title: B2_Saline_6 hrs

source_name: Lung sample from OVA-sensitized animal B2 challenged with Saline at 6 hrs


title: C6_0.1% MSA_6 hrs

status: Public on Oct 11 2015

type: RNA

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

country: USA

institute: Hoffmann-LaRoche

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix Mouse Genome 430 2.0  chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. Normalized data (VALUE) represents probesets that probesets passed the QC and curation processes.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Lung sample from naive animal C6 challenged with 0.1% MSA at 6 hrs

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).

extract_protocol: Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

tag: animal id

tag: sensitization

value: naive

tag: treatment

tag: time

value: 6 hrs

tag: tissue

value: lung

tag: genetic background

value: balb/c


title: 7.1_6_Mock

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

organism: Macaca fascicularis

source_name: Lung slice sample from animal 7 (tech replicate 1) at 6hr post-challenge with Mock

extract_protocol: RNA extraction was performed using the Qiagen RNeasy Mini Kit (Cat. 74004) – Fibrous Tissues protocol (includes proteinase K digestion to remove proteins).

tag: technical replicate

value: Mock


title: 3.1_2_Mock

source_name: Lung slice sample from animal 3 (tech replicate 1) at 2hr post-challenge with Mock


title: 7.1_2_Mock

source_name: Lung slice sample from animal 7 (tech replicate 1) at 2hr post-challenge with Mock


title: 7.1_2_Poly_IC

source_name: Lung slice sample from animal 7 (tech replicate 1) at 2hr post-challenge with Poly_IC

value: Poly IC


title: B8_Saline_6 hrs

source_name: Lung sample from OVA-sensitized animal B8 challenged with Saline at 6 hrs

value: OVA-sensitized

value: Saline


title: B7_Saline_6 hrs

source_name: Lung sample from OVA-sensitized animal B7 challenged with Saline at 6 hrs


title: B5_Saline_6 hrs

source_name: Lung sample from OVA-sensitized animal B5 challenged with Saline at 6 hrs


title: 3.1_6_Poly_IC

source_name: Lung slice sample from animal 3 (tech replicate 1) at 6hr post-challenge with Poly_IC


title: 2.1_2_Mock

source_name: Lung slice sample from animal 2 (tech replicate 1) at 2hr post-challenge with Mock


title: 3.1_24_Mock

source_name: Lung slice sample from animal 3 (tech replicate 1) at 24hr post-challenge with Mock


title: 8.1_24_Mock

source_name: Lung slice sample from animal 8 (tech replicate 1) at 24hr post-challenge with Mock


title: 3.1_2_Poly_IC

source_name: Lung slice sample from animal 3 (tech replicate 1) at 2hr post-challenge with Poly_IC


title: A1_Saline_6 hrs

source_name: Lung sample from naive animal A1 challenged with Saline at 6 hrs


title: A5_Saline_6 hrs

source_name: Lung sample from naive animal A5 challenged with Saline at 6 hrs


title: A4_Saline_6 hrs

source_name: Lung sample from naive animal A4 challenged with Saline at 6 hrs


title: B4_Saline_6 hrs

source_name: Lung sample from OVA-sensitized animal B4 challenged with Saline at 6 hrs


title: A6_Saline_6 hrs

source_name: Lung sample from naive animal A6 challenged with Saline at 6 hrs


title: 8.1_2_Mock

source_name: Lung slice sample from animal 8 (tech replicate 1) at 2hr post-challenge with Mock


title: A3_Saline_6 hrs

source_name: Lung sample from naive animal A3 challenged with Saline at 6 hrs


title: 8.1_24_Poly_IC

source_name: Lung slice sample from animal 8 (tech replicate 1) at 24hr post-challenge with Poly_IC


title: 8.1_6_Poly_IC

source_name: Lung slice sample from animal 8 (tech replicate 1) at 6hr post-challenge with Poly_IC


title: A7_Saline_6 hrs

source_name: Lung sample from naive animal A7 challenged with Saline at 6 hrs


title: A8_Saline_6 hrs

source_name: Lung sample from naive animal A8 challenged with Saline at 6 hrs


title: 2.1_6_Mock

source_name: Lung slice sample from animal 2 (tech replicate 1) at 6hr post-challenge with Mock


title: 8.1_2_Poly_IC

source_name: Lung slice sample from animal 8 (tech replicate 1) at 2hr post-challenge with Poly_IC


title: 2.1_6_Poly_IC

source_name: Lung slice sample from animal 2 (tech replicate 1) at 6hr post-challenge with Poly_IC


title: 7.1_24_Poly_IC

source_name: Lung slice sample from animal 7 (tech replicate 1) at 24hr post-challenge with Poly_IC


title: 8.1_6_Mock

source_name: Lung slice sample from animal 8 (tech replicate 1) at 6hr post-challenge with Mock


title: A2_Saline_6 hrs

source_name: Lung sample from naive animal A2 challenged with Saline at 6 hrs


title: 233204_OVA_0

source_name: Lung sample from OVA-sensitized animal 233204 at 0hr time point

tag: time (h)


title: 233209_OVA_0

source_name: Lung sample from OVA-sensitized animal 233209 at 0hr time point


title: 233205_OVA_0

source_name: Lung sample from OVA-sensitized animal 233205 at 0hr time point


title: NV-23_6h

source_name: Nasal scrape sample from animal NV-23 at 6hr time point

value: nasal epithelium

value: poly I:C


title: 233206_OVA_0

source_name: Lung sample from OVA-sensitized animal 233206 at 0hr time point


title: 3.1_6_Mock

source_name: Lung slice sample from animal 3 (tech replicate 1) at 6hr post-challenge with Mock


title: NV-24_0h

source_name: Nasal scrape sample from animal NV-24 at 0hr time point


title: NV-20_0h

source_name: Nasal scrape sample from animal NV-20 at 0hr time point


title: NV-24_6h

source_name: Nasal scrape sample from animal NV-24 at 6hr time point


title: AS-23_6h

source_name: Nasal scrape sample from animal AS-23 at 6hr time point

value: A. suum


title: 233199_PBS_0

source_name: Lung sample from naive animal 233199 at 0hr time point


title: AS-19_0h

source_name: Nasal scrape sample from animal AS-19 at 0hr time point


title: NV-22_0h

source_name: Nasal scrape sample from animal NV-22 at 0hr time point


title: 233198_PBS_0

source_name: Lung sample from naive animal 233198 at 0hr time point


title: 233201_PBS_0

source_name: Lung sample from naive animal 233201 at 0hr time point


title: AS-17_0h

source_name: Nasal scrape sample from animal AS-17 at 0hr time point


title: 233207_OVA_0

source_name: Lung sample from OVA-sensitized animal 233207 at 0hr time point


title: 233200_PBS_0

source_name: Lung sample from naive animal 233200 at 0hr time point


title: AS-22_6h

source_name: Nasal scrape sample from animal AS-22 at 6hr time point


title: NV-20_6h

source_name: Nasal scrape sample from animal NV-20 at 6hr time point


title: NV-21_0h

source_name: Nasal scrape sample from animal NV-21 at 0hr time point


title: 233197_PBS_0

source_name: Lung sample from naive animal 233197 at 0hr time point


title: 233208_OVA_0

source_name: Lung sample from OVA-sensitized animal 233208 at 0hr time point


title: 233203_OVA_0

source_name: Lung sample from OVA-sensitized animal 233203 at 0hr time point


title: 233202_OVA_0

source_name: Lung sample from OVA-sensitized animal 233202 at 0hr time point


title: AS-24_0h

source_name: Nasal scrape sample from animal AS-24 at 0hr time point


title: 233196_PBS_0

source_name: Lung sample from naive animal 233196 at 0hr time point


title: 233195_PBS_0

source_name: Lung sample from naive animal 233195 at 0hr time point


title: 233194_PBS_0

source_name: Lung sample from naive animal 233194 at 0hr time point


title: 233193_OVA_168

source_name: Lung sample from OVA-sensitized animal 233193 at 168hr time point


title: AS-24_6h

source_name: Nasal scrape sample from animal AS-24 at 6hr time point


title: NV-23_0h

source_name: Nasal scrape sample from animal NV-23 at 0hr time point


title: 233192_OVA_168

source_name: Lung sample from OVA-sensitized animal 233192 at 168hr time point


title: AS-17_6h

source_name: Nasal scrape sample from animal AS-17 at 6hr time point


title: 233191_OVA_168

source_name: Lung sample from OVA-sensitized animal 233191 at 168hr time point


title: 233190_OVA_168

source_name: Lung sample from OVA-sensitized animal 233190 at 168hr time point


title: AS-19_6h

source_name: Nasal scrape sample from animal AS-19 at 6hr time point


title: 233187_OVA_168

source_name: Lung sample from OVA-sensitized animal 233187 at 168hr time point


title: 233188_OVA_168

source_name: Lung sample from OVA-sensitized animal 233188 at 168hr time point


title: AS-22_0h

source_name: Nasal scrape sample from animal AS-22 at 0hr time point


title: NV-18_0h

source_name: Nasal scrape sample from animal NV-18 at 0hr time point


title: AS-21_0h

source_name: Nasal scrape sample from animal AS-21 at 0hr time point


title: 233186_OVA_168

source_name: Lung sample from OVA-sensitized animal 233186 at 168hr time point


title: 233185_PBS_168

source_name: Lung sample from naive animal 233185 at 168hr time point


title: 233184_PBS_168

source_name: Lung sample from naive animal 233184 at 168hr time point


title: NV-17_0h

source_name: Nasal scrape sample from animal NV-17 at 0hr time point


title: NV-18_6h

source_name: Nasal scrape sample from animal NV-18 at 6hr time point


title: AS-16_6h

source_name: Nasal scrape sample from animal AS-16 at 6hr time point


title: NV-21_6h

source_name: Nasal scrape sample from animal NV-21 at 6hr time point


title: AS-21_6h

source_name: Nasal scrape sample from animal AS-21 at 6hr time point


title: NV-22_6h

source_name: Nasal scrape sample from animal NV-22 at 6hr time point


title: 233181_PBS_168

source_name: Lung sample from naive animal 233181 at 168hr time point


title: AS-20_6h

source_name: Nasal scrape sample from animal AS-20 at 6hr time point


title: 233183_PBS_168

source_name: Lung sample from naive animal 233183 at 168hr time point


title: 233182_PBS_168

source_name: Lung sample from naive animal 233182 at 168hr time point


title: 233189_OVA_168

source_name: Lung sample from OVA-sensitized animal 233189 at 168hr time point


title: NV-16_0h

source_name: Nasal scrape sample from animal NV-16 at 0hr time point


title: NV-14_6h

source_name: Nasal scrape sample from animal NV-14 at 6hr time point


title: 233179_PBS_168

source_name: Lung sample from naive animal 233179 at 168hr time point


title: 233177_OVA_96

source_name: Lung sample from OVA-sensitized animal 233177 at 96hr time point


title: 233180_PBS_168

source_name: Lung sample from naive animal 233180 at 168hr time point


title: 233176_OVA_96

source_name: Lung sample from OVA-sensitized animal 233176 at 96hr time point


title: NV-16_6h

source_name: Nasal scrape sample from animal NV-16 at 6hr time point


title: NV-19_0h

source_name: Nasal scrape sample from animal NV-19 at 0hr time point


title: 233175_OVA_96

source_name: Lung sample from OVA-sensitized animal 233175 at 96hr time point


title: AS-23_0h

source_name: Nasal scrape sample from animal AS-23 at 0hr time point


title: 233178_PBS_168

source_name: Lung sample from naive animal 233178 at 168hr time point


title: 233173_OVA_96

source_name: Lung sample from OVA-sensitized animal 233173 at 96hr time point


title: AS-14_6h

source_name: Nasal scrape sample from animal AS-14 at 6hr time point


title: 233174_OVA_96

source_name: Lung sample from OVA-sensitized animal 233174 at 96hr time point


title: NV-15_6h

source_name: Nasal scrape sample from animal NV-15 at 6hr time point


title: 233172_OVA_96

source_name: Lung sample from OVA-sensitized animal 233172 at 96hr time point


title: NV-13_0h

source_name: Nasal scrape sample from animal NV-13 at 0hr time point


title: 233171_OVA_96

source_name: Lung sample from OVA-sensitized animal 233171 at 96hr time point


title: AS-15_6h

source_name: Nasal scrape sample from animal AS-15 at 6hr time point


title: AS-13_0h

source_name: Nasal scrape sample from animal AS-13 at 0hr time point


title: 233170_OVA_96

source_name: Lung sample from OVA-sensitized animal 233170 at 96hr time point


title: AS-16_0h

source_name: Nasal scrape sample from animal AS-16 at 0hr time point


title: NV-13_6h

source_name: Nasal scrape sample from animal NV-13 at 6hr time point


title: AS-18_0h

source_name: Nasal scrape sample from animal AS-18 at 0hr time point


title: 233169_PBS_96

source_name: Lung sample from naive animal 233169 at 96hr time point


title: AS-18_6h

source_name: Nasal scrape sample from animal AS-18 at 6hr time point


title: AS-15_0h

source_name: Nasal scrape sample from animal AS-15 at 0hr time point


title: 233165_PBS_96

source_name: Lung sample from naive animal 233165 at 96hr time point


title: AS-13_6h

source_name: Nasal scrape sample from animal AS-13 at 6hr time point


title: 233166_PBS_96

source_name: Lung sample from naive animal 233166 at 96hr time point


title: 233163_PBS_96

source_name: Lung sample from naive animal 233163 at 96hr time point


title: 233167_PBS_96

source_name: Lung sample from naive animal 233167 at 96hr time point


title: 233162_OVA_72

source_name: Lung sample from OVA-sensitized animal 233162 at 72hr time point


title: NV-14_0h

source_name: Nasal scrape sample from animal NV-14 at 0hr time point


title: 233161_OVA_72

source_name: Lung sample from OVA-sensitized animal 233161 at 72hr time point


title: NV-19_6h

source_name: Nasal scrape sample from animal NV-19 at 6hr time point


title: 233160_OVA_72

source_name: Lung sample from OVA-sensitized animal 233160 at 72hr time point


title: NV-8_0h

source_name: Nasal scrape sample from animal NV-8 at 0hr time point


title: 233168_PBS_96

source_name: Lung sample from naive animal 233168 at 96hr time point


title: 233159_OVA_72

source_name: Lung sample from OVA-sensitized animal 233159 at 72hr time point


title: AS-20_0h

source_name: Nasal scrape sample from animal AS-20 at 0hr time point


title: NV-12_6h

source_name: Nasal scrape sample from animal NV-12 at 6hr time point


title: 233164_PBS_96

source_name: Lung sample from naive animal 233164 at 96hr time point


title: NV-17_6h

source_name: Nasal scrape sample from animal NV-17 at 6hr time point


title: AS-11_6h

source_name: Nasal scrape sample from animal AS-11 at 6hr time point


title: 233156_OVA_72

source_name: Lung sample from OVA-sensitized animal 233156 at 72hr time point


title: 233157_OVA_72

source_name: Lung sample from OVA-sensitized animal 233157 at 72hr time point


title: AS-5_0h

source_name: Nasal scrape sample from animal AS-5 at 0hr time point


title: 233154_PBS_72

source_name: Lung sample from naive animal 233154 at 72hr time point


title: NV-9_6h

source_name: Nasal scrape sample from animal NV-9 at 6hr time point


title: AS-14_0h

source_name: Nasal scrape sample from animal AS-14 at 0hr time point


title: AS-7_0h

source_name: Nasal scrape sample from animal AS-7 at 0hr time point


title: 233152_PBS_72

source_name: Lung sample from naive animal 233152 at 72hr time point


title: 233158_OVA_72

source_name: Lung sample from OVA-sensitized animal 233158 at 72hr time point


title: 233153_PBS_72

source_name: Lung sample from naive animal 233153 at 72hr time point


title: NV-11_0h

source_name: Nasal scrape sample from animal NV-11 at 0hr time point


title: 233155_OVA_72

source_name: Lung sample from OVA-sensitized animal 233155 at 72hr time point


title: NV-12_0h

source_name: Nasal scrape sample from animal NV-12 at 0hr time point


title: 233149_PBS_72

source_name: Lung sample from naive animal 233149 at 72hr time point


title: 233148_PBS_72

source_name: Lung sample from naive animal 233148 at 72hr time point


title: NV-6_0h

source_name: Nasal scrape sample from animal NV-6 at 0hr time point


title: 233151_PBS_72

source_name: Lung sample from naive animal 233151 at 72hr time point


title: AS-9_0h

source_name: Nasal scrape sample from animal AS-9 at 0hr time point


title: 233147_PBS_72

source_name: Lung sample from naive animal 233147 at 72hr time point


title: NV-6_6h

source_name: Nasal scrape sample from animal NV-6 at 6hr time point


title: 233146_OVA_48

source_name: Lung sample from OVA-sensitized animal 233146 at 48hr time point


title: AS-7_6h

source_name: Nasal scrape sample from animal AS-7 at 6hr time point


title: AS-10_6h

source_name: Nasal scrape sample from animal AS-10 at 6hr time point


title: AS-10_0h

source_name: Nasal scrape sample from animal AS-10 at 0hr time point


title: 233145_OVA_48

source_name: Lung sample from OVA-sensitized animal 233145 at 48hr time point


title: 233150_PBS_72

source_name: Lung sample from naive animal 233150 at 72hr time point


title: AS-11_0h

source_name: Nasal scrape sample from animal AS-11 at 0hr time point


title: NV-10_0h

source_name: Nasal scrape sample from animal NV-10 at 0hr time point


title: NV-8_6h

source_name: Nasal scrape sample from animal NV-8 at 6hr time point


title: 233144_OVA_48

source_name: Lung sample from OVA-sensitized animal 233144 at 48hr time point


title: 233143_OVA_48

source_name: Lung sample from OVA-sensitized animal 233143 at 48hr time point


title: 233141_OVA_48

source_name: Lung sample from OVA-sensitized animal 233141 at 48hr time point


title: 1664_TS

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description: Gene expression data from mouse skin tumour metastasis

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates.  Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and a custom probe database which avoids SNPs in FVB and Spretus genomes. Matrix data were batch-corrected for plate and Log2 transformed.

label: biotin

source_name: thymus metastasis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in standard conditions with standard chow and water ad libitum

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were treated with a single dose of 25mg DMBA at 8 weeks followed by 200uL TPA 2x/week (10e-4 M solution). Primary tumors were surgically resected when they reached >1cm, and mice had metastatic disease at sacrifice.

tag: tumor type

value: MET

tag: histology

value: spindle

value: HrasKO

tag: Sex

value: M

tag: batch


title: NV-9_0h

source_name: Nasal scrape sample from animal NV-9 at 0hr time point


title: 233139_OVA_48

source_name: Lung sample from OVA-sensitized animal 233139 at 48hr time point


title: 233140_OVA_48

source_name: Lung sample from OVA-sensitized animal 233140 at 48hr time point


title: 233142_OVA_48

source_name: Lung sample from OVA-sensitized animal 233142 at 48hr time point


title: AS-12_0h

source_name: Nasal scrape sample from animal AS-12 at 0hr time point


title: 1664_LU

source_name: lung metastasis

value: SCC


title: 1664_LN_LWRT

source_name: lymph node metastasis


title: AS-12_6h

source_name: Nasal scrape sample from animal AS-12 at 6hr time point


title: 1664_SK

description: Gene expression data from mouse skin

source_name: dorsal skin

value: SK

value: normal


title: 233137_PBS_48

source_name: Lung sample from naive animal 233137 at 48hr time point

value: naive


title: 1456_CA

description: Gene expression data from mouse skin tumour

source_name: primary skin carcinoma

value: CA

value: WT


title: 1456_LU


title: 1664_LN_LWLT


title: 1456_TS


title: 1456_LN_UPRT


title: NV-10_6h

source_name: Nasal scrape sample from animal NV-10 at 6hr time point


title: 1664_RegCA_B


title: AS-5_6h

source_name: Nasal scrape sample from animal AS-5 at 6hr time point


title: 233136_PBS_48

source_name: Lung sample from naive animal 233136 at 48hr time point

value: lung

value: balb/c


title: 1456_PAP1

source_name: papilloma

value: PAP

value: papilloma


title: AS-9_6h

source_name: Nasal scrape sample from animal AS-9 at 6hr time point

value: nasal epithelium


title: 1664_LR

source_name: liver metastasis


title: 1664_CA


title: 1456_PAP2


title: AS-8_0h

source_name: Nasal scrape sample from animal AS-8 at 0hr time point

value: poly I:C


title: 233135_PBS_48

source_name: Lung sample from naive animal 233135 at 48hr time point


title: 233134_PBS_48

source_name: Lung sample from naive animal 233134 at 48hr time point


title: NV-7_0h

source_name: Nasal scrape sample from animal NV-7 at 0hr time point


title: NV-1_6h

source_name: Nasal scrape sample from animal NV-1 at 6hr time point


title: 1664_PAP1


title: NV-3_0h

source_name: Nasal scrape sample from animal NV-3 at 0hr time point


title: 1616_LU

source_name: lung metastasis


title: 1664_PAP2


title: 233132_PBS_48

source_name: Lung sample from naive animal 233132 at 48hr time point


title: 233131_PBS_48

source_name: Lung sample from naive animal 233131 at 48hr time point


title: 2022_CA_1_17


title: 2104_CA


title: NV-2_6h

source_name: Nasal scrape sample from animal NV-2 at 6hr time point


title: 233130_OVA_24

source_name: Lung sample from OVA-sensitized animal 233130 at 24hr time point

value: OVA-sensitized


title: 1984_CA

source_name: primary skin carcinoma


title: AS-8_6h

source_name: Nasal scrape sample from animal AS-8 at 6hr time point

value: A. suum


title: 233129_OVA_24

source_name: Lung sample from OVA-sensitized animal 233129 at 24hr time point


title: 1949_LN_UPRT

source_name: lymph node metastasis

value: MET

value: spindle


title: 1949_PAP1

source_name: papilloma

value: M


title: 233128_OVA_24

source_name: Lung sample from OVA-sensitized animal 233128 at 24hr time point


title: 1815_PAP3


title: 1456_SK

description: Gene expression data from mouse skin

source_name: dorsal skin


title: AS-6_6h

source_name: Nasal scrape sample from animal AS-6 at 6hr time point


title: AS-3_0h

source_name: Nasal scrape sample from animal AS-3 at 0hr time point


title: 233133_PBS_48

source_name: Lung sample from naive animal 233133 at 48hr time point


title: 233127_OVA_24

source_name: Lung sample from OVA-sensitized animal 233127 at 24hr time point


title: 1383_SK

description: Gene expression data from mouse skin


title: 233125_OVA_24

source_name: Lung sample from OVA-sensitized animal 233125 at 24hr time point


title: AS-2_0h

source_name: Nasal scrape sample from animal AS-2 at 0hr time point


title: 1616_LN_LWLT

value: SCC

value: HrasKO


title: 1383_TS

source_name: thymus metastasis


title: 233123_PBS_24

source_name: Lung sample from naive animal 233123 at 24hr time point


title: 1508_LU

source_name: lung metastasis

value: mixed


title: 1717_SK

description: Gene expression data from mouse skin

value: SK

value: normal


title: NV-5_6h

source_name: Nasal scrape sample from animal NV-5 at 6hr time point

value: naive


title: 1537_SK

description: Gene expression data from mouse skin


title: 1984_PAP3

value: WT


title: 1509_LU


title: 2022_PAP3


title: 1508_LN_UPRT


title: 2104_PAP3


title: 1383_LU


title: AS-4_0h

source_name: Nasal scrape sample from animal AS-4 at 0hr time point


title: 1815_PAP2


title: 233124_PBS_24

source_name: Lung sample from naive animal 233124 at 24hr time point

value: lung

value: balb/c


title: NV-1_0h

source_name: Nasal scrape sample from animal NV-1 at 0hr time point


title: NV-4_6h

source_name: Nasal scrape sample from animal NV-4 at 6hr time point


title: 1949_SK

description: Gene expression data from mouse skin


title: 1949_LN_LWRT

source_name: lymph node metastasis


title: 233126_OVA_24

source_name: Lung sample from OVA-sensitized animal 233126 at 24hr time point


title: 1706_LN_LWRT


title: NV-5_0h

source_name: Nasal scrape sample from animal NV-5 at 0hr time point


title: 233121_PBS_24

source_name: Lung sample from naive animal 233121 at 24hr time point


title: 233122_PBS_24

source_name: Lung sample from naive animal 233122 at 24hr time point


title: 233120_PBS_24

source_name: Lung sample from naive animal 233120 at 24hr time point


title: NV-4_0h

source_name: Nasal scrape sample from animal NV-4 at 0hr time point


title: AS-2_6h

source_name: Nasal scrape sample from animal AS-2 at 6hr time point


title: 2022_PAP2

source_name: papilloma

value: PAP

value: papilloma


title: 1407_SP

source_name: spleen metastasis


title: 2104_PAP1


title: 1984_PAP2


title: NV-2_0h

source_name: Nasal scrape sample from animal NV-2 at 0hr time point

value: nasal epithelium

value: poly I:C


title: 233119_PBS_24

source_name: Lung sample from naive animal 233119 at 24hr time point


title: 1815_LR

source_name: liver metastasis


title: 1509_CA

source_name: primary skin carcinoma

value: CA


title: 1949_RegCA_A_3_16


title: 1815_SK

description: Gene expression data from mouse skin

source_name: dorsal skin


title: AS-6_0h

source_name: Nasal scrape sample from animal AS-6 at 0hr time point

value: A. suum


title: 1616_CA


title: NV-3_6h

source_name: Nasal scrape sample from animal NV-3 at 6hr time point


title: 1706_LN_LWLT

source_name: lymph node metastasis

value: MET


title: 233118_PBS_24

source_name: Lung sample from naive animal 233118 at 24hr time point


title: 233116_OVA_6

source_name: Lung sample from OVA-sensitized animal 233116 at 6hr time point

value: OVA-sensitized


title: 1508_RegCA_B

value: spindle

value: M


title: 1407_LN_LWRT

value: HrasKO


title: 1383_LR

value: SCC


title: 233114_OVA_6

source_name: Lung sample from OVA-sensitized animal 233114 at 6hr time point


title: 233117_PBS_24

source_name: Lung sample from naive animal 233117 at 24hr time point


title: 2104_SK

description: Gene expression data from mouse skin

value: SK

value: normal


title: 233115_OVA_6

source_name: Lung sample from OVA-sensitized animal 233115 at 6hr time point


title: 2022_PAP1

value: WT


title: 1616_SK

description: Gene expression data from mouse skin


title: NV-7_6h

source_name: Nasal scrape sample from animal NV-7 at 6hr time point

value: naive


title: 1509_PAP2


title: 1984_PAP1


title: AS-1_6h

source_name: Nasal scrape sample from animal AS-1 at 6hr time point


title: 233113_OVA_6

source_name: Lung sample from OVA-sensitized animal 233113 at 6hr time point

value: lung

value: balb/c


title: 1949_RegCA_A_2_25


title: AS-1_0h

source_name: Nasal scrape sample from animal AS-1 at 0hr time point


title: AS-4_6h

source_name: Nasal scrape sample from animal AS-4 at 6hr time point


title: 233110_OVA_6

source_name: Lung sample from OVA-sensitized animal 233110 at 6hr time point


title: AS-3_6h

source_name: Nasal scrape sample from animal AS-3 at 6hr time point


title: 233112_OVA_6

source_name: Lung sample from OVA-sensitized animal 233112 at 6hr time point


title: 233111_OVA_6

source_name: Lung sample from OVA-sensitized animal 233111 at 6hr time point


title: NV4_24h

source_name: Nasal scrape sample from animal NV4 at 24hr time point

value: Naive


title: 1815_KD_LT

source_name: kidney metastasis


title: 1717_LU

source_name: lung metastasis


title: NV4_6h

source_name: Nasal scrape sample from animal NV4 at 6hr time point

value: nasal epithelium


title: 233109_OVA_6

source_name: Lung sample from OVA-sensitized animal 233109 at 6hr time point


title: 1508_RegCA_A

source_name: primary skin carcinoma


title: NV4_0h

source_name: Nasal scrape sample from animal NV4 at 0hr time point

value: poly I:C


title: 233107_PBS_6

source_name: Lung sample from naive animal 233107 at 6hr time point


title: 2022_LN_UPRT

source_name: lymph node metastasis


title: 1984_SK

description: Gene expression data from mouse skin

source_name: dorsal skin


title: 1509_PAP1

source_name: papilloma

value: PAP

value: papilloma


title: NV4_72h

source_name: Nasal scrape sample from animal NV4 at 72hr time point


title: NV2_72h

source_name: Nasal scrape sample from animal NV2 at 72hr time point


title: 1383_LN_UPLT

value: MET


title: 1537_LU


title: 2022_SK

description: Gene expression data from mouse skin


title: 1815_SP

source_name: spleen metastasis


title: 233105_PBS_6

source_name: Lung sample from naive animal 233105 at 6hr time point


title: 1407_LN_UPRT


title: 1717_LN_UPLT


title: 233108_PBS_6

source_name: Lung sample from naive animal 233108 at 6hr time point


title: 1949_CA_2_7

value: CA


title: NV2_6h

source_name: Nasal scrape sample from animal NV2 at 6hr time point


title: NV2_24h

source_name: Nasal scrape sample from animal NV2 at 24hr time point


title: 1706_LN_UPLT


title: 1508_CA


title: NV2_0h

source_name: Nasal scrape sample from animal NV2 at 0hr time point


title: 1407_CA

value: spindle


title: 233102_PBS_6

source_name: Lung sample from naive animal 233102 at 6hr time point


title: 1383_LN_LWLT

value: M


title: NV1_24h

source_name: Nasal scrape sample from animal NV1 at 24hr time point


title: 233104_PBS_6

source_name: Lung sample from naive animal 233104 at 6hr time point


title: 1537_LN_LWRT

value: HrasKO


title: 2022_LN_UPLT

value: SCC


title: 233103_PBS_6

source_name: Lung sample from naive animal 233103 at 6hr time point


title: 1509_SK

description: Gene expression data from mouse skin

value: SK


title: 1949_SP


title: 233100_OVA_2

source_name: Lung sample from OVA-sensitized animal 233100 at 2hr time point

value: OVA-sensitized


title: 233101_PBS_6

source_name: Lung sample from naive animal 233101 at 6hr time point


title: 1949_CA_1_12

source_name: primary skin carcinoma

value: mixed

value: WT


title: 1383_CA_B


title: NV1_0h

source_name: Nasal scrape sample from animal NV1 at 0hr time point


title: 1508_PAP2

source_name: papilloma


title: 233098_OVA_2

source_name: Lung sample from OVA-sensitized animal 233098 at 2hr time point

value: lung


title: AS4_24h

source_name: Nasal scrape sample from animal AS4 at 24hr time point

value: A. suum


title: 1706_CA


title: 1407_PAP2


title: 233106_PBS_6

source_name: Lung sample from naive animal 233106 at 6hr time point

value: naive

value: balb/c


title: 1815_LN_UPRT

source_name: lymph node metastasis


title: NV1_72h

source_name: Nasal scrape sample from animal NV1 at 72hr time point

value: Naive

value: nasal epithelium

value: poly I:C


title: AS4_72h

source_name: Nasal scrape sample from animal AS4 at 72hr time point


title: 233099_OVA_2

source_name: Lung sample from OVA-sensitized animal 233099 at 2hr time point


title: 1717_LN_LWLT

value: MET


title: 1706_PAP2

value: PAP

value: papilloma


title: 2104_DORSAL

source_name: dorsal metastasis

value: M


title: 1537_RegCA

value: CA

value: spindle

value: HrasKO


title: 1984_LN_UPLT


title: AS4_0h

source_name: Nasal scrape sample from animal AS4 at 0hr time point


title: 1984_LU

source_name: lung metastasis

value: SCC


title: AS4_6h

source_name: Nasal scrape sample from animal AS4 at 6hr time point


title: 1949_LU


title: 233096_OVA_2

source_name: Lung sample from OVA-sensitized animal 233096 at 2hr time point

value: OVA-sensitized


title: 233097_OVA_2

source_name: Lung sample from OVA-sensitized animal 233097 at 2hr time point


title: AS3_72h

source_name: Nasal scrape sample from animal AS3 at 72hr time point


title: 2022_RegCA_B_5_23

source_name: primary skin carcinoma

value: WT


title: AS3_24h

source_name: Nasal scrape sample from animal AS3 at 24hr time point


title: 1949_PAP3

source_name: papilloma


title: 233094_OVA_2

source_name: Lung sample from OVA-sensitized animal 233094 at 2hr time point

value: lung


title: 233095_OVA_2

source_name: Lung sample from OVA-sensitized animal 233095 at 2hr time point


title: 1815_LN_LWRT


title: AS3_6h

source_name: Nasal scrape sample from animal AS3 at 6hr time point

value: A. suum


title: 1717_CA


title: AS3_0h

source_name: Nasal scrape sample from animal AS3 at 0hr time point


title: 1383_CA_A


title: AS2_24h

source_name: Nasal scrape sample from animal AS2 at 24hr time point


title: 2022_CA_2_1


title: 233092_PBS_2

source_name: Lung sample from naive animal 233092 at 2hr time point

value: naive


title: 1984_RegCA_B


title: 233089_PBS_2

source_name: Lung sample from naive animal 233089 at 2hr time point

value: balb/c


title: 233091_PBS_2

source_name: Lung sample from naive animal 233091 at 2hr time point


title: 1508_PAP1


title: AS2_0h

source_name: Nasal scrape sample from animal AS2 at 0hr time point


title: 1407_PAP1


title: 2104_LN_LWRT

source_name: lymph node metastasis


title: 233093_OVA_2

source_name: Lung sample from OVA-sensitized animal 233093 at 2hr time point


title: AS2_72h

source_name: Nasal scrape sample from animal AS2 at 72hr time point


title: 233088_PBS_2

source_name: Lung sample from naive animal 233088 at 2hr time point


title: 1706_PAP1


title: 1815_CA


title: 1949_PAP2


title: AS1_24h

source_name: Nasal scrape sample from animal AS1 at 24hr time point


title: 1706_SK

description: Gene expression data from mouse skin

source_name: dorsal skin

value: SK

value: normal


title: 233087_PBS_2

source_name: Lung sample from naive animal 233087 at 2hr time point


title: 1717_PAP1

source_name: papilloma


title: 233090_PBS_2

source_name: Lung sample from naive animal 233090 at 2hr time point


title: AS1_0h

source_name: Nasal scrape sample from animal AS1 at 0hr time point

value: nasal epithelium

value: poly I:C


title: 1508_SK

description: Gene expression data from mouse skin


title: 1383_PAP2

value: PAP


title: AS1_6h

source_name: Nasal scrape sample from animal AS1 at 6hr time point


title: 1407_SK

description: Gene expression data from mouse skin


title: 233086_PBS_2

source_name: Lung sample from naive animal 233086 at 2hr time point


title: 1949_LN_UPLT

value: MET


title: E7.5_Flk-pos Foxf1-pos_sort2 [gene-level]

status: Public on Oct 10 2015

city: Manchester

first: Maud

last: Fleury

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

hyb_protocol: Labeled RNA was hybridised to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix), following the manufacturer’s instructions

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data were processed using Affymetrix Power Tools software package (Affymetrix) for RMA normalization and DABG detection. The expression level of a gene was calculated based on the median expression of its exonic probesets called present. Annotations and cross-mappings between probesets, exons and genes were obtained from Ensembl mouse genome build 70 using the R/BioConductor package annmap.

source_name: E7.5 embryo, sorted Flk-pos Foxf1-pos

label_protocol: RNA was used to produce biotinylated sense-strand DNA with the Whole Transcript Sense Target Labelling Assay (Affymetrix)

growth_protocol: sorted cells from E7.5 Foxf1::venus Knock-In embryos

extract_protocol: E7.5 embryos were dissociated, stained with antibodies, then 50 cells were sorted by FACS directly into lysis buffer from SuperAmp kit (Miltenyi)

treatment_protocol: not applicable

tag: sorted population

value: Flk-pos Foxf1-pos

tag: developmental stage

value: E7.5 embryo

tag: strain

value: foxf1::venus knock-in, C57BL/6 background


title: sigG5

city: New York

first: Patrick

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

institute: New York University

description: SigG regulon Replicate 5 : Strain PE452 (sigG::cat, sigK::erm) vs PE451 (sigK::erm) at 4 hours post-resuspension.

hyb_protocol: Hybridizations were incubated at 65˚C for 17 hours. After hybridization slides were washed using Agilent's Wash Buffer 1 and 2. Hybridizations were incubated at 65˚C for 17 hours. After hybridization slides were washed using Agilent's Wash Buffer 1 and 2.

scan_protocol: Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology

data_processing:
Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data were loaded into R using the marray package and normalized between arrays using loess normalization. Normalized log-ratios of gMedianSignal and rMedianSignal were collapsed for redundant probes taking the average.
Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data were loaded into R using the marray package and normalized between arrays using loess normalization. Normalized log-ratios of gMedianSignal and rMedianSignal were collapsed for redundant probes taking the average.

organism: Bacillus subtilis

source_name: sigG::cat sigK::erm

label_protocol:
6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare
6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare

extract_protocol:
RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit
RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit

tag: genotype/variation

value: sigG::cat sigK::erm


title: E7.5_Flk-pos Foxf1-pos_sort1 [gene-level]


title: G144_5m

city: Frederick

first: Xiaojun

last: Hu

state: MD

address: 1050 Boyles St.

department: CSP

institute: SAIC_Frederick, INc

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek software. RMA background correction with quantile normalization
Mouse430_2.na33.annot_core.mps

source_name: CD40L-KO mice lung, 5 months exposure

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

growth_protocol: CD40 knock-out (CD40-KO, strain B6, 129P2-Cd40tm1Kik/J) mice were subsequently bred at the NIH. Mice were housed in microisolator cages and kept in ventilated racks. All animal work was performed under a Clinical Center Animal Care and Use Committee-approved protocol.

extract_protocol: Lung tissue was collected and placed in RNAlater (Qiagen) for RNA extraction and in PBS for DNA extraction. Total RNA was isolated using Qiagen Rneasy kit. cDNA synthesis and amplification used Ambion  WT expression kit.

treatment_protocol: CD40-KO mice were exposed to P. murina infected seeder mice for 5 months.

value: 5month exposure


title: E7.5_Flk-neg Foxf1-pos_sort2 [gene-level]

source_name: E7.5 embryo, sorted Flk-neg Foxf1-pos

value: Flk-neg Foxf1-pos


title: Mouse heart at E12.5, Rhau KO rep3

city: Nanjing

first: Zhongzhou

last: Yang

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

country: China

institute: Nanjing University

description: Gene expression data from embryonic mouse heart

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and  Stain  Kit  (Cat#900720,  Affymetrix,  Santa  Clara,  CA,  US)in  Hybridization  Oven  645 (Cat#000331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

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

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

source_name: Embryonic mouse heart at the stage of  E12.5

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

growth_protocol: Mice were housed in accordance with the regulations on mouse welfare and ethics of Nanjing University in groups with 12-h dark-light cycles and had free access to food and water.

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

treatment_protocol: Mouse embryos of the appropriate stage were selected and hearts were dissected from each group of control and Rhau-deletion mice. After rinsing with PBS, selected hearts were directly put into Trizol for RNA extraction next.

value: Rhau KO

value: Heart


title: G143_5m

value: lung


title: Splenic_B220_B_cells

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

hyb_protocol: cRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using Affymetrix GeneChip Command Console Software (AGCC) and Console Software (Expression Console).

source_name: Primary B220_B cells isolated from 6-8 week old mice (C57BL/6)

label_protocol: Total RNA was labeled using the GeneChip 3' IVT Express Kit.

growth_protocol: Spnelic B220_B cells were purified using magnetic beads and an AutoMACS sorter (Miltenyi Biotec) that yielded purity of >98%.

treatment_protocol: Cells were harvested and RNA was immediately isolated.

tag: age

value: 6-8 week

tag: cell type

value: Splenic B220 B cells


title: C3_no

source_name: CD40L-KO mice lung, no exposure

value: no exposure


title: C1_no


title: Mouse heart at E12.5, wildtype rep3

value: wildtype


title: sigG4

description: SigG regulon Replicate 4 : Strain PE452 (sigG::cat, sigK::erm) vs PE451 (sigK::erm) at 4 hours post-resuspension.


title: sigW1.4_4

description: SigW regulon Replicate 4: A wild-type PY79 and PE2732 (sigW::erm) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at OD600nm of 1.4.

source_name: wildtype


title: sigD4_LL

description: SigD regulon Replicate 4: A wild-type PY79 and sigD mutant (PE2597) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during late-log (LL), and transition to stationary phase (T),


title: Mouse heart at E12.5, Rhau KO rep1


title: Mouse heart at E12.5, wildtype rep2


title: sigD3_T

description: SigD regulon Replicate 3: A wild-type PY79 and sigD mutant (PE2597) cultures were grown in parallel in Difco Sporulation Medium. Samples were collected during late-log (LL), and transition to stationary phase (T),


title: Splenic_CD4_T_cells

source_name: Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6)

growth_protocol: Splenic CD4_T cells were purified using magnetic beads and an AutoMACS sorter (Miltenyi Biotec) that yielded purity of >98%.

value: Splenic CD4 T cells


title: sigW1.4_3

description: SigW regulon Replicate 3: A wild-type PY79 and PE2732 (sigW::erm) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at OD600nm of 1.4.


title: Mouse heart at E12.5, Rhau KO rep2


title: G142_5m


title: E7.5_Flk-pos Foxf1-neg_sort2 [gene-level]

source_name: E7.5 embryo, sorted Flk-pos Foxf1-neg

value: Flk-pos Foxf1-neg


title: Embryonic_stem_cells

source_name: B6N-22 ES cells

growth_protocol: B6N-22 ES cells were cultivated on mitomycin C (MMC) -treated mouse embryonic fibroblast (MEF) in DMEM containing 0.1 mM 2-mercaptoethanol, 1000 units/ml leukemia inhibitory factor (LIF), nonessential amino acids (NEAA), sodium pyruvate and 20% fetal bovine serum (FBS)

value: Embryonic stem cells


title: E7.5_Flk-neg Foxf1-pos_sort1 [gene-level]


title: Mouse heart at E12.5, wildtype rep1


title: sigD4_T


title: sigD3_LL


title: E7.5_Flk-pos Foxf1-neg_sort1 [gene-level]


title: 684599_19193_2

type: genomic

city: Philadelphia

first: Katherine

last: Nathanson

state: PA

address: 421 Curie Blvd

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: Array-based comparative genomic hybridization (aCGH) was performed using the Agilent SurePrint G3 Human CGH 2x400K M microarrays following manufacturer’s instructions

scan_protocol: Scanned on Agilent scanner

data_processing: Images were quantified using Agilent Feature Extraction Software and extracted data were analyzed using BioDiscovery’s Nexus 7 copy-number software (Nexus Genomics Inc.)

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor

label_protocol: Tumor DNA was labeled using BioPrime® Array CGH Genomic Labeling System (Life Technologies, Grand Island, NY) according to manufacturer’s instructions

extract_protocol: DNA was extracted using sodium thiocyanate as described in Wilson et al. Clinical Cancer Research 20(12):3328-37, 2014.

tag: mutation status

value: WT

value: melanoma

source_name: Pooled Normal

tag: gender

value: Female

tag: sample type

value: reference


title: 684581_13655_1

value: BRAF V600E

tag: tissue


title: 678042_11291_2

value: NRAS Q61K


title: Tumor_09/137_HGU133 Plus 2.0+3' IVT kit

city: Ankara

first: Nevin

last: Belder

state: Tandogan

address: De gol

department: Biotechnology

country: Turkey

institute: Ankara University

description: Gene expression data from tumor FFPE tissue

hyb_protocol: Labeled products were hybridized onto two Affymetrix microarray platforms (Human Genome U133 Plus 2.0 and U133_X3P). 15 ug amplified and labeled samples with the 3’ IVT kit were hybridized to these two Affymetrix microarray platforms following manufacturers’ recommendations (Affymetrix GeneChip® Expression Wash, Stain and Scan User Guide, P/N 702731 ). 3.5 ug amplified and  labeled products using Nugen Ovation FFPE WTA system and  Encore Biotin Module were also hybridized to these two Affymetrix microarray platforms following Nugen specifications. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed on a GeneChip Scanner 3000 7G

data_processing: Array images and the CEL files were generated using the Affymetrix® GeneChip® Command Console® Software v 3.0.1 Raw data were processed with the RMA procedure using Expression Console. Gene expression data was analyzed using Partek Genomic Suite 6.6 software (Partek Inc., St. Louis, MO, USA) for the three tumor samples that had matched controls.

source_name: Colorectal Cancer FFPE Tissue

label_protocol: 3’ IVT Kit (Affymetrix, Santa Clara, CA) and the Ovation FFPE WTA System (NuGEN San Carlos, CA, USA) were used for amplification and labelling. 100 ng of input RNA was used to generate the amplified Ribo-SPIA product (NuGEN). Amplified cDNA samples were fragmented and labelled using Encore Biotine Module (NuGEN). 500 ng  total RNA was used  as input for Affymretix 3' IVT kit. The samples were amplified and labeled using the Affymetrix 3'IVT labeling kit according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using Qiagen RNeasy FFPE kit according to the manufacturer's instructions except deparaffinization step.

value: Tumor

tag: platform

value: HGU133 Plus 2.0

tag: kit

value: 3' IVT kit


title: Tumor_10/12_HGU133 Plus 2.0+3' IVT kit


title: Tumor_08/95_HGU133 Plus 2.0+Nugen Ovation FFPE WTA System Kit

value: Nugen Ovation FFPE WTA System Kit


title: Tumor_08/40_HGU133 Plus 2.0+Nugen Ovation FFPE WTA System Kit


title: Tumor_10/12_HGU133 Plus 2.0+Nugen Ovation FFPE WTA System Kit


title: Tumor_09/137_HGU133 Plus 2.0+Nugen Ovation FFPE WTA System Kit


title: 660273_17278_1

value: BRAF V600R


title: 670380_13518_1


title: 660093_11290_2

value: BRAF V600K


title: 660274_19191_2

value: BRAF G469A_Het


title: 665926_19000_2

value: KIT KIT576P


title: 660638_13517_1


title: 665928_11291_1

value: NRAS Q61R


title: 668711_19193_1


title: 665954_13517_2

value: GNAQ Q209L


title: 684016_19002_2


title: 670367_19002_1


title: 684566_19001_1


title: Tumor_08/40_HGU133 Plus 2.0+3' IVT kit


title: 659968_19191_1


title: 660529_13607_2


title: 665955_13500_1


title: 665925_19192_1


title: 665956_19192_2

value: ND ND


title: 665929_17278_2


title: 670371_13608_2


title: 12 hour biofilm cells compared to mid-log cells

city: Wageningen

first: Janneke

last: Wijman

address: Bomenweg 2

country: Netherlands

institute: Wageningen UR

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.

organism: Bacillus cereus ATCC 10987

source_name: 12 hour biofilm cells sample 1

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

source_name: mid-logarithmic phase cells sample 2


title: 657195_17229_2


title: mid-log cells compared to 12 hour biofilm cells

description: No extra description.

source_name: mid-logarithmic phase cells sample 1

source_name: 12 hour biofilm cells sample 2


title: 653680_19190_2


title: 657193_17229_1

value: WT


title: 655705_13516_2

value: melanoma


title: Stationary phase cells compared to 24 hour biofilm cells

description: No extra description.

source_name: Stationary phase cells sample 1

source_name: 24 hour biofilm cells sample 2


title: 653576_17228_1

value: Female


title: 653523_19011_1

value: NRAS Q61H

value: reference


title: 657108_17228_2


title: 660091_17277_2


title: 653416_19190_1


title: 651594_11290_1


title: 651474_17269_2


title: 651532_13654_2


title: mid-log cells compared to stationary phase cells

description: No extra description.

source_name: Stationary phase cells sample 2


title: stationary phase cells compared to mid-log cells

description: No extra description.


title: 24 hour biofilm cells compared to stationary phase cells

description: No extra description.

source_name: 24 hour biofilm cells sample 1


title: 24 hour biofilm cells compared to mid-log cells

description: No extra description.


title: mid-log cells compared to 24 hour biofilm cells

description: No extra description.


title: 651563_13655_1

value: BRAF K601E


title: 651561_17270_1

value: BRAF V600E


title: Tumor_08/95_HGU133 Plus 2.0+3' IVT kit

value: Tumor

value: HGU133 Plus 2.0


title: Stationary phase cells compared to 12 hour biofilm cells

description: No extra description.


title: 12 hour biofilm cells compared to stationary phase cells

description: No extra description.


title: 651471_13515_2


title: 651462_11289_2


title: 651466_17213_1


title: 24 hour biofilm cells compared to 12 hour biofilm cells

description: No extra description.


title: 649968_11289_1


title: 651468_17213_2


title: 646330_17269_1


title: 651467_19189_2


title: 646326_17268_1


title: 646347_17210_2


title: 650350_13515_1


title: 653508_13516_1


title: E7.5_Flk-neg Foxf1-pos_sort1 [exon-level]

description:
0513_VK(9)2_ep_MoEx_Pool2.CEL
RNA expression value

source_name: E7.5 embryo, sorted Flk-neg Foxf1-pos

value: Flk-neg Foxf1-pos

value: E7.5 embryo

value: foxf1::venus knock-in, C57BL/6 background


title: 12 hour biofilm compared to 24 hour biofilm

description: No extra description.


title: E7.5_Flk-pos Foxf1-pos_sort2 [exon-level]

description:
0513_VK(9)5_ep_MoEx_Pool5.CEL
RNA expression value

source_name: E7.5 embryo, sorted Flk-pos Foxf1-pos

value: Flk-pos Foxf1-pos


title: 646329_17268_2


title: E7.5_Flk-pos Foxf1-pos_sort1 [exon-level]

description:
0513_VK(9)3_ep_MoEx_Pool3.CEL
RNA expression value


title: 641433_17177_2


title: 644952_11288_1

value: BRAF V600K


title: E7.5_Flk-pos Foxf1-neg_sort2 [exon-level]

description:
0513_VK(9)4_ep_MoEx_Pool4.CEL
RNA expression value

value: Flk-pos Foxf1-neg


title: 639754_17205_2


title: 639968_13501_2

value: NRAS Q61R


title: CD5

city: Ann Arbor

first: Hiroko

last: Nagao-kitamoto

address: 1150 W Medical Center Dr,

institute: The University of Michigan Medical school

description: Gene expression data from colon micosa of CD-Mb colonized mouse (as control)

hyb_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.1 ST Arrays , that were stained, washed and scanned following standard procedures.

data_processing: Background correction and normalization was performed using the RMA-Sketch implementation in Affymetrix Expression Console

source_name: CD-Mb colonized hGB mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Colon mucosa was collected from human microbiota (HC, UC, CD) colonized GF mouse (6-10 weeks old).

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

treatment_protocol: Colon tissue (the middole part, 2-3 mm) was cut into pieces and snap frozen and store at -80C freezed unti RNA extraction.

value: colon


title: 639805_13607_1

value: ND ND


title: E7.5_Flk-pos Foxf1-neg_sort1 [exon-level]

description:
0513_VK(9)1_ep_MoEx_Pool1.CEL
RNA expression value


title: CD3

scan_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.1 ST Arrays , that were stained, washed and scanned following standard procedures.


title: CD4


title: 644988_11288_2

value: melanoma


title: 643166_17210_1

value: WT

value: Female


title: 644703_11287_2

value: reference


title: 637821_17173_2


title: 639745_17177_1

value: NRAS G13C


title: 630837_13420_2

value: BRAF V600E


title: 637196_17173_1


title: 630886_19189_1


title: 630763_13420_1

value: NRAS Q61K


title: 634311_17205_1


title: 630758_17203_2

value: NRAS Q61L


title: 630327_13419_2


title: E7.5_Flk-neg Foxf1-pos_sort2 [exon-level]

description:
0513_VK(9)6_ep_MoEx_Pool6.CEL
RNA expression value

value: Flk-neg Foxf1-pos


title: 630772_17204_1


title: 630833_19000_1


title: 639761_13608_1


title: 627568_17285_2


title: CD1


title: CD2


title: UC5

description: Gene expression data from colon micosa of UC-Mb colonized mouse (as control)

source_name: UC-Mb colonized hGB mouse


title: UC4


title: HC4

description: Gene expression data from colon micosa of HC-Mb colonized mouse (as control)

source_name: HC-Mb colonized hGB mouse


title: 629882_17203_1


title: UC2


title: UC3


title: UC1


title: 626420_13654_1


title: HC3


title: 627372_17172_1


title: 627367_17171_2


title: GF2

description: Gene expression data from colon micosa of WT- GF mouse (as control)

source_name: WT-GF mouse


title: 627515_17172_2

source_name: Tumor


title: 627379_18999_2

source_name: Pooled Normal


title: 626885_13419_1


title: 624887_13417_1


title: 624083_17285_1


title: 624059_13653_2


title: 627370_19011_2

value: NRAS Q61P


title: 626410_13417_2

value: BRAF V600R


title: HC1


title: 624087_17202_1


title: 624890_17202_2


title: 624872_18999_1


title: 624085_13416_1


title: 626428_13500_2


title: G125_+/-_5m

data_processing:
Data were processed using Partek software. RMA background correction with quantile normalization
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: Control mice lung, 5 month exposure

growth_protocol: CD40 ligand knock-out (CD40L-KO, strain B6, 129S-Tnfsf5tm1lmx) were subsequently bred at the NIH. Mice were housed in microisolator cages and kept in ventilated racks. All animal work was performed under a Clinical Center Animal Care and Use Committee-approved protocol.

treatment_protocol: CD40L-KO -/- mice and, as controls, CD40L +/-, which were littermates of the CD40L-KO mice, were exposed to P. murina infected seeder mice for 5 months.

value: lung

tag: genetic background

tag: treatment

value: 5month exposure

tag: mouse strain


title: G122_+/-_5m


title: 623409_17201_2


title: 624433_13416_2


title: 623492_19001_2


title: X-13

city: Houston

first: LI

last: SHEN

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

description:
a520780-00-942088-113015-4217786-32904
a520780-00-942086-113015-4217786-32604

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Affymetrix OncoScan Console 1.1 software was acquired to yield log R ratios (LRR) and B allele frequencies (BAF) for each SNP in each sample using the TuScan algorithm. Computations were performed relative to the normal reference provided by Affymetrix

source_name: tumor tissue

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Samples were grown according to standard conditions.

extract_protocol: Tumor areas within samples were marked by the Pathologist on an H&E stained slide. These areas were used to guide the acquisition of a 0.6mm core biopsy from the FFPE block. The FFPE tissue sections were extracted with xylene, washed with ethanol, and DNA was isolated using the Recover All Total Nucleic Acid Isolation kit for FFPE (Life Technologies, catalog-AM1975). The average DNA recovered was 36.6ng/mL (range 2.6-203.3)

value: Xenograft

tag: preservation method

value: FFPE


title: 622999_13415_2


title: X-14

description:
a520780-00-941877-103115-4214911-68658
a520780-00-942067-113015-4217786-19944


title: 623407_17170_2

value: BRAF K601E


title: 619783_17283_2


title: 624080_11287_1


title: G121_+/-_5m


title: G119_-/-_5m

source_name: CD40L-KO mice lung, 5 month exposure


title: X-11

description:
a520780-00-942000-103115-4214911-73398
a520780-00-942073-113015-4217786-28958


title: G118_-/-_5m


title: 618093_17281_2


title: X-8

description:
a520780-00-941870-103115-4214911-83878
a520780-00-941875-103115-4214911-69395


title: 621745_17271_2


title: HC2

value: colon


title: G116_-/-_5m


title: 618804_17283_1

value: melanoma


title: X-6

description:
a520780-00-941872-103115-4214911-84123
a520780-00-941880-103115-4214911-69094


title: X-9

description:
a520780-00-941876-103115-4214911-69546
a520780-00-941998-103115-4214911-73164


title: 618086_13653_1


title: GF1


title: G115_-/-_5m


title: G113_+/-_no

source_name: Control mice lung, no exposure

value: no exposure


title: X-3

description:
a520780-00-941877-103115-4214911-68626
a520780-00-941878-103115-4214911-68856


title: 618073_17281_1

value: Female


title: 627366_17171_1

value: ND ND

value: reference


title: G112_-/-_no

source_name: CD40L-KO mice lung, no exposure


title: 618050_17280_2

value: BRAF V600E


title: P-36

description:
a520780-00-941880-103115-4214911-69020
a520780-00-941879-103115-4214911-68927

value: Patient sample


title: G109_-/-_no

source_name: CD40-KO mice lung, 5 months exposure


title: G111_-/-_no


title: G110_+/-_no


title: X-1

description:
a520780-00-941878-103115-4214911-68859
a520780-00-941999-103115-4214911-73200


title: 618011_13501_1

value: NRAS Q61K


title: 617891_13415_1

value: WT


title: P-35

description:
a520780-00-941874-103115-4214911-69289
a520780-00-941994-103115-4214911-70841


title: P-32

description:
a520780-00-942074-113015-4217786-29027
a520780-00-941878-103115-4214911-68844


title: P-34

description:
a520780-00-942074-113015-4217786-29059
a520780-00-941880-103115-4214911-69012


title: P-31

description:
a520780-00-942061-113015-4217786-19197
a520780-00-942075-113015-4217786-29164


title: P-33

description:
a520780-00-942060-113015-4217786-19078
a520780-00-941874-103115-4214911-69324


title: 617498_17170_1

value: NRAS Q61R


title: Matched control of TT08_X3P Array+Nugen Ovation FFPE WTA System Kit

description: Gene expression data from matched normal FFPE tissues

source_name: Normal Colorectum Mucosa (FFPE)

value: Normal

value: Nugen Ovation FFPE WTA System Kit


title: 617405_13612_2

value: NRAS G13R


title: Matched control of TT31_X3P Array+Nugen Ovation FFPE WTA System Kit


title: 617428_17280_1


title: 617381_17279_2

value: GNAQ Q209L


title: 617251_13612_1

value: BRAF V600D


title: 617306_17279_1


title: P-29

description:
a520780-00-941879-103115-4214911-68975
a520780-00-942061-113015-4217786-19223

value: FFPE


title: 617378_13651_2


title: 622351_17201_1


title: Tumor_10/12_X3P Array+Nugen Ovation FFPE WTA System Kit

description: Gene expression data from tumor FFPE tissue

source_name: Colorectal Cancer FFPE Tissue

value: Tumor


title: Tumor_08/95_X3P Array+Nugen Ovation FFPE WTA System Kit


title: CD4UnExpC57_4

data_processing:
Data were processed using Partek software. RMA background correction with quantile normalization
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: CD4 cells from unexposed  mouse

growth_protocol: Healthy C57 black (C57BL/6) mice were obtained from the National Cancer Institute. Mice were housed in microisolator cages and kept in ventilated racks. All animal work was performed under a Clinical Center Animal Care and Use Committee-approved protocol.

extract_protocol: Lung CD4 cells and alveolar macrophages were obtained by bronchoalveolar lavage from C57BL/6 mice and were purified using bead for CD4 cells (Miltenyi) and adherence to plastic for  24 hours for alveolar macrophages.Due to the small number of cells recovered, cells from 5 animals were combined in 4 separate pools and each pool was analyzed separately. Because the RNA yield from macrophages was low even after combining cells, RNA was amplified by the Ovation Pico WTA System V2 (NuGen) prior to processing for microarray analysis. cDNA synthesis and amplification used Ambion  WT expression kit.

treatment_protocol: C57BL/6 mice (expressing either CD45.1 or CD45.2) exposeure 35 days

value: CD4 cells

value: Not expose to Pneumocystis

tag: mouse


title: Tumor_09/137_X3P Array+Nugen Ovation FFPE WTA System Kit


title: CD4UnExpC57_3


title: P-26

description:
a520780-00-941870-103115-4214911-83891
a520780-00-942088-113015-4217786-32828


title: 617241_17271_1

value: melanoma

value: Female


title: P-27

description:
a520780-00-941871-103115-4214911-84009
a520780-00-942059-113015-4217786-19033


title: Tumor_08/40_X3P Array+Nugen Ovation FFPE WTA System Kit


title: P-28

description:
a520780-00-941874-103115-4214911-69280
a520780-00-942092-113015-4217786-23646


title: P-25

description:
a520780-00-941878-103115-4214911-68750
a520780-00-941873-103115-4214911-69181


title: Tumor_10/12_X3P Array+3' IVT kit

value: 3' IVT kit


title: 617231_13611_2

value: BRAF V600K

value: reference


title: P-24

description:
a520780-00-941996-103115-4214911-71099
a520780-00-941998-103115-4214911-73123

value: Patient sample


title: 616465_13611_1

value: BRAF V600E


title: P-30

description:
a520780-00-942068-113015-4217786-20147
a520780-00-942073-113015-4217786-28930


title: CD4UnExpC57_1_8


title: 616326_13519_1

value: WT


title: CD4UnExpC57_1_7


title: 615693_13609_2


title: CD4ExpC57_2

source_name: CD4 cells from exposed mouse

value: Expose to Pneumocystis


title: 616463_13651_1


title: CD4ExpC57_1_6


title: CD4ExpC57_1_5


title: P-20

description:
a520780-00-941999-103115-4214911-73262
a520780-00-941871-103115-4214911-84023


title: Tumor_08/95_X3P Array+3' IVT kit


title: Matched control of TT01_X3P Array+Nugen Ovation FFPE WTA System Kit

value: Normal

value: Nugen Ovation FFPE WTA System Kit


title: P-23

description:
a520780-00-941869-103115-4214911-83774
a520780-00-941880-103115-4214911-69010


title: MOUnExpC57_12

source_name: macrophage from unexposed  mouse

value: macrophage


title: P-22

description:
a520780-00-941869-103115-4214911-83819
a520780-00-941999-103115-4214911-73243


title: CD4ExpC57_1


title: Tumor_08/40_X3P Array+3' IVT kit


title: Tumor_09/137_X3P Array+3' IVT kit


title: P-21

description:
a520780-00-941877-103115-4214911-68700
a520780-00-941873-103115-4214911-69123


title: P-19

description:
a520780-00-941870-103115-4214911-83944
a520780-00-941995-103115-4214911-70977


title: MOUnExpC57_11


title: 616547_13519_2


title: 615484_13518_2


title: P-18

description:
a520780-00-941997-103115-4214911-73030
a520780-00-941879-103115-4214911-68913


title: P-17

description:
a520780-00-941873-103115-4214911-69179
a520780-00-941995-103115-4214911-70957


title: 615393_13652_2


title: P-16

description:
a520780-00-941878-103115-4214911-68864
a520780-00-941870-103115-4214911-83872


title: MOUnExpC57_1_15


title: 615412_13609_1


title: Control, repeat 3

city: Shanghai

first: Jie

last: Xu

address: Shandong Rd 145

department: Shanghai Renji Hospital

institute: Shanghai Institute for Digestive Diseases

description: miRNA expression profile

hyb_protocol: The labeled RNA was consequently hybridized for sixteen hours to an Affymetrix GeneChip miRNA array according to the product manual.

scan_protocol: Microarrays were washed and stained in the Affymetrix Fluidics Station 450, and scanned on the Affymetrix G3000 GeneArray Scanner.

data_processing: The image files were analyzed using the Affymetrix software (Expression Console)

source_name: Control cells expressing the empty vector

label_protocol: A total of 200 ng small RNA was used in sample preparation with a FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere).

growth_protocol: The human H1299 (p53-null) cells were maintained in DMEM medium (Gibco, Gaithersburg, MD, USA) supplemented with 10% fetal bovine serum (Invitrogen) and cultured in a humidified incubator at 37 °C under 5% CO2.

extract_protocol: RNA was extracted with Rneasy mini Kit from QIAGEN following the product manual.

treatment_protocol: Before transfection, cells were seeded into normal growth medium at 50% confluence in six-well tissue plates. The FuGENE HD transfection reagent (Promega, Fitchburg, WI, USA) was applied according to the product manual. Briefely, the transfection complex was made by 1 μg plasmid, 3 μl FuGENE HD and 100 μl media. Six hours after the complex was added to the cells, normal culture media was used to culture cells for additional 48 h

value: Cultured cancer cells

tag: cell line


title: Control, repeat 2

description: miRNA expression profile


title: Mutant p53, repeat 3

description: miRNA expression profile

source_name: Cells expressing the R282W mutant


title: Control, repeat 1

description: miRNA expression profile


title: Mutant p53, repeat 2

description: miRNA expression profile


title: MOExpC57_10

source_name: macrophage from exposed mouse


title: 615391_13652_1

value: NRAS Q61K


title: MOExpC57_9


title: P-14

description:
a520780-00-941998-103115-4214911-73154
a520780-00-941996-103115-4214911-71146

value: FFPE


title: Mutant p53, repeat 1

description: miRNA expression profile


title: MOExpC57_1_14


title: P-15

description:
a520780-00-941880-103115-4214911-69008
a520780-00-941878-103115-4214911-68818


title: MOExpC57_1_13


title: P-12

description:
a520780-00-941996-103115-4214911-71152
a520780-00-941996-103115-4214911-71105


title: P-13

description:
a520780-00-941994-103115-4214911-70903
a520780-00-941874-103115-4214911-69287


title: P-10

description:
a520780-00-941876-103115-4214911-69582
a520780-00-941873-103115-4214911-69150


title: P-6

description:
a520780-00-941996-103115-4214911-71061
a520780-00-941995-103115-4214911-70952


title: P-7

description:
a520780-00-941995-103115-4214911-70966
a520780-00-941881-103115-4214911-70712


title: P-11

description:
a520780-00-941869-103115-4214911-83763
a520780-00-941877-103115-4214911-68635


title: P-9

description:
a520780-00-941880-103115-4214911-69086
a520780-00-941880-103115-4214911-69053


title: M_cell_SpeG_4-17

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

hyb_protocol: All labeled nucleic acids were hybridized to Agilent SurePrint G3 human V2 GE 8 × 60K arrays that had been tiled with 50599 probes of human genes (Agilent) at 65oC for 17 h. After washing and drying, the array chips were scanned using an Agilent microarray scanner at 535 nm for Cy3-CTP

scan_protocol: The scanned images were quantified and analyzed by Feature Extraction 10.5.1.1 software (Agilent). The background values were corrected by spatial detrend surface value, and normalized by quantile

data_processing: The expression levels of the genes on each array group were analyzed using DAVID database (http://david.abcc.ncifcr.gov). The heap map with those more than 2 fold-change up- or down-regulated genes of each group was constructed based on their normalized values using GeneSpring multi-omic analysis software (Agilent).

source_name: speG mutant-infected in vitro M cells

label_protocol: The total RNA samples were reverse transcribed to cDNAs that were then labeled with Cy3-CTP (CyDye, Agilent) with an Agilent Low Input Quick-Amp Labeling kit (Agilent) according to the manufacturer’s instruction. Thus, the Cy3-labled cRNAs were fragmented into 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 min.

growth_protocol: In vitro M cell culture model was established as previously described with minor modification. Raji B cells, a cell line of human Burkitt’s lymphoma purchased from the Bioresource Collection and Research Center Taiwan (BCRC No. 60116, originally from ATCC No. CCL-86), were grown in 90% RPMI 1640 medium (Gibco, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% L-glutamine (Gibco), 1.5 g/L sodium bicarbonate (Sigma, St. Louis, MO), 4.5 g/L glucose (Sigma), 10 mM HEPES (Sigma), and 1.0 mM sodium pyruvate (Sigma) at 37oC in 5% CO2. Caco-2 cells, a C2BBe1 clone of a Caucasian human’s colon adenocarcinoma purchased from the Bioresource Collection and Research Center Taiwan (BCRC No. 60182, originally from ATCC No. CRL-2102), were grown in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 10% FBS (Sigma), 100 μM non-essential amino acids (Sigma), 1% L-glutamine (Gibco), and 0.01 mg/ml transferrin (Sigma) at 37oC in 5% CO2.

extract_protocol: The total RNAs of both cells from the above three conditions were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction, and preformed RNA clean-up by using RNeasy Mini Kit (Qiagen, Valencia, CA). The RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA) and the integrity of RNA samples were validated by the ratio of absorbance at 260 nm and 280 nm as well as RIN (RNA integrity number) using a Bioanalyzer 2100 (Agilent Technology, Palo Alto, CA) with an RNA 6000 Nano LabChip kit (Agilent).

treatment_protocol: In vitro M cells and Caco-2 cells were treated with S. Typhimurium WT and ΔspeG at a MOI of 25, or LB broth as non-infection control, for 1 h in duplicate.

value: M cells

tag: agent

value: Salmonella typhimurium speG mutant


title: P-4

description:
a520780-00-941870-103115-4214911-83901
a520780-00-941879-103115-4214911-68942


title: P-8

description:
a520780-00-941869-103115-4214911-83786
a520780-00-941999-103115-4214911-73286


title: Mid-log cells compared to 12 hour biofilm cells

description: No extra description.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 100% laser intensity, and 10 micron scan resolution.

organism: Bacillus cereus ATCC 14579

source_name: mid-logarithmic phase cells sample 2

extract_protocol: RNA was extracted as described by van Schaik et al., 2004

tag: strain

source_name: 12 hour biofilm cells sample 2


title: 12 hour biofilm cells compared to mid-log cells

description: No extra description.

source_name: 12 hour biofilm cells sample 1


title: P-3

description:
a520780-00-941878-103115-4214911-68803
a520780-00-941871-103115-4214911-83985

source_name: tumor tissue


title: M_cell_SpeG


title: MOUnExpC57_1_16

value: Not expose to Pneumocystis


title: P-5

description:
a520780-00-941870-103115-4214911-83924
a520780-00-941880-103115-4214911-69071


title: P-2

description:
a520780-00-941878-103115-4214911-68794
a520780-00-941878-103115-4214911-68825


title: Stationary phase cells compared to 24 hour biofilm cells

description: No extra description.

source_name: Stationary phase cells sample 1

source_name: 24 hour biofilm cells sample 2


title: M_cell_WT

source_name: SL1344-infected in vitro M cells

value: Salmonella typhimurium wild-type (SL1344)


title: CaCO2_SpeG

source_name: speG mutant-infected Caco-2 cells


title: P-1

description:
a520780-00-941877-103115-4214911-68705
a520780-00-941876-103115-4214911-69540


title: Stationary phase cells compared to mid-logarithmic phase cells

description: No extra description.


title: CaCO2_WT

source_name: SL1344-infected Caco-2 cells


title: M_cell_WT_4-17


title: CaCO2_SpeG_4-17


title: CaCO2_WT_4-17


title: M_cell_LB

source_name: in vitro M cells

value: uninfected


title: 12 hour biofilm compared to mid-log cells

description: No extra description.


title: mid-log cells compared to stationary cells

description: No extra description.

source_name: mid-logarithmic phase cells sample 1

source_name: Stationary phase cells sample 2


title: M_cell_LB_4-17


title: 24 hour biofilm compared to 12hour biofilm

description: No extra description.

source_name: 24 hour biofilm

source_name: 12 hour biofilm


title: stationary phase cells compared to 12 h biofilm

description: No extra description.


title: Mid-log cells compared to 24 hour biofilm

description: No extra description.


title: Hippocampus_6189781050_Control_5

status: Public on Oct 09 2015

city: Woolloongabba

first: Suyinn

last: Chong

state: QLD

address: 37 Kent St

country: Australia

institute: Mater Research Institute - The University of Queensland

description: SAMPLE 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed using GenomeStudio  (1.9.0) following the manufacturer's protocol.

label_protocol: Standard Illumina Labelling protocol

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following the manufacturer's protocol.

treatment_protocol: Ethanol-exposed mice were exposed to ethanol in utero from 0.5 to 8.5 days post-coitum

value: 12 weeks

value: male

tag: exposed to

value: none (control)

value: hippocampus


title: Hippocampus_6189781012_Control_2

description: SAMPLE 8

tag: age


title: 24 hour biofilm compared to stationary phase cells

description: No extra description.

source_name: 24 hour biofilm cells sample 1


title: CaCO2_LB

source_name: Caco-2 cells

tag: cell type


title: Hippocampus_6189781050_Control_4

description: SAMPLE 10


title: 12 hour biofilm compared to stationary phase cells

description: No extra description.


title: CaCO2_LB_4-17


title: Hippocampus_6189781012_Control_3

description: SAMPLE 9


title: Hippocampus_6189781050_Control_6

description: SAMPLE 12


title: Hippocampus_6189781050_EtOH_6

description: SAMPLE 6

value: ethanol in utero from 0.5 to 8.5 days post-coitum


title: Hippocampus_6189781012_Control_1

description: SAMPLE 7


title: Hippocampus_6189781050_EtOH_4

description: SAMPLE 4


title: Hippocampus_6189781012_EtOH_3

description: SAMPLE 3


title: Biofilm 12 h compared to biofilm 24 h

description: No extra description.


title: Hippocampus_6189781012_EtOH_1

description: SAMPLE 1


title: Hippocampus_6189781050_EtOH_5

description: SAMPLE 5


title: Hippocampus_6189781012_EtOH_2

description: SAMPLE 2


title: Trisomy 21, V3036

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
V3036
Gene expression data.

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

source_name: cultured fibroblasts, trisomy 21

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix).

growth_protocol: Standard protocols for culture of amnion cells and chorionic villi cells.

extract_protocol: Total RNA was isolated from each cell culture using a Nucleospin RNA II kit, according to manufacturer’s instructions.

treatment_protocol: After removal of the medium, trypsin EDTA was added and left to incubate for 15 minutes at 37°C. The cells were harvested, centrifuged at 1000 rpm for 10 minutes, washed with PBS and centrifuged again. The PBS was removed and the cells were lysed directly by addition of RA1 lysis buffer from a Nucleospin RNA II kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany).

tag: genotype/variation

value: trisomy 21

value: chorionic villi (fibroblasts)

tag: Sex

value: female

tag: gestational age (weeks of gestation)


title: Trisomy 21, V3020

description:
V3020
Gene expression data.


title: Trisomy 21, V3018

description:
V3018
Gene expression data.


title: Control, V3010

description:
V3010
Gene expression data.

source_name: cultured fibroblasts, control

value: control


title: Control, V3011

description:
V3011
Gene expression data.


title: Control, V3012

description:
V3012
Gene expression data.


title: Control, 23559

description:
23559
Gene expression data.

source_name: cultured amniocytes, control

value: amniocytes


title: Control, V3007

description:
V3007
Gene expression data.


title: Trisomy 21, V3009

description:
V3009
Gene expression data.


title: Control, V3026

description:
V3026
Gene expression data.


title: Trisomy 13, 23552

description:
23552
Gene expression data.

source_name: cultured amniocytes, trisomy 13

value: trisomy 13


title: Control, 23567

description:
23567
Gene expression data.


title: Trisomy 21, V2997

description:
V2997
Gene expression data.


title: Control, 23548

description:
23548
Gene expression data.


title: Control, 23551

description:
23551
Gene expression data.


title: Trisomy 18, 23570

description:
23570
Gene expression data.

source_name: cultured amniocytes, trisomy 18

value: trisomy 18


title: Control, 23549

description:
23549
Gene expression data.


title: Control, 23541

description:
23541
Gene expression data.


title: Trisomy 13, 23553

description:
23553
Gene expression data.


title: Trisomy 18, 23542

description:
23542
Gene expression data.


title: Control, 23547

description:
23547
Gene expression data.


title: 2cell_embryo_TG3_rep3

status: Public on Oct 08 2015

city: Ste-anne-de-Bellevue

first: Sarah

last: Kimmins

state: Quebec

address: 21,111 Rue Lakesshore

country: Canada

institute: McGill University

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 2.0 ST Arrays (Affymetrix) and scanned at Genome Quebec Innovation Center.

data_processing: CEL files for embryo microarray data were read into R (version 3.1.0), where the Bioconductor package oligo was used to calculate transcript-cluster level expression values with the RMA (Robust Multi-array Average) algorithm. Differential expression analysis between the experimental groups was conducted using the limma package

source_name: 2-cell embryo, KDM1A Transgenic

label_protocol: Double-stranded cDNA was generated from the amplified cRNA with the SensationPlus WT kit (Affymetrix) and labelled according to manufacturer's instructions.

growth_protocol: Mice were watered and fed standard mouse chow ad libitum and housed under conditions of controlled light (12-hour light, 12-hour dark cycle) at 21°C and 50% humidity

extract_protocol: Plug positive females were sacrificed 46-48 hours post hCG injection, and oviducts were flushed with PBS + 0.01% BSA to collect 2-cell embryos. On average, 26 embryos were pooled per group for total RNA extraction by PicoPure RNA extraction kit (Life Technologies).

treatment_protocol: C57BL/6 female mice were superstimulated with 5IU of eCG and hCG prior to mating with C57BL/6, KDM1A transgenic, and nonTG male mice.

tag: genotype

value: KDM1A TG

tag: tissue

value: 2-cell embryo


title: 2cell_embryo_TG3_rep2


title: 2cell_embryo_nonTG3_rep1

source_name: 2-cell embryo, nonTG

value: nonTG


title: 2cell_embryo_C57BL/6_rep2

source_name: 2-cell embryo,Control


title: 2cell_embryo_nonTG3_rep2


title: 2cell_embryo_TG3_rep1


title: 2cell_embryo_C57BL/6_rep3


title: patient 69 liver donor - whole liver tissue miRNA - miRNA-DON-69

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

hyb_protocol: Hybridization was performed on Affymetrix GeneChip miRNA 2.0 arrays using standard protocols available at www.affymetrix.com.

scan_protocol: Standard Affymetrix protocols were also used for staining, washing, and scanning of the arrays (available at www.affymetrix.com).

data_processing: Affymetrix probeset summaries were computed using the RMA algorithm.  Data were then imported to BRB-ArrayTools and only the 2226 human miRNAs present in the chip were filtered and used for the subsequent analyses. Median normalization, group comparisons and multivariate analyses were made using BRB-ArrayTools and R packages.

source_name: specimen obtained from explanted liver of patient 69

label_protocol: 500ng of total RNA, including microRNA, was poly(A) tailed and then directly ligated to a fluorescent dendrimer (a branched single and double stranded DNA molecule conjugated to biotin) using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix)

extract_protocol: Total RNA, including microRNA,was extracted from frozen liver specimens using the miRNeasy Mini Kit (Qiagen).

value: whole liver

tag: phenotype

value: liver donor


title: patient 62 liver donor - whole liver tissue miRNA - miRNA-DON-62

source_name: specimen obtained from explanted liver of patient 62


title: 2cell_embryo_C57BL/6_1


title: sperm_nonTG3_rep2

data_processing: CEL files for sperm and embryo data were separately read into R (version 3.1.0), where the Bioconductor package oligo was used to calculate transcript-cluster level expression values with the RMA (Robust Multi-array Average) algorithm. Differential expression analysis between the experimental groups was conducted using the limma package

source_name: Sperm, nonTG

extract_protocol: Cells were homogenized by vortexing in buffer RLT (Qiagen RNeasy) supplemented with 50mM β-mercaptoethanol and 100mg 0.2mm steel beads.  RNA was extracted through Qiazol (Qiagen) followed by chloroform.  The aqueous layer containing RNA was processed with RNeasy RNA extraction kit. (Qiagen). RNA extracts were pooled from four or five males to give a total of ~20 x10^6 sperm/replicate (C57BL/6, 1 replicate, n= 5; TG, 3 replicates, n=4 per replicate; nonTG, 3 replicates, n=4 per replicate).

treatment_protocol: To generate experimental groups we microinjected the transgenic construct into C57BL/6 zygotes and obtained two female transgenic founders.  We subsequently transmitted the transgene by heterozygous males bred to C57BL/6 females for three generations and classified males with the transgene TG3 and the wild-type littermates nonTG3

value: sperm


title: Control, 23540

description:
23540
Gene expression data.


title: sperm_nonTG3_rep3


title: patient 56 liver donor - whole liver tissue miRNA - miRNA-DON-56

source_name: specimen obtained from explanted liver of patient 56


title: Control, 23539

description:
23539
Gene expression data.


title: patient 37 liver donor - whole liver tissue miRNA - miRNA-DON-37

source_name: specimen obtained from explanted liver of patient 37


title: patient 36 liver donor - whole liver tissue miRNA - miRNA-DON-36

source_name: specimen obtained from explanted liver of patient 36


title: sperm_TG3_rep3

source_name: Sperm, KDM1A Transgenic


title: patient 25 liver donor - whole liver tissue miRNA - miRNA-DON-25

source_name: specimen obtained from explanted liver of patient 25


title: patient 18 liver donor - whole liver tissue miRNA - miRNA-DON-18

source_name: specimen obtained from explanted liver of patient 18


title: patient 68 with liver angioma - whole liver tissue miRNA - miRNA-ANG-68

source_name: specimen obtained from explanted liver of patient 68

value: hepatic resection for liver angioma


title: patient 29 liver donor - whole liver tissue miRNA - miRNA-DON-29

source_name: specimen obtained from explanted liver of patient 29


title: sperm_TG3_rep1


title: patient 8 liver donor - whole liver tissue miRNA - miRNA-DON-8

source_name: specimen obtained from explanted liver of patient 8


title: patient 64 with liver angioma - whole liver tissue miRNA - miRNA-ANG-64

source_name: specimen obtained from explanted liver of patient 64


title: patient 65 with liver angioma - whole liver tissue miRNA - miRNA-ANG-65

source_name: specimen obtained from explanted liver of patient 65


title: patient 55 with liver angioma - whole liver tissue miRNA - miRNA-ANG-55

source_name: specimen obtained from explanted liver of patient 55


title: patient 16 liver donor - whole liver tissue miRNA - miRNA-DON-16

source_name: specimen obtained from explanted liver of patient 16


title: patient 86 with liver angioma - whole liver tissue miRNA - miRNA-ANG-86

source_name: specimen obtained from explanted liver of patient 86


title: sperm_TG3_rep2


title: patient 2 with liver angioma - whole liver tissue miRNA - miRNA-ANG-2

source_name: specimen obtained from explanted liver of patient 2


title: patient 32 with ALF - whole liver tissue miRNA - miRNA-ALF-32-3

source_name: specimen obtained from explanted liver of patient 32

value: from OLT of HBV-associated acute liver failure


title: patient 23 with liver angioma - whole liver tissue miRNA - miRNA-ANG-23

source_name: specimen obtained from explanted liver of patient 23


title: patient 32 with ALF - whole liver tissue miRNA - miRNA-ALF-32-2


title: sperm_nonTG3_rep1

source_name: Sperm, nonTG


title: patient 32 with ALF - whole liver tissue miRNA - miRNA-ALF-32-1


title: sperm_C57BL/6

source_name: Sperm, Control


title: patient 241 with ALF - whole liver tissue miRNA - miRNA-ALF-241-2

source_name: specimen obtained from explanted liver of patient 241


title: patient 241 with ALF - whole liver tissue miRNA - miRNA-ALF-241-1


title: patient 31 with ALF - whole liver tissue miRNA - miRNA-ALF-31-1

source_name: specimen obtained from explanted liver of patient 31


title: patient 219 with ALF - whole liver tissue miRNA - miRNA-ALF-219-5

source_name: specimen obtained from explanted liver of patient 219


title: patient 31 with ALF - whole liver tissue miRNA - miRNA-ALF-31-2


title: patient 219 with ALF - whole liver tissue miRNA - miRNA-ALF-219-4


title: patient 219 with ALF - whole liver tissue miRNA - miRNA-ALF-219-2


title: patient 219 with ALF - whole liver tissue miRNA - miRNA-ALF-219-3


title: patient 219 with ALF - whole liver tissue miRNA - miRNA-ALF-219-1


title: patient 31 with ALF - whole liver tissue miRNA - miRNA-ALF-31-3


title: ED70

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

description: Freshwater Sample 70

hyb_protocol: Cy5-cDNA (600 ng) was denatured at 95°C in a final volume of 34 µl with Agilent 100X Blocking Agent and 2X Hi-RPM GE Hyb buffer. After adding 11 µl of Agilent-CGHblock, the labeled cDNA was finally hybridized on a sub-array. Hybridization was performed for 17 hours at 65°C in a rotating hybridization oven (20 RPM) prior to washing

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3 µm and 20 bits). Data were then obtained with the Agilent Feature Extraction software (10.7.1.1) according to the appropriate GE protocol (GE1_107_Sep09).

data_processing: Normalization and statistical analysis were performed using GeneSpring software (Agilent). Data were scale-normalized using the median value of each array. To identify differentially expressed genes between gill ionocytes from trout maintained in freshwater or adapted to seawater, a T-test with a Benjamini-Hochberg correction (p-value<0.05) was performed on a set of genes previously selected with a Fold Change>3. Clustering analysis was performed and visualized using CLUSTER and TREEVIEW software (Eisen et al., 1998). For clustering, the data were log transformed, median-centered and an average linkage clustering was carried out.

organism: Oncorhynchus mykiss

source_name: freshwater adapted rainbow trout

label_protocol: The labeling and hybridization steps of the amplified cDNA were performed following the “Gene Expression FFPE Workflow” Agilent protocol (starting from step 5 with minor modifications). Briefly, 1.65 µg of amplified cDNA was labeled using the Genomic DNA ULS Labeling Kit (1 µl of ULS-Cy5 per µg of DNA) at a final volume of 20 µl. The labeled cDNA was then purified using an Agilent KREApure column according to the standard protocol. The yield (~100%) and the degree of labeling (between 1.5% and 3%) of Cy5-cDNA were checked using a Nanodrop ND-1000 spectrophotometer (Labtech, Palaiseau, France).

extract_protocol: Arcturus Veritas (Excilone, Beynes, France) was used to capture ionocytes from frozen gill sections. The infrared laser was adjusted to produce spot sizes between 10 and 15 µm in diameter, which allowed consistent capture of cells onto CapSure LCM caps (Life Technologies). A mean of 400 labeled ionocytes were selected and captured from each animal. RNA was extracted using the PicoPure RNA isolation kit (Excilone) following the manufacturer’s recommendations and with 1 U of DNase (Invitrogen, Life Technologies, Saint Aubin, France) treatment for 15 min at room temperature. Ionocyte RNA from four freshwater and four seawater trout was ampliﬁed and puriﬁed using the Ovation picoSL WTA system V2 RNA Ampliﬁcation kit (NuGEN Technologies, Leek, Netherlands) according to the manufacturer’s instructions. Ampliﬁed cDNA was quantiﬁed using a NanoDrop Spectrophotometer (Labtech, Palaiseau, France).

tag: tissue type

value: gill

value: Ionocyte


title: EM77

description: Seawater Sample 77

source_name: seawater adapted rainbow trout


title: EM74

description: Seawater Sample 74


title: EM76

description: Seawater Sample 76


title: patient 56 liver donor - whole liver tissue mRNA - mRNA-DON-56

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

source_name: specimen obtained from explanted liver of patient 56

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).


title: EM75

description: Seawater Sample 75


title: patient 64 with liver angioma - whole liver tissue mRNA - mRNA-ANG-64


title: patient 23 with liver angioma - whole liver tissue mRNA - mRNA-ANG-23


title: patient 55 with liver angioma - whole liver tissue mRNA - mRNA-ANG-55


title: ED72

description: Freshwater Sample 72


title: patient 29 liver donor - whole liver tissue mRNA - mRNA-DON-29

source_name: specimen obtained from explanted liver of patient 29


title: ED67

description: Freshwater Sample 67


title: W6nk2 under control

city: Hangzhou

first: Hongyan

last: Sun

address: Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University

institute: Zhejiang University

description: Gene expression data from leaves under Cd treatment

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

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

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

organism: Hordeum vulgare

source_name: Barley leaves at seedling stage

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: Healthy seeds were surface sterilized with 2% H2O2 for 30 min and then rinsed with deionized water and soaked for 4 h. The seeds were germinated and grown hydroponically as described by Chen et al.(2010).

treatment_protocol: There were 2 treatments: control (BNS without Cd), 5 uM Cd

value: Fresh leaves


title: W6nk2 under Cd treatment

department: Department of Agronomy, College of Agriculture and Biotechnology

description: Gene expression data from leaves under control condition


title: Zhenong8 under Cd treatment


title: ED71

description: Freshwater Sample 71


title: patient 8 liver donor - whole liver tissue mRNA - mRNA-DON-8

source_name: specimen obtained from explanted liver of patient 8


title: patient 37 liver donor - whole liver tissue mRNA - mRNA-DON-37

source_name: specimen obtained from explanted liver of patient 37


title: patient 25 liver donor - whole liver tissue mRNA - mRNA-DON-25

source_name: specimen obtained from explanted liver of patient 25


title: patient 62 liver donor - whole liver tissue mRNA - mRNA-DON-62

source_name: specimen obtained from explanted liver of patient 62


title: patient 86 with liver angioma - whole liver tissue mRNA - mRNA-ANG-86

source_name: specimen obtained from explanted liver of patient 86


title: patient 2 with liver angioma - whole liver tissue mRNA - mRNA-ANG-2

source_name: specimen obtained from explanted liver of patient 2


title: Zhenong8 under control


title: patient 68 with liver angioma - whole liver tissue mRNA - mRNA-ANG-68

source_name: specimen obtained from explanted liver of patient 68


title: patient 65 with liver angioma - whole liver tissue mRNA - mRNA-ANG-65

source_name: specimen obtained from explanted liver of patient 65


title: patient 69 liver donor - whole liver tissue mRNA - mRNA-DON-69

source_name: specimen obtained from explanted liver of patient 69


title: patient 16 liver donor - whole liver tissue mRNA - mRNA-DON-16

source_name: specimen obtained from explanted liver of patient 16


title: patient 18 liver donor - whole liver tissue mRNA - mRNA-DON-18

source_name: specimen obtained from explanted liver of patient 18


title: patient 36 liver donor - whole liver tissue mRNA - mRNA-DON-36

source_name: specimen obtained from explanted liver of patient 36