC in vitro LPS-treated rep1

description: replicate 1


title: GFAP-EGC in vitro LPS-treated rep2

description: replicate 2


title: E22_Bl003_BRP009


title: E23_Bl002_BRP009


title: E22_Bl002_BRP009


title: Mother_BRP008


title: Rrm3-Flag YRA1∆i

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: GAL::YRA1∆i Rrm3 exp1 and exp2

hyb_protocol: Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run. 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

organism: Saccharomyces cerevisiae

source_name: Rrm3-Flag ChIP DNA from WRBb-9B overexpressing YRA1, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in minimal medium + Glucose 2%  to mid-log phase at 30°C. In samples with Rrm3-Flag ChIP, yeast cells were grown minimal medium + Galactose 2%

extract_protocol: ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-HA polyclonal antibody (Abcam) was used for ChIP. Anti-FLAG M2 monoclonal (Sigma-Aldrich)

value: WRBb-9B+ pRS413-GAL::YRA1∆i

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG + pRS413-GAL::YRA1Δi

tag: cell cycle stage

value: asynchronous

source_name: Input DNA from WRBb-9B


title: GFAP-EGC in vitro rep3

description: replicate 3


title: GFAP-EGC in vitro rep1

description: replicate 1


title: GFAP-EGC in vitro rep2

description: replicate 2


title: E22_Bl008_BRP009

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified byGenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: E22_Bl004_BRP009

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).\


title: OE HA-Yra1Δi

description: HA-Yra1∆i exp1 and exp2

source_name: HA-Yra1 ChIP DNA from W303-A1 overexpressing YRA1, asynchronous culture

value: W303-1A+ pRS413-GAL::YRA1∆i

source_name: Input DNA from W303-1A+ pRS413-GAL::YRA1∆i


title: Grandfather_BRP008