title: Pb-ARv567es_Tg_transgenic_mouse_prostate_879

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: whole prostate of Pb-ARv567es transgenic mouse

hyb_protocol: Hybridizations to Agilent 44K whole mouse genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the GE2_105_Jan09 protocol with default settings. We normalized the raw data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of NA to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers.  Data was further normalized using between-array quantile normalization.  All normalizations were performed using the Limma package in R.

label_protocol: amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol:
ch1:Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp II aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.
ch2:Whole prostate was harvested directly into TRIzol® Reagent (Invitrogen). Samples were homogenized using autoclaved glassware on ice and purified following the TRIzol manufacturer’s protocol. Total RNA was then further purified by RNeasy mini kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp II aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

value: Swiss-Webster

value: Adult

tag: tissue

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

tag: protocol

value: second round aRNA

value: 19 wks

value: whole prostate

value: one round aRNA

tag: genotype/variation

value: ARv567es transgenic


title: Pb-ARv567es_Wt_control_littermate_prostate_922

status: Public on Sep 11 2014

type: RNA

country: USA

description: whole prostate of Pb-ARv567es control littermate

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

value: wildtype


title: Pb-ARv567es_Wt_control_littermate_prostate_923


title: Pb-ARv567es_Tg_transgenic_mouse_prostate_888


title: Pb-ARv567es_Wt_control_littermate_prostate_921


title: Pb-ARv567es_Tg_transgenic_mouse_prostate_859


title: Pb-ARv567es_Tg_transgenic_mouse_prostate_896


title: Ct3

city: Badalona

first: Miguel

middle: A

last: Peinado

state: Barcelona

address: Ctra. de Can Ruti, camí de les escoles, s/n

country: Spain

institute: IGTP

description: ATCC cell line

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: CT26 colorectal cell line replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit - Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNeasy Mini Kit or RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

value: colorectal cell line

tag: cell line


title: Ct1

description: ATCC cell line

source_name: CT26 colorectal cell line replicate1


title: C2

description: Whole tissue

source_name: Colon replicate2

value: colon


title: Pb-ARv567es_Wt_control_littermate_prostate_114-6


title: C3

description: Whole tissue

source_name: Colon replicate3


title: C1

description: Whole tissue

source_name: Colon replicate1


title: Ct2

description: ATCC cell line

source_name: CT26 colorectal cell line replicate2


title: Ade3

description: Macroscopic adenoma. Whole tissue

source_name: Adenoma replicate3

value: adenoma

value: APCmin/+


title: Adj2

description: Whole tissue

source_name: Tissue adjacent to adenoma replicate1

value: tissue adjacent to adenoma


title: Ade1

description: Macroscopic adenoma. Whole tissue

source_name: Adenoma replicate1


title: Ade2

description: Macroscopic adenoma. Whole tissue

source_name: Adenoma replicate2


title: Adj3

description: Whole tissue

source_name: Tissue adjacent to adenoma replicate2


title: CNT-2_NR8383

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

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

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

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

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

organism: Rattus norvegicus

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

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

growth_protocol: Rat alveolar macrophages NR8383 were seeded into each well of a 96-well plate and grown in the F-12K with 15% heat-inactivated fetal bovine serum medium for 24 hours.

extract_protocol: After 24 hours, total RNA was extracted from the cells using the RNeasy mini (Qiagen, Tokyo, Japan) according to the manufactures instructions. Total RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

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

tag: cell type

value: alveolar macrophages

tag: treatment

tag: time


title: IP1

description: Whole tissue

source_name: Small intestine replicate1

value: small intestine


title: IP3

description: Whole tissue

source_name: Small intestine replicate3


title: FUR_noCPR_1

city: Szeged

first: Balazs

last: Bogos

address: Temesvári krt. 62-64

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre of the Hungarian Academy of Sciences

description: Escherichia coli liquid culture, incubated in LB medium, BW25113

hyb_protocol: Hybridization of the cDNAs was conducted at UD-GenoMed Medical Genomic Technologies Ltd. (4032, Debrecen, Nagyerdei Krt. 98. Tel: +36 30 494 6496) using Affymetrix Genechip® E. coli Genome 2.0 Array (Affymetrix) as described by the manufacturer.

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files (DAT/CEL).

data_processing: CHP files were generated using Affymetrix Expression Control.  Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

label: biotin

organism: Escherichia coli K-12

source_name: Non-treated, fur mutant sample at T0, biological rep 1

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

growth_protocol: Escherichia coli BW25113 and fur mutant strains were cultivated at 37Co in 25 ml of LB medium using Erlenmeyer flasks. 1 ml of OVN culture was transferred to 20 ml of fresh LB medium and cells were incubated in the presence or absence of ciprofloxacin (100 ng/ml).

extract_protocol: Samples for microarray analyses were taken before ciprofloxacin treatment (t0) and then at 1 hour post-treatment (t1). Cell concentration was adjusted to 109 cells/ml and cultures were treated with ciprofloxacin in Erlenmeyer flasks using 20 ml fresh LB. ~109 cells were taken at each timepoint as samples for RNA isolation. In order to stabilize RNA, RNA Bacteria Protect Reagent (Qiagen) was added to the samples according to the instructions of the manufacturer and then samples were stored overnight at -80°C. Total RNA was isolated by using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Sample concentration was estimated using the NanoDrop 1000 (Thermoscientific) spectrophotometer.

treatment_protocol: We compared the microarray-determined mRNA profiles (Affymetrix E. coli Genome 2.0 Array) of Δfur and WT genotypes in response to ciprofloxacin treatment (100 ng/ml) with those of untreated cultures. We used two biological replicates per genotype.

tag: background strain

value: fur-knockout mutant


title: FUR_noCPR_2

source_name: Non-treated, fur mutant sample at T0, biological rep 2


title: CNT-1_NR8383

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

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


title: WT_CPR_2

source_name: Cirpofloxacin treated WT sample at T1h, biological rep 2

value: wild type


title: plasma circulating DNA from cancer-free individual Sample 3-95

type: genomic

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: Sample 3-95

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina GolodenGate methylation cancer panel I using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: plasma sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified with phenol/chloform according to standard manul instructions

value: female

tag: disease state

value: cancer-free individual

value: plasma sample from cancer-free individual

tag: sample type

value: plasma circulating DNA


title: WT_noCPR_2

source_name: Non-treated, WT control at T0, biological rep 2


title: Control for CNT-1 or CNT-2_NR8383

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

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

value: untreated control for CNT-1 or CNT-2


title: IP2

description: Whole tissue

source_name: Small intestine replicate2


title: WT_CPR_1

source_name: Cirpofloxacin treated WT sample at T1h, biological rep 1


title: FUR_CPR_2

source_name: Cirpofloxacin treated fur mutant sample at T1h, biological rep 2


title: FUR_CPR_1

source_name: Cirpofloxacin treated fur mutant sample at T1h, biological rep 1


title: plasma circulating DNA from cancer-free individual Sample 3-96

description: Sample 3-96

value: male


title: plasma circulating DNA from cancer-free individual Sample 3-94

description: Sample 3-94


title: plasma circulating DNA from cancer-free individual Sample 3-93

description: Sample 3-93


title: plasma circulating DNA from cancer-free individual Sample 3-92

description: Sample 3-92


title: 4-dun1_Sup_1

status: Public on Sep 12 2014

city: Taipei

first: Cheng-Fu

last: Kao

address: 128, Academia Rd., Sec. 2, Nankang

department: Institute of Cellular and Organismic Biology

institute: Academia Sinica

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files] TXT results were produced by GCOS using a custom CDF which summarizes probes into sets covering 50 basepairs ranges.
The discrimination of positive and negative signals for the binding were obtained by comparing IP fraction with Sup (supernatant) fraction. The reliability of strength of signal was judged by detection p-value of each locus (p-value 0.025) and presented as lowess normalized log2 ratio (IP/Sup) discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction.

organism: Saccharomyces cerevisiae

source_name: SUP of BrdU of dun1-1 (YCL023)

label_protocol: Synthesis of cDNA, IVT amplification, and end-labeled with biotin-N11-ddATP following the Affymetrix GeneChip Expression Anaysis protocol

growth_protocol: Cells were grown in YPD.

extract_protocol: For the analysis of BrdU incorporated regions, total DNA from 3X108 cells was purified by Quiagen Genomic-tip system (P/N10223, QIAGEN, Germany). DNA was sheared to 300bp by sonication, denatured, and mixed with 2μg of anti-mouse IgG1 dynabeads (P/N110.12, Dynal AS, Norway) bound anti-BrdU monoclonal antibody (MI-11-3, MBL). Immunoprecipitation and purification of antibody bound DNA fraction was carried out following the protocol of Cimbora et al. (Mol. Cel. Biol. 20, 5581-5591, 2000). Purified DNA was random primed and amplified by the WGA2 GenomePlex Complete Genome Amplification Kit. 2μg of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling.

treatment_protocol: G1 synchronization was performed by α−factor treatment (2 μg/ml), S synchronization release from factor block in 200 mM HU for 90 min

tag: fraction

value: supernatant

tag: chip antibody

tag: phase

value: S

value: Glu


title: plasma circulating DNA from cancer-free individual Sample 3-91

description: Sample 3-91


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-86

description: Sample 3-86

value: Esophageal squamous cell carcinoma

value: plasma sample from patient


title: plasma circulating DNA from cancer-free individual Sample 3-88

description: Sample 3-88


title: plasma circulating DNA from cancer-free individual Sample 3-90

description: Sample 3-90


title: plasma circulating DNA from cancer-free individual Sample 3-89

description: Sample 3-89


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-85

description: Sample 3-85


title: DBA/2J Liver, High Fat Diet

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing: Samples were analyzed using Affymetrix Expression Console.

source_name: Mouse liver

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice are housed 5 per cage in IVC GM500 cages (Tecniplast, 500 cm2) according to the Swiss cantonal rules.

extract_protocol: Trizol extraction of total RNA was performed on all individuals -- approximately 5 per cohort, for roughly 400 animals in all. Sample concentrations were then measured by Nanodrop, and then all individuals from a cohort were evenly pooled together. These cohort pools were then cleaned up with a Qiagen RNEasy kit prior to preparation for microarray.

treatment_protocol: Mice were fed ad libitum chow diet (Harlan 2018) or high fat diet (Harlan 06414) throughout their lifetime. For high fat cohorts, the diet started at 8 weeks of age until sacrifice at 29 weeks. All animals were fasted overnight (6pm to 9am) before sacrifice.

value: liver

tag: genotype


title: C57BL/6J Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from cancer-free individual Sample 3-87

description: Sample 3-87

tag: gender


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-84

description: Sample 3-84

tag: tissue


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-81

description: Sample 3-81


title: BXD103 Liver, Chow Diet

description: Gene expression data


title: BXD101 Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-80

description: Sample 3-80


title: BXD100 Liver, High Fat Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-82

description: Sample 3-82


title: BXD98 Liver, High Fat Diet

description: Gene expression data


title: DBA/2J Liver, Chow Diet

description: Gene expression data


title: WT_noCPR_1

source_name: Non-treated, WT control at T0, biological rep 1


title: BXD100 Liver, Chow Diet

description: Gene expression data


title: C57BL/6J Liver, High Fat Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-83

description: Sample 3-83


title: BXD101 Liver, High Fat Diet

description: Gene expression data


title: BXD97 Liver, High Fat Diet

description: Gene expression data


title: BXD99 Liver, High Fat Diet

description: Gene expression data


title: BXD98 Liver, Chow Diet

description: Gene expression data


title: BXD103 Liver, High Fat Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-79

description: Sample 3-79


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-78

description: Sample 3-78


title: BXD99 Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-74

description: Sample 3-74


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-77

description: Sample 3-77


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-75

description: Sample 3-75


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-72

description: Sample 3-72


title: BXD97 Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-71

description: Sample 3-71


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-69

description: Sample 3-69


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-70

description: Sample 3-70


title: BXD95 Liver, High Fat Diet

description: Gene expression data


title: BXD96 Liver, High Fat Diet

description: Gene expression data


title: BXD96 Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-68

description: Sample 3-68


title: BXD89 Liver, High Fat Diet

description: Gene expression data


title: BXD90 Liver, High Fat Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-76

description: Sample 3-76


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-67

description: Sample 3-67


title: BXD95 Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-73

description: Sample 3-73


title: BXD92a Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-66

description: Sample 3-66


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-65

description: Sample 3-65


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-64

description: Sample 3-64


title: BXD90 Liver, Chow Diet

description: Gene expression data


title: BXD89 Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-63

description: Sample 3-63


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-62

description: Sample 3-62


title: BXD85 Liver, High Fat Diet

description: Gene expression data


title: BXD87 Liver, High Fat Diet

description: Gene expression data


title: BXD85 Liver, Chow Diet

description: Gene expression data


title: BXD84 Liver, High Fat Diet

description: Gene expression data


title: BXD83 Liver, High Fat Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-60

description: Sample 3-60


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-59

description: Sample 3-59


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-58

description: Sample 3-58


title: BXD84 Liver, Chow Diet

description: Gene expression data


title: BXD87 Liver, Chow Diet

description: Gene expression data


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-61

description: Sample 3-61


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-54

description: Sample 3-54

source_name: surgical tissue

value: tumor tissue

value: genomic DNA


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-53

description: Sample 3-53

value: normal tissue


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 3-57

description: Sample 3-57


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-56

description: Sample 3-56


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-55

description: Sample 3-55


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-52

description: Sample 3-52


title: BXD81 Liver, Chow Diet

description: Gene expression data


title: BXD80 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-51

description: Sample 3-51


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-49

description: Sample 3-49


title: BXD79 Liver, Chow Diet

description: Gene expression data


title: BXD79 Liver, High Fat Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-50

description: Sample 3-50


title: BXD75 Liver, High Fat Diet

description: Gene expression data


title: BXD81 Liver, High Fat Diet

description: Gene expression data


title: BXD75 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-47

description: Sample 3-47


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-48

description: Sample 3-48


title: BXD73 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-46

description: Sample 3-46


title: BXD80 Liver, High Fat Diet

description: Gene expression data


title: BXD71 Liver, High Fat Diet

description: Gene expression data


title: BXD70 Liver, High Fat Diet

description: Gene expression data


title: BXD73 Liver, High Fat Diet

description: Gene expression data


title: BXD71 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-44

description: Sample 3-44


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-45

description: Sample 3-45


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-41

description: Sample 3-41


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-42

description: Sample 3-42


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-43

description: Sample 3-43


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-40

description: Sample 3-40


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-39

description: Sample 3-39


title: BXD69 Liver, High Fat Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-38

description: Sample 3-38


title: BXD68 Liver, High Fat Diet

description: Gene expression data


title: BXD66 Liver, High Fat Diet

description: Gene expression data


title: BXD69 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-36

description: Sample 3-36


title: BXD70 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-35

description: Sample 3-35


title: BXD66 Liver, Chow Diet

description: Gene expression data


title: BXD65 Liver, Chow Diet

description: Gene expression data


title: BXD65 Liver, High Fat Diet

description: Gene expression data


title: BXD63 Liver, High Fat Diet

description: Gene expression data


title: BXD63 Liver, Chow Diet

description: Gene expression data


title: BXD64 Liver, Chow Diet

description: Gene expression data


title: BXD64 Liver, High Fat Diet

description: Gene expression data


title: BXD68 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-34

description: Sample 3-34


title: BXD62 Liver, High Fat Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-37

description: Sample 3-37


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-32

description: Sample 3-32


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-33

description: Sample 3-33


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-30

description: Sample 3-30


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-28

description: Sample 3-28


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-27

description: Sample 3-27


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-25

description: Sample 3-25


title: BXD61 Liver, High Fat Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-24

description: Sample 3-24


title: BXD61 Liver, Chow Diet

description: Gene expression data


title: BXD56 Liver, High Fat Diet

description: Gene expression data


title: BXD55 Liver, High Fat Diet

description: Gene expression data


title: BXD56 Liver, Chow Diet

description: Gene expression data


title: BXD62 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-29

description: Sample 3-29


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-26

description: Sample 3-26


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-22

description: Sample 3-22


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-20

description: Sample 3-20


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-21

description: Sample 3-21


title: BXD51 Liver, High Fat Diet

description: Gene expression data


title: BXD51 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-31

description: Sample 3-31


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-19

description: Sample 3-19


title: BXD55 Liver, Chow Diet

description: Gene expression data


title: BXD60 Liver, Chow Diet

description: Gene expression data


title: BXD50 Liver, High Fat Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-23

description: Sample 3-23


title: BXD48 Liver, Chow Diet

description: Gene expression data


title: BXD48 Liver, High Fat Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-18

description: Sample 3-18


title: BXD49 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-17

description: Sample 3-17


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-16

description: Sample 3-16


title: BXD49 Liver, High Fat Diet

description: Gene expression data


title: BXD45 Liver, High Fat Diet

description: Gene expression data


title: BXD44 Liver, High Fat Diet

description: Gene expression data


title: BXD45 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-14

description: Sample 3-14


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-13

description: Sample 3-13


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-12

description: Sample 3-12


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-11

description: Sample 3-11


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-10

description: Sample 3-10


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-15

description: Sample 3-15


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-9

description: Sample 3-9


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-6

description: Sample 3-6


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-8

description: Sample 3-8


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-7

description: Sample 3-7


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-5

description: Sample 3-5


title: BXD83 Liver, Chow Diet

description: Gene expression data


title: BXD43 Liver, High Fat Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-4

description: Sample 3-4


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-3

description: Sample 3-3


title: BXD43 Liver, Chow Diet

description: Gene expression data


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-2

description: Sample 3-2


title: BXD44 Liver, Chow Diet

description: Gene expression data


title: Whole trachea Scnn1b-T, PND 10, biological replicate 3

city: Chapel Hill

first: Hong

last: Dang

state: NC

address: 7027 Thurston-Bowles Bldg. CB#7248

department: CF Center

institute: UNC Chapel Hill

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3618, 3619)

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16 hours at 45 degrees. Washing and staining was performed in the Affymetrix GeneChip Fluidics Station 450, protocol FS450_0007.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets. PND10 samples were further adjusted through Batchremoval by comparing to the rest of the samples.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Scnn1b-Tg, trachea

label_protocol: RNAs were processed for hybridization to Affymetrix Mouse Gene ST 1.0 microarrays using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit and Ambion WT Expression Kit, according to manufacturer's recommended protocol.

growth_protocol: Mouse whole trachea;  mice grown under specific-pathogen-free conditions in micro-isolator cages

extract_protocol: Whole lungs were dissected and stored in RNALater until extraction using Qiagen RNAeasy columns, followed by ethanol precipitation

treatment_protocol: Not applicable;  no treatment;  mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42.

value: C57Bl/6N Tac

tag: age (postnatal day)


title: Whole trachea Scnn1b-T, PND 42, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 2998, 3001)


title: Whole trachea Scnn1b-T, PND 42, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3035, 3057)


title: Whole trachea Scnn1b-T, PND 10, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3599, 3600)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-Tg males (animal numbers 22818, 2886, 2887, 2888)


title: genomic DNA from esophageal squamous cell carcinoma Sample 3-1

description: Sample 3-1


title: plasma circulating DNA from cancer-free individual Sample 2-95

description: Sample 2-95


title: Whole trachea Scnn1b-T, PND 3, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2783, 2784, 2785)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2662, 2664, 2665)


title: plasma circulating DNA from cancer-free individual Sample 2-96

description: Sample 2-96


title: Whole trachea Scnn1b-T, PND 0, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2419, 2420)

value: PND 0 (<24 hrs)


title: Whole trachea Scnn1b-T, PND 10, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3589, 3597)


title: Whole trachea WT, PND 42, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 3036, 3037)

source_name: Wildtype, trachea

value: Wildtype


title: Whole trachea Scnn1b-T, PND 0, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2376, 2409)


title: Whole trachea Scnn1b-T, PND 0, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2369, 2377)


title: plasma circulating DNA from cancer-free individual Sample 2-94

description: Sample 2-94

value: cancer-free individual


title: plasma circulating DNA from cancer-free individual Sample 2-93

description: Sample 2-93

value: plasma sample from cancer-free individual


title: plasma circulating DNA from cancer-free individual Sample 2-92

description: Sample 2-92

value: plasma circulating DNA


title: plasma circulating DNA from cancer-free individual Sample 2-91

description: Sample 2-91


title: plasma circulating DNA from cancer-free individual Sample 2-90

description: Sample 2-90


title: plasma circulating DNA from cancer-free individual Sample 2-89

description: Sample 2-89


title: plasma circulating DNA from cancer-free individual Sample 2-87

description: Sample 2-87


title: plasma circulating DNA from cancer-free individual Sample 2-88

description: Sample 2-88


title: Whole trachea WT, PND 42, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 2996, 2997)


title: Whole trachea WT, PND 10, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) from a post natal day 10 wild-type male (animal number 3616)


title: Whole trachea WT, PND 3, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2791, 2793)


title: Whole trachea WT, PND 10, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 wild-type males (animal numbers 3588, 3590)


title: Whole trachea WT, PND 3, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2792, 2781)


title: Whole trachea WT, PND 10, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 wild-type males (animal numbers 3598, 3601)


title: Whole trachea WT, PND 0, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively); pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2377, 2410)


title: Whole trachea WT, PND 42, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 2999, 3033)


title: plasma circulating DNA from cancer-free individual Sample 2-82

description: Sample 2-82


title: plasma circulating DNA from cancer-free individual Sample 2-85

description: Sample 2-85


title: Whole trachea Scnn1b-T, PND 42, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3002, 3013)


title: Whole trachea WT, PND 0, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2418, 2421)


title: plasma circulating DNA from cancer-free individual Sample 2-83

description: Sample 2-83


title: Whole trachea WT, PND 3, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2782, 2817)


title: plasma circulating DNA from cancer-free individual Sample 2-86

description: Sample 2-86


title: plasma circulating DNA from cancer-free individual Sample 2-81

description: Sample 2-81


title: plasma circulating DNA from cancer-free individual Sample 2-79

description: Sample 2-79


title: plasma circulating DNA from cancer-free individual Sample 2-80

description: Sample 2-80


title: plasma circulating DNA from cancer-free individual Sample 2-84

description: Sample 2-84


title: plasma circulating DNA from cancer-free individual Sample 2-78

description: Sample 2-78

value: female


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-77

description: Sample 2-77

value: male


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-76

description: Sample 2-76


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 3

description: whole lung (left lobe) sample from post natal day 42 Scnn1b-transgenic male (animal number 3035)

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Scnn1b-Tg, whole lung

growth_protocol: Mouse whole lung (left lobe);  mice grown under specific-pathogen-free conditions in micro-isolator cages


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-73

description: Sample 2-73


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-74

description: Sample 2-74


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-72

description: Sample 2-72


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-71

description: Sample 2-71


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3013, 3034)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2752, 2754)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-70

description: Sample 2-70


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-69

description: Sample 2-69


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2783, 2784)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2664, 2665)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-68

description: Sample 2-68


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 2998, 3002)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 2-75

description: Sample 2-75


title: Whole lung WT, PND 42, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 2996, 3036)

source_name: Wildtype, whole lung


title: Whole lung WT, PND 42, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 3037, 3058)


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-67

description: Sample 2-67


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 1

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2375, 2376)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2662, 2663)


title: Whole lung WT, PND 42, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 3067, 3068)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2688, 2746)


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 3

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2420, 2422)


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 2

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2409, 2419)


title: Whole lung WT, PND 10, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2745, 2753)


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-66

description: Sample 2-66


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-65

description: Sample 2-65


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-64

description: Sample 2-64


title: Whole lung WT, PND 10, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2685, 2689)


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-62

description: Sample 2-62


title: Whole lung WT, PND 3, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2817, 2884)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2760, 2761)


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-58

description: Sample 2-58


title: Whole lung WT, PND 0, biological replicate 3

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2418, 2421)


title: Whole lung WT, PND 10, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2683, 2684)


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-59

description: Sample 2-59


title: Whole lung WT, PND 3, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2781, 2782)


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-57

description: Sample 2-57


title: Whole lung WT, PND 3, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2792, 2793)


title: Whole lung WT, PND 0, biological replicate 1

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2370, 2374)


title: Whole lung WT, PND 0, biological replicate 2

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2377, 2410)


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-60

description: Sample 2-60


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-63

description: Sample 2-63


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-54

description: Sample 2-54


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-55

description: Sample 2-55


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-53

description: Sample 2-53


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-51

description: Sample 2-51


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-52

description: Sample 2-52


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-48

description: Sample 2-48


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-49

description: Sample 2-49


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-47

description: Sample 2-47


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-44

description: Sample 2-44


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-50

description: Sample 2-50


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-61

description: Sample 2-61


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-46

description: Sample 2-46


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-56

description: Sample 2-56


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-43

description: Sample 2-43


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-45

description: Sample 2-45


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-42

description: Sample 2-42


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-37

description: Sample 2-37


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-35

description: Sample 2-35


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-41

description: Sample 2-41


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-40

description: Sample 2-40


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-38

description: Sample 2-38


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-32

description: Sample 2-32


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-36

description: Sample 2-36


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-39

description: Sample 2-39


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-27

description: Sample 2-27


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-28

description: Sample 2-28


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-26

description: Sample 2-26


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-31

description: Sample 2-31


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-25

description: Sample 2-25


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-30

description: Sample 2-30


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-29

description: Sample 2-29


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-34

description: Sample 2-34


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-23

description: Sample 2-23


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-24

description: Sample 2-24


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-20

description: Sample 2-20


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-22

description: Sample 2-22


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-19

description: Sample 2-19


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-18

description: Sample 2-18


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-33

description: Sample 2-33


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-17

description: Sample 2-17


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-16

description: Sample 2-16


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-15

description: Sample 2-15


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-14

description: Sample 2-14


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-13

description: Sample 2-13


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-11

description: Sample 2-11


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-12

description: Sample 2-12


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-9

description: Sample 2-9


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-10

description: Sample 2-10


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-8

description: Sample 2-8


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-5

description: Sample 2-5


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-7

description: Sample 2-7


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-6

description: Sample 2-6


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-21

description: Sample 2-21


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-3

description: Sample 2-3


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-2

description: Sample 2-2


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-1

description: Sample 2-1


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 2

description: purified macrophages

hyb_protocol: Hybridization was performed at 48 degrees using the GeneTitan plate system.

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets.
MoGene-1_1-st-v1.r4.pgf
MoGene-1_1-st-v1.r4.mps

source_name: Scnn1b-Tg, macrophages, germ-free facility

label_protocol: 12 ng of RNA was used to generate cDNA using Ovation Pico WTA system V2 kig (NuGEN Technologies, CA).

growth_protocol: Mouse lung lavage macrphages purified by negative selection through from a Lys-6G column;  mice grown either under specific-pathogen-free conditions in micro-isolator cages or in a germ-free environment

extract_protocol: Magnetic activated cell sorting uas used to purify macrophages from lung lavage samples using Ant-Ly-6G MicroBeads (Miltenyi Biotec, MA).  Ly-6G negative cells (macrophages) were pelleted, snap-frozen and stored at -80 C.  Frozen macrophage pellets were lysed and homogenized in lysis buffer and QIAshedder (Qiagen).  Genomic DNA was eliminated using gDNA eliminator spin columns;  RNA was isolated using Purelink RNA mini kits (Invitrogen).

treatment_protocol: Mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42.  At PND 42 macrophages were also isolated from wildtype and Scnn1b-transgenic mice grown in a germ-free environment.

tag: animal facility type

value: germ-free


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 3

description: purified macrophages

source_name: Wildtype, macrophages, germ-free facility

tag: strain


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 2

description: purified macrophages

source_name: Scnn1b-Tg, macrophages, specific pathogene free facility

value: specfic pathogen free


title: plasma circulating DNA from cancer-free individual Sample 1-96

description: Sample 1-96

source_name: plasma sample


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 2

description: purified macrophages

source_name: Wildtype, macrophages, germ-free free facility


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 2

description: purified macrophages


title: plasma circulating DNA from cancer-free individual Sample 1-95

description: Sample 1-95


title: plasma circulating DNA from cancer-free individual Sample 1-94

description: Sample 1-94


title: plasma circulating DNA from cancer-free individual Sample 1-93

description: Sample 1-93


title: Whole trachea WT, PND 0, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2370, 2374)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 1

description: purified macrophages


title: genomic DNA from esophageal squamous cell carcinoma Sample 2-4

description: Sample 2-4


title: plasma circulating DNA from cancer-free individual Sample 1-91

description: Sample 1-91


title: plasma circulating DNA from cancer-free individual Sample 1-92

description: Sample 1-92


title: plasma circulating DNA from cancer-free individual Sample 1-90

description: Sample 1-90


title: plasma circulating DNA from cancer-free individual Sample 1-89

description: Sample 1-89


title: plasma circulating DNA from cancer-free individual Sample 1-88

description: Sample 1-88


title: plasma circulating DNA from cancer-free individual Sample 1-87

description: Sample 1-87


title: Purified lung lavage macrophages WT, PND 42, biological replicate 4

description: purified macrophages

source_name: Wildtype, macrophages, specfic pathogen free facility


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 4

description: purified macrophages


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-84

description: Sample 1-84


title: Purified lung lavage macrophages WT, PND 42, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 3, biological replicate 4

description: purified macrophages


title: plasma circulating DNA from cancer-free individual Sample 1-85

description: Sample 1-85


title: SF2969 (HG-U133A)

city: San Francisco

first: Joseph

last: Costello

state: CA

department: NeuroSurgery

institute: UCSF

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: R/Bioconductor RMA processing with custom CDF v.18.0.0, ENTREZG

source_name: GBM tumor

label_protocol: Approximately 1-5 ug of total RNA was processed to produce biotynylated cRNA targets

extract_protocol: RNA was isolated using Trizol and purified with Qiagen RNeasy columns

tag: site

tag: age

tag: survival

tag: censored

value: no


title: SF2919 (HG-U133A)


title: Ba/F3_c-kitV814_rep4 vs Ba/F3_normal_rep8

city: Takatsuki City

first: Masutani

last: Ryota

state: Osaka

address: Daigaku-machi

department: clinical central laboratory

institute: osaka medical college hospital

hyb_protocol: Samples were soluble in Hybridization buffer and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Scanned on a GenePix® 4400A (Molecular Devices). Images were quantified using Array-Pro Analyzer ® Ver.4.5 (Media Cybernetics）.

data_processing: LOESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Array-Pro Analyzer ® Ver.4.5 (Media Cybernetics） was used.

source_name: an IL-3-dependent mouse cell line (Ba/F3), c-kitV814 expressed cell

label_protocol: RNA labeling was carried out with miRCURY LNA™ microRNA, Hi-Power Labeling kit (Exiqon) using 1 μg of total RNA according to the manufacturer’s instructions.

growth_protocol: Ba/F3 was cultured in RPMI 1640 (Nacalai Tesque) supplemented with 10% FBS and 1X Penicillin-Streptomycin in the presence of 1.0 ng/mL recombinant mouse IL-3 (rmIL-3)(kirin) at 37 °C and 5% CO2.

extract_protocol: Total RNA was extracted from 6.00E+06 cells using TRIzol reagent (Invitrogen).

treatment_protocol: Ba/F3_normal_rep8: nothing. Ba/F3_c-kitV814_rep4: pMSCV-KIT.D816V-IRES-GFP retroviral vectors were transfected into plat-E cells using FuGENE6 Transfection reagent according to the manufacturer’s instructions. Retroviral supernatant was added to RetroNectin (TaKaRa) coated plates and Ba/F3 cells were infected in the presence of polybrene. WT or V814 protein expression was determined by flow cytometry with, PE-anti human CD4 (BioLegend) and/or APC-anti mouse c-kit (BioLegend), and sorting was performed using FACSAria flow cytometer (Becton Dickinson). MEK inhibitor treated Ba/F3_c-kitV814_rep2: Ba/F3 expressed c-kitV814 cells were incubated in the presence of 10 µM MEK1/2 inhibitor (PD325901; Cayman Chemical), for 48 hours at 37 °C and 5% CO2.

value: C3H mouse

tag: cell type

value: IL3 dependent pro B cell, expressed mutation:c-kitV814

source_name: an IL-3-dependent mouse cell line (Ba/F3), normal control

value: IL3 dependent pro B cell


title: SF3076 (HG-U133A)

value: yes


title: SF2777 (HG-U133A)


title: MEK inhibitor treated Ba/F3_c-kitV814_rep2 vs Ba/F3_c-kitV814_rep4

source_name: an IL-3-dependent mouse cell line (Ba/F3), MEK inhibitor treated c-kitV814 expressed cell

value: IL3 dependent pro B cell, expressed mutation:c-kitV814, Treate:MEK inhibitor


title: SF2894 (HG-U133A)

value: Multifocal


title: Purified lung lavage macrophages WT, PND 3, biological replicate 3

description: purified macrophages

value: C57Bl/6N Tac


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-83

description: Sample 1-83

value: Esophageal squamous cell carcinoma

value: plasma sample from patient


title: SF2935 (HG-U133A)


title: plasma circulating DNA from cancer-free individual Sample 1-86

description: Sample 1-86

value: cancer-free individual


title: Purified lung lavage macrophages WT, PND 10, biological replicate 3

description: purified macrophages

value: Wildtype


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-81

description: Sample 1-81

value: plasma circulating DNA


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-82

description: Sample 1-82


title: Purified lung lavage macrophages WT, PND 3, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 3, biological replicate 2

description: purified macrophages


title: SF2774 (HG-U133A)


title: Purified lung lavage macrophages WT, PND 0, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 0, biological replicate 1

description: purified macrophages


title: SF2760 (HG-U133A)


title: SF2737 (HG-U133A)


title: Purified lung lavage macrophages WT, PND 0, biological replicate 3

description: purified macrophages


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-79

description: Sample 1-79


title: SF2969 (HG-U133B)

data_processing: R/Bioconductor RMA processing with custom CDF v.16.0.0, ENTREZG

value: female


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-78

description: Sample 1-78

value: male


title: SF2704 (HG-U133A)


title: SF2919 (HG-U133B)


title: SF2935 (HG-U133B)


title: SF2670 (HG-U133A)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-74

description: Sample 1-74


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-77

description: Sample 1-77


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-76

description: Sample 1-76


title: SF3076 (HG-U133B)


title: SF2777 (HG-U133B)


title: SF2703 (HG-U133A)


title: SF2434 (HG-U133A)


title: SF2399 (HG-U133A)


title: SF2894 (HG-U133B)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-80

description: Sample 1-80


title: SF2774 (HG-U133B)


title: SF2413 (HG-U133A)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-75

description: Sample 1-75


title: SF2737 (HG-U133B)


title: SF2560 (HG-U133A)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-71

description: Sample 1-71


title: SF2704 (HG-U133B)


title: SF2208 (HG-U133A)


title: SF2315 (HG-U133A)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-70

description: Sample 1-70


title: SF2760 (HG-U133B)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-73

description: Sample 1-73


title: SF2670 (HG-U133B)


title: SF2703 (HG-U133B)


title: SF2560 (HG-U133B)


title: SF2159 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-66

description: Sample 1-66

value: tumor tissue

value: genomic DNA


title: SF2167 (HG-U133A)

value: no


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-72

description: Sample 1-72


title: SF1913 (HG-U133A)


title: plasma circulating DNA from esophageal squamous cell carcinoma Sample 1-69

description: Sample 1-69


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-68

description: Sample 1-68


title: SF2434 (HG-U133B)


title: SF2413 (HG-U133B)


title: SF2399 (HG-U133B)


title: SF2077 (HG-U133A)


title: SF1881 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-65

description: Sample 1-65


title: SF1751 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-62

description: Sample 1-62


title: SF2208 (HG-U133B)


title: SF1750 (HG-U133A)


title: SF2315 (HG-U133B)


title: SF1605 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-64

description: Sample 1-64


title: SF1701 (HG-U133A)


title: SF1653 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-67

description: Sample 1-67


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-63

description: Sample 1-63


title: SF2077 (HG-U133B)


title: SF2159 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-58

description: Sample 1-58

value: normal tissue


title: SF1481 (HG-U133A)


title: SF2167 (HG-U133B)


title: SF1547 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-61

description: Sample 1-61


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-57

description: Sample 1-57


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-59

description: Sample 1-59


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-60

description: Sample 1-60


title: SF1913 (HG-U133B)


title: SF1475 (HG-U133A)


title: SF1388 (HG-U133A)


title: SF1751 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-56

description: Sample 1-56


title: SF1881 (HG-U133B)


title: SF1750 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-55

description: Sample 1-55


title: SF1461 (HG-U133A)


title: SF1198 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-54

description: Sample 1-54


title: Collagen gel w/ PDGF-BB

city: Ann Arbor

first: William

last: Giannobile

state: Michigan

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

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 450.

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

data_processing: The data were analyzed with Expression Console.

source_name: HGF cells in gel w growth factor

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

growth_protocol: HGF cells were suspended in BME with 1% FBS

extract_protocol: Trizol method of RNA extraction was performed to manufacturer's instructions.

treatment_protocol: Collagen scaffolds and gel (w/ and w/o PDGF-BB) was overlaid with HGF cells in BME and harvested after 1-14 days for RNA extraction

value: gingival fibroblasts

tag: scaffold

value: gel

tag: growth factor

value: w/ PDGF-BB


title: Collagen gel w/o PDGF-BB

source_name: HGF cells in gel w/o growth factor

value: w/o PDGF-BB


title: Collagen scaffold w/ PDGF-BB

source_name: HGF cells in scaffold w growth factor

value: collagen


title: Collagen scaffold w/o PDGF-BB

source_name: HGF cells in scaffold w/o growth factor


title: SF1653 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-53

description: Sample 1-53

source_name: surgical tissue

tag: disease state

tag: sample type


title: SF1167 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-51

description: Sample 1-51


title: SF1605 (HG-U133B)


title: SF1368 (HG-U133A)

value: yes


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-50

description: Sample 1-50

value: Esophageal squamous cell carcinoma


title: SF1547 (HG-U133B)


title: SF1701 (HG-U133B)


title: SF1166 (HG-U133A)


title: SF0918 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-49

description: Sample 1-49


title: SF0921 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-52

description: Sample 1-52


title: Tumor epthelial component - sample 1660

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from microdissected ovarian tumor epthelial component

hyb_protocol: For each sample, 15 microgram of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array.

scan_protocol: GeneChip Scanner 3000 (Affymetrix) was used for array scanning and data collection.

data_processing: Microarray data analysis software, GeneSpring V.11.0.2 (Agilent Technologies Inc.) was used to perform the primary data analysis. RMA summerization algorithm was used and baseline transformation to median of all samples were performed.

label: Biotin

source_name: Microdissected ovarian tumor epthelial component

label_protocol: RNA samples were amplified and labeled using the two-cycle amplification protocol (Affymetrix).

extract_protocol:
Cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). Normal human ovarian surface epithelium (HOSE) specimens were obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
Frozen sections were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol and stained by 1% methyl green. Air-dried tissue sections were then taken for microdissection using a MD LMD laser microdissecting microscope (Leica). Different types of tissues were dissected and harvested. Total RNA was isolated using the RNeasy Micro kit (Qiagen).


title: NJchip16 (HG-U133A)

source_name: Non-neoplastic brain tissue


title: SF1475 (HG-U133B)


title: Tumor epthelial component - sample 1231

value: Microdissected ovarian tumor epthelial component


title: N99A_36 (HG-U133A)


title: Tumor epthelial component - sample 799


title: Tumor epthelial component - sample 872


title: Tumor epthelial component - sample 1064


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-48

description: Sample 1-48


title: Tumor epthelial component - sample 778


title: Tumor epthelial component - sample 780


title: SF1388 (HG-U133B)


title: SF1461 (HG-U133B)


title: Tumor epthelial component - sample 765


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-47

description: Sample 1-47


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-44

description: Sample 1-44


title: SF1198 (HG-U133B)


title: N7A41 (HG-U133A)


title: SF1368 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-43

description: Sample 1-43


title: SF1167 (HG-U133B)


title: N88A_34 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-46

description: Sample 1-46


title: SF1166 (HG-U133B)


title: N21A48 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-42

description: Sample 1-42


title: MDAN3122 (HG-U133A)


title: SF0921 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-45

description: Sample 1-45


title: Tumor epthelial component - sample 467


title: SF0918 (HG-U133B)


title: MDAN3116 (HG-U133A)


title: MDAN3121 (HG-U133A)


title: Tumor epthelial component - sample 714


title: Tumor epthelial component - sample 744


title: Tumor epthelial component - sample 443


title: Tumor epthelial component - sample 434


title: Tumor epthelial component - sample 629


title: Tumor epthelial component - sample 427


title: N3886 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-40

description: Sample 1-40


title: NJchip16 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-41

description: Sample 1-41


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-39

description: Sample 1-39


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-38

description: Sample 1-38


title: N99A_36 (HG-U133B)


title: N88A_34 (HG-U133B)


title: MDAN2512 (HG-U133A)


title: Tumor epthelial component - sample 412


title: MDAN3114 (HG-U133A)


title: MDAN1818 (HG-U133A)


title: MDAN1486 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-37

description: Sample 1-37


title: N7A41 (HG-U133B)


title: Tumor epthelial component - sample 402


title: Tumor epthelial component - sample 396


title: N3886 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-34

description: Sample 1-34


title: Tumor epthelial component - sample 394


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-33

description: Sample 1-33


title: Tumor epthelial component - sample 389


title: MDA43291 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-35

description: Sample 1-35


title: MDA34826 (HG-U133A)


title: MDAN3121 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-36

description: Sample 1-36


title: MDA8662 (HG-U133A)


title: MDAN1248 (HG-U133A)


title: N21A48 (HG-U133B)


title: MDAN3116 (HG-U133B)


title: Tumor epthelial component - sample 393


title: MDAN3122 (HG-U133B)


title: MDAN3114 (HG-U133B)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-31

description: Sample 1-31


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-30

description: Sample 1-30


title: MDAN2512 (HG-U133B)


title: MDA28435 (HG-U133A)


title: MDA20194 (HG-U133A)


title: MDAN1248 (HG-U133B)


title: MDAN1486 (HG-U133B)


title: Tumor epthelial component - sample 380


title: MDA13818 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-28

description: Sample 1-28


title: MDA18395 (HG-U133A)


title: Tumor epthelial component - sample 386


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-27

description: Sample 1-27


title: MDA1153 (HG-U133A)


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-26

description: Sample 1-26


title: Tumor epthelial component - sample 349


title: Tumor epthelial component - sample 351


title: M8FE-with 15mM iron-log phase-rep3

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Iron-resistant Saccharomyces cerevisiae, log. Phase, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.5 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Fresh precultures of yeast cells were diluted to an OD600 of 0.1 in fresh minimal medium in the presence and absence of 15mM [NH4]2[Fe][SO4]2 stress factor.  They were cultivated at 30°C and 150 rpm untill they reach the OD600 value of about 1.00. Cells were harvested at this OD600 value.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Three replicates for WT (reference Saccharomyces cerevisiae strain) and M8FE were treated with 15mM [NH4]2[Fe][SO4]2 stress factor. Stress factor was added in the beginning of culture incubation. Cultures were grown until an OD600 of ~1.00. Samples were washed with fresh YMM prior of the RNA extraction.

tag: background strain

value: CEN.PK 113.7D (MATa)

tag: genotype/variation

tag: treatment

value: treated with 15mM [NH4]2[Fe][SO4]2


title: Tumor epthelial component - sample 377


title: Tumor epthelial component - sample 332


title: Tumor epthelial component - sample 326


title: MDA8662 (HG-U133B)

tag: gender


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-29

description: Sample 1-29

tag: tissue


title: Tumor epthelial component - sample 324


title: SF1481 (HG-U133B)


title: M8FE-with 15mM iron-log phase-rep2

source_name: Iron-resistant Saccharomyces cerevisiae, log. Phase, replicate 2


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-32

description: Sample 1-32


title: MDA34826 (HG-U133B)


title: Tumor epthelial component - sample 321


title: M8FE-with 15mM iron-log phase-rep1

source_name: Iron-resistant Saccharomyces cerevisiae, log. Phase, replicate 1


title: MDA28435 (HG-U133B)


title: Wild Type-with 15mM iron-log phase-rep2

source_name: Saccharomyces cerevisiae, log. Phase, replicate 2

value: wild type


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-24

description: Sample 1-24


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-25

description: Sample 1-25


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-23

description: Sample 1-23


title: MDA43291 (HG-U133B)


title: MDAN1818 (HG-U133B)


title: MDA20194 (HG-U133B)

value: female


title: Wild Type-with 15mM iron-log phase-rep1

source_name: Saccharomyces cerevisiae, log. Phase, replicate 1


title: MDA24843 (HG-U133B)

value: male


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-22

description: Sample 1-22


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-21

description: Sample 1-21

value: tumor tissue


title: MDA18395 (HG-U133B)


title: Wild Type-with 15mM iron-log phase-rep3

source_name: Saccharomyces cerevisiae, log. Phase, replicate 3


title: M8FE-without iron-log phase-rep2


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-20

description: Sample 1-20

value: genomic DNA


title: Tumor epthelial component - sample 317


title: Human ovarian surface epthelium - sample 2234

description: Gene expression data from microdissected ovarian surface epthelium

source_name: Microdissected ovarian surface epthelium


title: Human ovarian surface epthelium - sample 2230

value: Microdissected ovarian surface epthelium


title: Human ovarian surface epthelium - sample 2228


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-19

description: Sample 1-19


title: MDA13818 (HG-U133B)

source_name: GBM tumor


title: M8FE-without iron-log phase-rep3


title: MDA1153 (HG-U133B)

value: no


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-17

description: Sample 1-17


title: M8FE-without iron-log phase-rep1


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-18

description: Sample 1-18

value: normal tissue


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-15

description: Sample 1-15


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-16

description: Sample 1-16


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-14

description: Sample 1-14


title: Human ovarian surface epthelium - sample 2226


title: Wild Type-without iron-log phase-rep1


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-13

description: Sample 1-13


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-12

description: Sample 1-12


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-11

description: Sample 1-11


title: Wild Type-without iron-log phase-rep3


title: Ovarian cancer stroma - sample 1660

description: Gene expression data from microdissected ovarian cancer stroma

source_name: Microdissected ovarian cancer stroma

value: Microdissected ovarian cancer stroma


title: Ovarian cancer stroma - sample 1064


title: Human ovarian surface epthelium - sample 2225


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-10

description: Sample 1-10


title: Wild Type-without iron-log phase-rep2


title: Ovarian cancer stroma - sample 799


title: Ovarian cancer stroma - sample 872


title: Ovarian cancer stroma - sample 794


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-8

description: Sample 1-8


title: Human ovarian surface epthelium - sample 2237


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-7

description: Sample 1-7


title: Ovarian cancer stroma - sample 780


title: Ovarian cancer stroma - sample 629


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-9

description: Sample 1-9


title: Ovarian cancer stroma - sample 778


title: Ovarian cancer stroma - sample 467


title: Ovarian cancer stroma - sample 765


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-6

description: Sample 1-6


title: Ovarian cancer stroma - sample 744


title: Tumor epthelial component - sample 388


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-5

description: Sample 1-5


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-4

description: Sample 1-4


title: MDA24843 (HG-U133A)


title: Hutt60_LCL

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

department: Human Genetics

institute: University of Chicago

hyb_protocol: As directed by manufacturer

scan_protocol: As directed by manufacturer

data_processing: Quantile normalization followed by BQMI normalization

label: Cy3, Cy5

source_name: LCL

label_protocol: Bisulfite conversion

extract_protocol: DNeasy Blood and Tissue Kits (Qiagen)

tag: cell type (precursor used to generate ipscs)

value: LCL

tag: passage

value: Female


title: Ovarian cancer stroma - sample 443


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-3

description: Sample 1-3


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-2

description: Sample 1-2


title: Ovarian cancer stroma - sample 434


title: genomic DNA from esophageal squamous cell carcinoma Sample 1-1

description: Sample 1-1


title: H19101_LCL

value: Male


title: H19114_LCL


title: Ovarian cancer stroma - sample 412


title: Ovarian cancer stroma - sample 431


title: Ovarian cancer stroma - sample 396


title: Ovarian cancer stroma - sample 427


title: H20961_FB

source_name: dermal fibroblast

value: dermal fibroblast


title: C40280_FB

organism: Pan troglodytes


title: H28834_FB


title: H18489_LCL


title: Dox + CHIR, rep2

city: New York

first: Matthias

last: Stadtfeld

address: 540 First Avenue Skirball Lab 4-1

institute: NYU School of Medicine

hyb_protocol: GeneChip 3'IVT Express Kit

scan_protocol: GeneChip Hybridization Wash and Stain Kit

data_processing: The data were analyzed using GeneSpring 11 with default settings, normalized using GCRMA

label: biotin-conjugated

source_name: day 4 SSEA1+ cells, Dox + CHIR

label_protocol: GeneChip 3'IVT Express Kit

growth_protocol: Reprogrammable MEFs were cultured for four days in the presence of dox and other compounds

extract_protocol: Total RNA extracted from SSEA1+ cells with the RNeasy mini kit (QIAGEN)

treatment_protocol: On day 4, cells were harvested and stained with biotinylated anti-SSEA1 antibody, followed by APC-conjugated Streptavidin and then anti-APC microbeads (Milteny Biotec) and enrichment using MACS separation columns (Milteny Biotec)

tag: cell-type

value: reprogrammable MEFs

tag: cutured with

value: Dox + CHIR

tag: time point

value: day 4 culture

tag: cell subpopulation

value: SSEA1+ cells


title: Hutt45_LCL


title: Ovarian cancer stroma - sample 402


title: Ovarian cancer stroma - sample 388


title: Dox + CHIR, rep1


title: C40210_FB


title: Dox + 3c, rep1

source_name: day 4 SSEA1+ cells, Dox + 3c

value: Dox + 3c


title: Ovarian cancer stroma - sample 393


title: Ovarian cancer stroma - sample 389


title: C8861_FB


title: C4955_FB


title: Dox + iAlk5, rep1

source_name: day 4 SSEA1+ cells, Dox + iAlk5

value: Dox + iAlk5


title: Dox + 3c, rep2


title: Ovarian cancer stroma - sample 386


title: Dox + iAlk5, rep2


title: Ovarian cancer stroma - sample 377


title: Dox + AA, rep2

source_name: day 4 SSEA1+ cells, Dox + AA,

value: Dox + AA


title: Ovarian cancer stroma - sample 351


title: Hutt60_iPSC

source_name: induced pluripotent stem cell line

tag: cell line

value: induced pluripotent stem cell line


title: C3649_FB


title: C3651_FB


title: Dox + AA, rep1


title: Ovarian cancer stroma - sample 349


title: C3647_FB


title: H19114_iPSC


title: H20961_iPSC


title: Dox alone, rep2

source_name: day 4 SSEA1+ cells, Dox alone

value: Dox alone


title: Ovarian cancer stroma - sample 345


title: C40280_iPSC


title: Ovarian cancer stroma - sample 332


title: Dox alone, rep1


title: H28834_iPSC


title: Ovarian cancer stroma - sample 324


title: Hutt45_iPSC


title: Cre-24h-3-3

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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: RMA by software Partek

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: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

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

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: strain

tag: cell type

value: mouse embryonic fibroblasts

value: Cre

tag: time


title: H19101_iPSC


title: Cre-24h-3-2


title: H18489_iPSC


title: Ovarian cancer stroma - sample 326


title: Cre-24h-3-1


title: Normal ovarian stroma - sample 47

description: Gene expression data from microdissected normal ovarian stroma

source_name: Microdissected normal ovarian stroma

value: Microdissected normal ovarian stroma


title: Ovarian cancer stroma - sample 317

value: Microdissected ovarian cancer stroma


title: seed at 50 DAF, biological rep2

city: Ames

first: Ling

last: Li

state: IA

address: 443 Bessey Hall

department: Department of Genetics, Development, and Cell Biology

institute: Iowa State University

description: developing soybean seeds

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

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

organism: Glycine max

source_name: soybean Evans seed at 50 day after flowering

growth_protocol: Glycine max variety Evans was grown in the field under standard agronomic practice at the Bruner Research Farm near Ames, IA.

treatment_protocol: Flowers at mid-plant nodes were tagged as they opened and pods were harvested during rapid seed filling at 20, 25, 30, 35, 40, 45, and 50 days after flowering (DAF).

tag: cultivar

value: Evans

value: developing seed

tag: genotype


title: Cre-0h-1-3


title: seed at 50 DAF, biological rep1

description: developing soybean seeds


title: Cre-0h-1-2


title: seed at 45 DAF, biological rep2

description: developing soybean seeds

source_name: soybean Evans seed at 45 day after flowering


title: Cre-0h-1-1


title: Ovarian cancer stroma - sample 380


title: C4955_iPSC

value: Male


title: 16WT1-KTS-24h-3


title: Normal ovarian stroma - sample 43


title: Normal ovarian stroma - sample 18


title: seed at 40 DAF, biological rep2

description: developing soybean seeds

source_name: soybean Evans seed at 40 day after flowering


title: Normal ovarian stroma - sample 41


title: C40210_iPSC

value: Female


title: 16WT1-KTS-24h-2


title: seed at 45 DAF, biological rep1

description: developing soybean seeds


title: C3649_iPSC


title: 16WT1-KTS-24h-1


title: Normal ovarian stroma - sample 28


title: 10WT1-KTS-0h-2


title: Normal ovarian stroma - sample 14


title: seed at 30 DAF, biological rep2

description: developing soybean seeds

source_name: soybean Evans seed at 30 day after flowering


title: C8861_iPSC


title: 10WT1-KTS-0h-3


title: C3651_iPSC


title: seed at 40 DAF, biological rep1

description: developing soybean seeds


title: C3647_iPSC


title: seed at 25 DAF, biological rep2

description: developing soybean seeds

source_name: soybean Evans seed at 25 day after flowering


title: seed at 30 DAF, biological rep1

description: developing soybean seeds


title: Normal ovarian stroma - sample 13


title: 7WT1+KTS-24h3-3


title: seed at 25 DAF, biological rep1

description: developing soybean seeds


title: te_lbf1_04

city: Villeneuve d'Ascq

first: Chantreau

last: Maxime

state: Nord

address: Université de lille 1

institute: Université de Lille 1

hyb_protocol: Following manufacture's instruction for One-Color Microarray base gene Expression Analysis (Agilent Technologies)

scan_protocol: Using an Axon GenePix 4000B scanner (Molecular Devices) piloted by GenePix Pro 6.0 software (Axon)

data_processing: After background noise elimination, medians values of overall hybridization were normalized by robust local regression (Yang et al., 2002). Artefact spots were manually eliminated. Differential analysis was performed with the method varmixt (Delmar et al., 2005) , available in the package anapuce of the software R. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance (Delmar et al., 2005). The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER) (Ge et al., 2003). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.05

organism: Linum usitatissimum

source_name: flax outer stem tissues

growth_protocol: plants were grown under field conditions at the University of Lille, France

extract_protocol: Total RNA was extracted from peeled outer tissues using the TriReagent (Molecular Research Center) method

tag: developmental stage

value: vegetative

value: Diane

value: EMS mutant from family lbf1