title: FACH_liver_ClearwaterRiver_nonmigratingsubyearling_rep4

city: Cook

first: Helena

last: Christiansen

address: 5501A Cook-Underwood Rd

department: Western Fisheries Research Center

institute: U.S. Geological Survey

description: Gene expression profiling of natural subyearling fall Chinook Salmon from the Snake and Clearwater rivers

hyb_protocol: Sample hybridization was performed according to the manufacturer's protocols using the Agilent One-Color Microarray-Based Gene Expression Analysis Manual (Low Input Quick Amp Version).

scan_protocol: Microarray slides were scanned with Agilent G2505C Microarray Scanner.

data_processing: The raw array data were extracted from the scanned images using Agilent Feature Extraction 10.10 (FE). The raw intensity values from these files was imported into the software package “R”, which was used for diagnostic plots, normalization and final data analysis.

organism: Oncorhynchus tshawytscha

source_name: liver, wild fish, Clearwater River, non-migrating subyearling, replicate 4

label_protocol: Sample labeling was performed according to the manufacturer's protocols using the Agilent One-Color Microarray-Based Gene Expression Analysis Manual (Low Input Quick Amp Version).

extract_protocol: Total RNA was extracted from 20–30 mg RNAlater-preserved liver tissue using an RNeasy kit (Qiagen, Inc., Valencia, CA) with recommended on-column DNase digestion following the manufacturer’s instructions.  We checked RNA concentration and quality with a BioMate 3 UV spectrophotometer (Thermo Electron Corporation, Madison, WI). The concentration was also confirmed using the NanoDrop® ND-1000 UV-Vis Spectrophotometer, and RNA samples were analyzed using an Agilent 2100 Bioanalyzer Lab-On-A-Chip Agilent 6000 Series II chip to determine the integrity of the samples.

value: liver

tag: developmental stage

value: non-migrating subyearling

tag: collection site

value: Clearwater River transition zone

tag: collection date


title: siControl_48hr_rep1

status: Public on Jun 20 2014

type: RNA

city: Suita

first: Yukio

last: Kawahara

state: Osaka

address: 2-2 Yamada-oka

department: Graduate School of Medicine

country: Japan

institute: Osaka University

description: Gene expression  48 hr after Control siRNA transfection

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.   On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE microarray kit 8x60k Ver2.0 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.    After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides  (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with GeneSpring GX 12.6.0 (Agilent) using default parameters (Grit temptate 039494_D_F_20120628, FE protocol GE1_1010_Sep10, QC Metric GE1_QCMT_Sep10).

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T, siControl, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Low Input Quick Amp labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini column purification (QIAGEN, Valencia, CA).    Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HEK293T cells were grown in DMEM medium with 10% FBS in 6-cm dish at 37 ºC in a humidified incubator with 5% CO2

extract_protocol: Total RNA was extracted using TRIZOL reagent followed by further purification with PureLink RNA Mini Kit (Life Technologies) following the manufacturer's recommendations.    The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For the knockdown experiment, either Ataxin-2 siRNA or Control siRNA was transfected at the final concentration of 10 nM into 2 x 10^4 HEK293T cells using Lipofectamine RNAiMAX (Life Technologies).   For the overexpression experiment, 8 μg of either pFN21A-Halo-Ataxin-2 or pFN21A-Halo was transfected into HEK293T cells that were 90% confluent in 6-cm dish using Lipofectamine 2000 (Life Technologies).   Twenty-four hours after transfection, the cell culture medium was replaced with fresh medium, and the cells were incubated for additional 24 hrs at 37 ºC in a humidified incubator with 5% CO2

tag: cell

tag: condition

value: Control siRNA


title: TLwV14d_1

city: Heidelberg

first: Anja

last: Runge

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description:
replicate 1
Chip ID: 6085341051
Position: F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

organism: Mus musculus

source_name: Tumor liver vehicle-treated 14d

label_protocol: not provided

extract_protocol: twice TRIZOL extraction according to the manufactur's protocol

treatment_protocol: 60 mg/kg oral application of Sorafenib for 14d and 83d (LT) or equal amount of vehicle solution for 14d

tag: strain

tag: age

value: 12-15 weeks

tag: tissue


title: FACH_liver_ClearwaterRiver_nonmigratingsubyearling_rep2

state: WA

country: USA

source_name: liver, wild fish, Clearwater River, non-migrating subyearling, replicate 2


title: siControl_48hr_rep2

source_name: HEK293T, siControl, replicate 2


title: P60_wt cones, replicate 1 [array]

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: Light adapted for 6h.

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed using the Affymetrix GCC Scan Control V. 3.0.0.1214 on GeneChip Scanner 3000 with autoloader.

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.15) 'affy' package using the rma() function.

source_name: FACS-sorted cones, P60 wild type mice

label_protocol: The sense-strand cDNA obtained was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: The animals were maintained under a 12-hour light-dark cycle. Conditional DGCR8 knockout mice were crossed to the cone-specific Cre recombinase driver line D4-cre resulting in C-DGCR8 KO mice. To visualize cones, C-DGCR8 KO line mice were crossed to the floxed tdTomato reporter line Ai9. D4-cre or D4-cre/Ai9 animals served as wild type controls.

extract_protocol: Cones were isolated by FACS from wild type and C-DGCR8 KO mice at different time points (P30, P40, P50, P60, and P90). RNA extraction was performed with Trizol or Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer's instructions. Quantitative and qualitative analysis was performed using 2100 Bioanalyzer.

tag: strain/background

tag: genotype/variation

value: wild type (D4-cre/Ai9 tdTomato)

value: retina

tag: cell type

value: cone photoreceptors

value: postnatal day 60


title: P50_wt cones, replicate 2 [array]

description: Light adapted for 6h.

source_name: FACS-sorted cones, P50 wild type mice

value: postnatal day 50


title: FACH_liver_ClearwaterRiver_nonmigratingsubyearling_rep3

source_name: liver, wild fish, Clearwater River, non-migrating subyearling, replicate 3


title: mussel_gill_2week_Pb_rep4

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

hyb_protocol: Labeled cRNA was hybridized to the custom 15,000 probe array using the protocols of Agilent Technologies (AMADID # 031786).  Each microarray slide contained eight arrays (8 x 15k format).  To hybridize all fifty-two samples, a total of seven slides were used.  Replicate samples  from each treatment were hybridized to different slides to minimize any slide effects on gene expression.

scan_protocol: DNA microarrays were scanned at five micron resolution using an Agilent DNA Microarray Scanner G2565CA (Agilent Technologies) at the University of Massachusetts Medical School in Worchester, MA.

data_processing: Feature extraction was performed using Feature Extraction Software 9.5.1 (Agilent Technologies) and intensity values were normalized by quantile normalization with median polish in Arraystar (DNAstar, Madison, Wisconsin).  Differentially expressed sequences were identified by performing t-test with false discovery rate (FDR) correction (Benjamini Hochberg) between each treatment and the same time-point control or by ANOVA with FDR correction (Benjamini Hochberg) across all treatments at the same time-point.  Differentially expressed sequences were determined in two different data sets: (1) those uploaded and normalized with all treatments and controls at 1, 2, and 4 weeks, and (2) those uploaded and normalized with all the treatments and controls, including the initial samples

organism: Mytilus edulis

source_name: week 2, Pb exposed

label_protocol: Total RNA was prepared for microarray hybridization using the Quick Amp One Color Labeling kit and One Color RNA Spike-in kit (cy3) following the manufacturer’s protocols (Agilent Technologies, Santa Clara, CA).

growth_protocol: One hundred and twenty M. edulis between 50 – 60 mm in length were collected in January 2011, from Bourne MA (41.7402 N  70.6157W).    Mussels were collected by hand, at approximately the +0.15 m tidal height (4.1°C, 35 PSU salinity), and transported in a cooler back to the University of Massachusetts Boston.  Once in the lab, mussels were cleaned of epifauna/flora, rinsed in cold tapwater, and placed in a 69 L (18 gal) aquarium containing 5 µm filtered seawater at 11oC  for acclimation (8 d).  Mussels were fed Isochrysis galbana (tropical strain) and Thalassiosira weissflogii every two days during the acclimation period (but not during the experiment since metals would adhere to algal cells). Over the course of the acclimation period (and experiment), mussels were subjected to a 10 h:14 h light:dark cycle, and salinities ranging from 30 to 32 PSU.

extract_protocol: RNAlater preserved gill tissue was held at -20oC until analysis.  At that time, RNAlater was removed and the tissue was washed with TriReagent (Molecular Research Center, Cincinnati, OH) to remove residual RNAlater.  Then, 0.75 ml of TriReagent was added to each sample, tissue was homogenized for 5 min at 30 vibrations/s using a Tissue Lyser bead mill (Qiagen Inc., Valencia, CA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK), and RNA was isolated from the homogenate according to the TriReagent manufacturer’s methods.  RNA was precipitated on an RNAeasy spin column and treated on the column with DNAse I (Qiagen).  RNA was then eluted from the spin column with RNAse free water.

treatment_protocol: Mussels were exposed to 0.54 µM of the chloride salt of each metal alone or in combination: cadmium (Sigma Aldrich, St. Louis, MO) (61.26 µg/l Cd), lead (Sigma Aldrich, St. Louis, MO) (111.68 µg/l Pb ) and a Cd/Pb mixture (61.26 µg/l Cd + 111.68 µg/l Pb) or an unexposed control.  At three time points (1 week, 2 weeks, and 4 weeks) seven mussels were removed from each tank, length was recorded, and mussels were dissected.  Gill tissue was dissected from the body and divided, with a ~100 mg sample preserved in RNAlater.

value: gill

tag: exposure

value: 0.54 µM Pb


title: siAtaxin-2_48hr_rep3

description: Gene expression  48 hr after Ataxin-2 knockdown

source_name: HEK293T, siAtaxin-2, replicate 3

value: Ataxin-2 siRNA


title: P40_wt cones, replicate 2 [array]

description: Light adapted for 6h.

source_name: FACS-sorted cones, P40 wild type mice

value: postnatal day 40


title: siAtaxin-2_48hr_rep2

source_name: HEK293T, siAtaxin-2, replicate 2


title: mussel_gill_2week_Pb_rep5


title: FACH_liver_ClearwaterRiver_nonmigratingsubyearling_rep1

source_name: liver, wild fish, Clearwater River, non-migrating subyearling, replicate 1


title: FACH_liver_SnakeRiver_latemigratingsubyearling_rep4

source_name: liver, wild fish, Snake River, late migrating subyearling, replicate 4

value: migrating subyearling

value: Lower Granite Dam


title: FACH_liver_SnakeRiver_latemigratingsubyearling_rep3

source_name: liver, wild fish, Snake River, late migrating subyearling, replicate 3


title: siAtaxin-2_48hr_rep1

source_name: HEK293T, siAtaxin-2, replicate 1


title: mussel_gill_2week_Pb_rep3


title: P40_wt cones, replicate 1 [array]

description: Light adapted for 6h.


title: P50_wt cones, replicate 1 [array]

description: Light adapted for 6h.


title: mussel_gill_2week_Cd_rep6

source_name: week 2, Cd exposed

value: 0.54 µM Cd


title: P30_wt cones, replicate 2 [array]

description: Light adapted for 6h.

source_name: FACS-sorted cones, P30 wild type mice

value: postnatal day 30


title: mussel_gill_2week_Cd_rep3


title: mussel_gill_2week_Pb_rep1


title: mussel_gill_2week_Mixture_rep4

source_name: week 2, Cd + Pb exposed


title: FACH_liver_SnakeRiver_latemigratingsubyearling_rep1

source_name: liver, wild fish, Snake River, late migrating subyearling, replicate 1

value: liver


title: P30_wt cones, replicate 1 [array]

description: Light adapted for 6h.


title: mussel_gill_2week_Cd_rep5


title: mussel_gill_2week_Cd_rep2


title: FACH_liver_SnakeRiver_earlymigratingsubyearling_rep4

source_name: liver, wild fish, Snake River, early migrating subyearling, replicate 4


title: mussel_gill_2week_ctrl_rep7

source_name: week 2, no exposure


title: FACH_liver_SnakeRiver_earlymigratingsubyearling_rep3

source_name: liver, wild fish, Snake River, early migrating subyearling, replicate 3


title: FACH_liver_SnakeRiver_latemigratingsubyearling_rep2

source_name: liver, wild fish, Snake River, late migrating subyearling, replicate 2


title: mussel_gill_2week_ctrl_rep3


title: Potassium chloride treated small neurospheres  biological replicate 1

city: St lucia Brisbane

first: Zong-Hong

last: Zhang

state: Queensland

address: QBI Building (#79)

country: Australia

institute: QBI

hyb_protocol: Fragmentation and biotin labelling of the cDNA was carried out using Encore Biotin module (NuGEN) for Affymetrix GeneChip Mouse Gene 1.0 ST arrays. Labelled cDNA was hybridised to arrays in an oven at 45°C.

scan_protocol: Hybridised arrays were scanned using the Affymetrix GeneChip Scanner and the scanned data (.CEL files) was transferred to the Partek Genomics Suite and data analysis

data_processing: CEL files generated by AGCC were uploaded onto Partek software and the data analysis was carried out using the gene expression analysis workflow. Steps performed in Partek included: 1) robust microarray averaging (RMA) to normalize the data; 2) principal component analysis (PCA) to check for sample outliers; 3) analysis ofvariance (ANOVA) to generate p -values

label: Biotin

label_protocol: RNA was isolated from neurospheres generatedin presence of either N or K (n=3 each, two biological replicates 249 in common with the RNA-Seq data) and converted to cDNA using Applause WT-Amp ST kit (NuGEN).

growth_protocol: Mouse neurosphere cells treated by potassium chloride (KCl) and norepinephrine. Briefly, adult (8–12 week old) male C57BL/6J mice were used for all in vitro experiments conducted in this study. All mice were housed in groups and maintained on a 12-hour light/dark cycle with ad libitum access to food and water. After mice were sacrificed by cervical dislocation, the neural precursor activity was examined as previous described by our group.

extract_protocol: Total RNA was extracted from neurospheres using TRIzol Reagent (Life Technologies) and chloroform (Sigma-Aldrich) followed by precipitation and washing with isopropanol and ethanol respectively. RNA samples were treated with the Ambion DNA-free kit (Life Technologies) according to the manufacturer’s instructions to remove any contamination from genomic DNA.

treatment_protocol: The isolated hippocampal tissue was minced to obtain a single cell suspension. The cell suspension was cultured in complete neurosphere medium containing EGF and bFGF, in the presence of norepinephrine (10 μM) or potassium chloride (15mM). The primary neurospheres were collected on day 14 for each treatment.

value: adult (8–12 week old)

tag: gender

value: male

value: hippocampal tissue

value: primary neurospheres

tag: treated with

value: potassium chloride (15mM)


title: Potassium chloride treated small neurospheres  biological replicate 3


title: mussel_gill_2week_ctrl_rep2


title: Potassium chloride treated small neurospheres  biological replicate 2


title: FACH_liver_SnakeRiver_nonmigratingsubyearlingparr_rep4

source_name: liver, wild fish, Snake River, non-migrating subyearling parr, replicate 4

value: non-migrating subyearling parr

value: Lower Granite Reservoir rearing site


title: FACH_liver_SnakeRiver_earlymigratingsubyearling_rep1

source_name: liver, wild fish, Snake River, early migrating subyearling, replicate 1


title: Norepinephrine treated small neurospheres biological replicate 2

value: norepinephrine (10 μM)


title: Norepinephrine treated small neurospheres biological replicate 3


title: FACH_liver_SnakeRiver_earlymigratingsubyearling_rep2

source_name: liver, wild fish, Snake River, early migrating subyearling, replicate 2


title: FACH_liver_SnakeRiver_nonmigratingsubyearlingparr_rep3

source_name: liver, wild fish, Snake River, non-migrating subyearling parr, replicate 3


title: mussel_gill_1week_Mixture_rep7

source_name: week 1, Cd + Pb exposed

value: gill


title: mussel_gill_1week_Mixture_rep5


title: mussel_gill_2week_ctrl_rep1


title: FACH_liver_SnakeRiver_nonmigratingsubyearlingparr_rep1

source_name: liver, wild fish, Snake River, non-migrating subyearling parr, replicate 1


title: Norepinephrine treated small neurospheres biological replicate 1


title: FACH_liver_SnakeRiver_nonmigratingsubyearlingparr_rep2

source_name: liver, wild fish, Snake River, non-migrating subyearling parr, replicate 2


title: Col treated with COR vs Col 0 treated with COR + CORMO_Rep 3

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

country: Spain

institute: CNB-CSIC

description:
Biological replicate 3 of 4. Col -0 (CT) treated 2 hours with Coronatine vs Col-0 treated 2 hours with Coronatine + CORMO_Rep 3
R3_Cor vs Cor+CORMO
3. Col treated with Cor vs Col treated with Cor+CORMO

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Images were scanned at 5mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and they were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0 seedlings

label_protocol: 200 ng of total RNA was reverse transcribed used T7 promotor  primer and the cDNA was converted to aRNA using T7 RNA polimerase, wich simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two color Microarray-Based GeneExpression Analysis Protocol )

growth_protocol: Seedlings were grown 7 days under a 16-h light/8-h dark cycle at 21ºC in 0,5xMS1 solid and after they grown 2 days in 0,5xMS1 liquid

extract_protocol: The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).

treatment_protocol: Then 12 seedlings by biological replicate were treated with EtOH (CT), Cor (0.5uM) or  Cor-MO (10uM)

tag: ecotype

value: Col

value: seedling

tag: treatment

value: COR

value: COR+CORMO


title: Col treated with COR vs Col 0 treated with COR + CORMO_Rep 4

description:
Biological replicate 4 of 4. Col -0 (CT) treated 2 hours with Coronatine vs Col-0 treated 2 hours with Coronatine + CORMO_Rep 4
R4_Cor vs Cor+CORMO
4. Col treated with Cor vs Col treated with Cor+CORMO


title: mussel_gill_1week_Mixture_rep3


title: mussel_gill_1week_Pb_rep6

source_name: week 1, Pb exposed

value: 0.54 µM Pb


title: Col treated with COR vs Col 0 treated with COR + CORMO_Rep 2

description:
Biological replicate 2 of 4. Col -0 (CT) treated 2 hours with Coronatine vs Col-0 treated 2 hours with Coronatine + CORMO_Rep 2
R2_Cor vs Cor+CORMO
2. Col treated with Cor vs Col treated with Cor+CORMO


title: mussel_gill_1week_Mixture_rep1


title: Col treated with COR  vs Col 0 treated with COR + CORMO_Rep 1

description:
Biological replicate 1 of 4. Col -0 (CT) treated 2 hours with Coronatine vs Col-0 treated 2 hours with Coronatine + CORMO_Rep 1
R1_ Cor vs Cor+CORMO
1. Col treated with Cor vs Col treated with Cor+CORMO


title: mussel_gill_1week_Pb_rep2


title: mussel_gill_1week_Pb_rep4


title: Col vs Col treated with CORMO_Rep 2

description:
Biological replicate 2of 4. Col -0 (CT)  vs Col-0 treated 2 hours with CORMO_Rep 2
R2_ CT vs CORMO
2. Col vs Col treated with CORMO

value: untreated

value: CORMO


title: Col vs Col treated with CORMO_Rep 4

description:
Biological replicate 4 of 4. Col -0 (CT)  vs Col-0 treated 2 hours with CORMO_Rep 4
R4_ CT vs CORMO
4. Col vs Col treated with CORMO


title: mussel_gill_1week_Pb_rep1


title: Col vs Col treated with CORMO_Rep 3

description:
Biological replicate 3 of 4. Col -0 (CT)  vs Col-0 treated 2 hours with CORMO_Rep 3
R3_ CT vs CORMO
3. Col vs Col treated with CORMO


title: P90_wt cones, replicate 1 [array]

description: Light adapted for 6h.

source_name: FACS-sorted cones, P90 wild type mice

value: wild type (D4-cre/Ai9 tdTomato)

value: retina

value: cone photoreceptors

value: postnatal day 90


title: mussel_gill_1week_Cd_rep7

source_name: week 1, Cd exposed

value: 0.54 µM Cd


title: Imatinib 48h/Control 48h biological replica 3 technical replica 1

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

description:
Imatinib 48h/Control 48h 3
ch1: Non-treated paired adult worms (48h) biological replica 3 - technical replica 1_Cy3
ch2: Imatinib-treated paired adult worms (48h) biological replica 3- technical replica 1 _Cy5

hyb_protocol: Samples were combined and hybridized on a custom oligoarray with 4 x 44k elements produced by Agilent Technologies (GPL8606), the hybridization and washing steps were perfomed according to agilent instructions

scan_protocol: The washed slides were scanned using the equipament GenePix4000B (molecular devices)

data_processing: Data was extracted using Feature Extraction software (Agilent Technologies), the intensities were LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Schistosoma mansoni

source_name: Control 48h 3_ Cy3

label_protocol: All samples were linearly amplified and labeled using Agilent protocol with Low input RNA amplification kit

growth_protocol: worms were obtained by portal perfusion in 42-days infected hamsters

extract_protocol: RNA from all samples was extract using Trizol reagent (invitrogen)  followed by DNAse treatment using RNeasy kit (QIAGEN) according to manufacturer´s instructions.

treatment_protocol: adult paired worms were treated with 50 µM Imatinib during 24h and 48h with the respectives controls (non-treated worms)

value: adult

tag: agent

value: Non-treated

tag: time

source_name: Imatinib 48h 3_Cy5

value: Imatinib-treated


title: mussel_gill_1week_Cd_rep3


title: mussel_gill_1week_Cd_rep4


title: Sorghum leaf_combined_R16_rep1

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

description: 3 day not watered, followed by 50C incubation for 3 hrs

hyb_protocol: The labeled cRNA was hybridized using Agilent's Hybridization Kit to the microarrays. The slides were then washed in Wash Solution 1 (0.005% Triton X-102), Wash Solution 2 (0.005% Triton X-102) acetonitrile and dried using Agilent's Stabilization and Drying Solution

scan_protocol: The slides were scanned with the Agilent G2505C Microarray Scanner. For data extraction and quality control, the Agilent Feature Extraction Software (v.10.7.3.1) was used.

data_processing: Data was processed using default GeneSpring GX12.5 protocol: Threshold: 1.0; Logbase: 2; Data normalisation: shift to 75th percentile; Baseline transformation: median of all samples

organism: Sorghum bicolor

source_name: Sorghum bicolor leaf, combined stress (3 day water withdrawal then 50 degree incubation for 3 hrs)

label_protocol: RNA from Sorghum samples and Agilent One-Color RNA Spike-In RNA were labeled with reagents supplied in the Agilent Quick Amp Labeling Kit, One-Color. The labeled cRNA was then purified with the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK).

growth_protocol: Seeds of Sorghum R16 variety (Sorghum bicolor L. Moench.) were imbibed overnight in water and surface-sown singly onto soaked 42mm Jiffy peat pellets (LBS horticulture Ltd, Lancashire, UK). Seedlings were grown in a controlled growth chamber at 28°C day, 23°C night, 12 h photoperiod, 0% humidity

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen Sussex, UK). The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyzer (Palo Alto, CA) and the Agilent RNA 6000 Nano Kit (Cat no # 5067-1511)

treatment_protocol: Plants were subjected either to control (no treatment), heat, drought or combined heat and drought conditions. Drought stress was applied by withholding water from 14 days after sowing. At the point when the photosynthetic efficiency of the un-watered plants first showed a significant difference to the watered plants, they were subject to either heat shock by incubation in the dark at 50 °C for 3 h (heat and combined treatment) or 28 °C for 3 h (control and drought treatment). The youngest 3 leaves were sampled and tissue was pooled for each treatment set.

tag: variety

value: 14 days after sowing

value: Leaf

value: Heat&Drought


title: Imatinib 48h/Control 48h biological replica 2 technical replica 2 (dye swap)

description:
Imatinib 48h/Control 48h 2_s
ch1: Imatinib-treated paired adult worms (48h) biological replica 2- technical replica 2 _Cy3 (dye swap)
ch2: Non-treated paired adult worms (48h) biological replica 2 - technical replica 2_Cy5 (dye swap)
dye swap

source_name: Imatinib 48h 2_Cy3

tag: developmental stage

source_name: Control 48h 2_ Cy5


title: Imatinib 48h/Control 48h biological replica 3 technical replica 2 (dye swap)

description:
Imatinib 48h/Control 48h 3_s
ch1: Imatinib-treated paired adult worms (48h) biological replica 3- technical replica 2 _Cy3 (dye swap)
ch2: Non-treated paired adult worms (48h) biological replica 3 - technical replica 2_Cy5 (dye swap)
dye swap

source_name: Imatinib 48h 3_Cy3

source_name: Control 48h 3_ Cy5


title: Sorghum leaf_combined_R16_rep3


title: Sorghum leaf_heat_R16_rep3

description: 3 day watered, followed by 50C incubation for 3 hrs

source_name: Sorghum bicolor leaf, heat shock (watered, 50 degrees incubation 3 hrs)

value: Heat


title: mussel_gill_1week_Cd_rep2

value: gill


title: mussel_gill_1week_ctrl_rep5

source_name: week 1, no exposure


title: Slide 344292

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Average ratio of inter slide replicates

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F532 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences)

growth_protocol: Cells were grown GM17 medium and harvested at OD600 of 0.2.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006; Shafeeq et al., 2011). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: Wild type

source_name: F635 Mean

value: lacR Mutant


title: Sorghum leaf_heat_R16_rep2


title: Imatinib 24h/Control 24h biological replica 2 technical replica 2 (dye swap)

description:
Imatinib 24h/Control 24h 2_s
ch1: Imatinib-treated paired adult worms (24h) biological replica 2- technical replica 2 _Cy3 (dye swap)
ch2: Non-treated paired adult worms (24h) biological replica 2 - technical replica 2_Cy5 (dye swap)
dye swap

source_name: Imatinib 24h 2_Cy3

source_name: Control 24h 2_ Cy5


title: PAPI25 [SNP]

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Hybridised to SNP6

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Raw data were analysed using the CRMAv2 algorithm in the aroma.affymetrix package.

molecule: genomic DNA

source_name: Papillary carcinoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted using the Qiagen DNA Blood and Tissue kit

tag: subtype

value: Invasive papillary carcinoma

tag: grade

tag: er

value: ER+

value: HER-


title: mussel_gill_1week_ctrl_rep3


title: Sorghum leaf_combined_R16_rep2

tag: age


title: PAPI26 [SNP]

description: Hybridised to SNP6

value: Encapsulated papillary carcinoma

tag: pr

value: PR+


title: Slide 345471

description: Sample 1

growth_protocol: Cells were grown LM17 medium and harvested at OD600 of 0.2.

value: LacT mutant

value: Wild-type


title: mussel_gill_1week_ctrl_rep2

tag: tissue


title: Sorghum leaf_heat_R16_rep1


title: Imatinib 24h/Control 24h biological replica 2 technical replica 1

description:
Imatinib 24h/Control 24h 2
ch1: Non-treated paired adult worms (24h) biological replica 2 - technical replica 1_Cy3
ch2: Imatinib-treated paired adult worms (24h) biological replica 2- technical replica 1 _Cy5

source_name: Control 24h 2_ Cy3

value: adult

source_name: Imatinib 24h 2_Cy5


title: PAPI24 [SNP]

description: Hybridised to SNP6


title: PAPI23 [SNP]

description: Hybridised to SNP6

value: Solid papillary carcinoma

value: PR-


title: PAPI4 [SNP]

description: Hybridised to SNP6


title: Slide 344291

description: Average ratio of inter slide replicates

tag: genotype/variation


title: PAPI21 [SNP]

description: Hybridised to SNP6


title: mussel_gill_1week_ctrl_rep1


title: mussel_gill_initial_rep6

source_name: initial sample, no exposure


title: Slide 343741

description: Sample 3

growth_protocol: Cells were grown to OD600 of 0.2 in M17 medium+ 0.5 % (w/v) Lactose (LM17) compared to M17 medium+ 0.5 % (w/v) Glucose (GM17)

tag: condition

value: Glucose

value: Lactose


title: Sorghum leaf_drought_R16_rep2

description: 3 day not watered, followed by 28C incubation for 3 hrs

source_name: Sorghum bicolor leaf, drought stressed (3 day water withdrawal, 28 degree incubation)

value: 14 days after sowing

value: Leaf

value: Drought


title: Sorghum leaf_drought_R16_rep1


title: Imatinib 24h/Control 24h biological replica 1 technical replica 2 (dye swap)

description:
Imatinib 24h/Control 24h 1_s
ch1: Imatinib-treated paired adult worms (24h) biological replica 1- technical replica 2 _Cy3 (dye swap)
ch2: Non-treated paired adult worms (24h) biological replica 1 - technical replica 2_Cy5 (dye swap)
dye swap

source_name: Imatinib 24h 1_Cy3

value: Imatinib-treated

source_name: Control 24h 1_ Cy5

value: Non-treated


title: Slide 343740

description: Sample 2


title: PAPI22 [SNP]

description: Hybridised to SNP6


title: Slide 343739

description: Sample 1


title: Col vs Col treated with CORMO_Rep 1

description:
Biological replicate 1 of 4. Col -0 (CT)  vs Col-0 treated 2 hours with CORMO_Rep 1
R1_ CT vs CORMO
1. Col vs Col treated with CORMO

source_name: Arabidopsis thaliana Col-0 seedlings

value: Col

value: seedling

value: untreated

value: CORMO


title: PAPI27 [SNP]

description: Hybridised to SNP6

value: ER+

value: PR+

value: HER-


title: PAPI18 [SNP]

description: Hybridised to SNP6

value: Encapsulated papillary carcinoma


title: mussel_gill_initial_rep5

value: gill

tag: exposure


title: Sorghum leaf_control_R16_rep3

description: 3 day watered followed by 28C incubation for 3 hrs

source_name: Sorghum bicolor leaf, control (no treatment - watered, 28 degree incubation for 3 hrs )

value: Control


title: Imatinib 48h/Control 48h biological replica 1 technical replica 1

description:
Imatinib 48h/Control 48h 1
ch1: Non-treated paired adult worms (48h) biological replica 1 - technical replica 1_Cy3
ch2: Imatinib-treated paired adult worms (48h) biological replica 1- technical replica 1 _Cy5

source_name: Control 48h 1_ Cy3

value: adult

source_name: Imatinib 48h 1_Cy5


title: PAPI14 [SNP]

description: Hybridised to SNP6

value: Invasive papillary carcinoma


title: Sorghum leaf_drought_R16_rep3

value: 14 days after sowing


title: mussel_gill_initial_rep3


title: Imatinib 48h/Control 48h biological replica 1 technical replica 2 (dye swap)

description:
Imatinib 48h/Control 48h 1_s
ch1: Imatinib-treated paired adult worms (48h) biological replica 1- technical replica 2 _Cy3 (dye swap)
ch2: Non-treated paired adult worms (48h) biological replica 1 - technical replica 2_Cy5 (dye swap)
dye swap

source_name: Imatinib 48h 1_Cy3

source_name: Control 48h 1_ Cy5


title: PAPI2 [SNP]

description: Hybridised to SNP6


title: Imatinib 24h/Control 24h biological replica 3 technical replica 2 (dye swap)

description:
Imatinib 24h/Control 24h 3_s
ch1: Imatinib-treated paired adult worms (24h) biological replica 3- technical replica 2 _Cy3 (dye swap)
ch2: Non-treated paired adult worms (24h) biological replica 3 - technical replica 2_Cy5 (dye swap)
dye swap

source_name: Imatinib 24h 3_Cy3

source_name: Control 24h 3_ Cy5


title: Slide 344294

description: Average ratio of inter slide replicates

source_name: F532 Mean

growth_protocol: Cells were grown to OD600 of 0.2 in M17 medium+ 0.5 % (w/v) Galactose (GaM17) compared to M17 medium+ 0.5 % (w/v) Glucose (GM17)

value: Glucose

source_name: F635 Mean

value: Galactose


title: PAPI12 [SNP]

description: Hybridised to SNP6

source_name: Papillary carcinoma


title: Slide 344293

description: Average ratio of inter slide replicates


title: mussel_gill_initial_rep2


title: Imatinib 48h/Control 48h biological replica 2 technical replica 1

description:
Imatinib 48h/Control 48h 2
ch1: Non-treated paired adult worms (48h) biological replica 2 - technical replica 1_Cy3
ch2: Imatinib-treated paired adult worms (48h) biological replica 2- technical replica 1 _Cy5

source_name: Control 48h 2_ Cy3

source_name: Imatinib 48h 2_Cy5

value: Imatinib-treated


title: Imatinib 24h/Control 24h biological replica 3 technical replica 1

description:
Imatinib 24h/Control 24h 3
ch1: Non-treated paired adult worms (24h) biological replica 3 - technical replica 1_Cy3
ch2: Imatinib-treated paired adult worms (24h) biological replica 3- technical replica 1 _Cy5

source_name: Control 24h 3_ Cy3

value: Non-treated

source_name: Imatinib 24h 3_Cy5


title: Sorghum leaf_control_R16_rep2

value: Leaf


title: PAPI20 [SNP]

description: Hybridised to SNP6

value: PR-


title: light-hs, rep3

status: Public on Jun 19 2014

city: changsha

first: Junyi

last: Song

address: Deya Road 888

country: China

institute: National University of Defense Techonolgy

description:
B3= light-hs-rep3
Gene expression data from Arabidopsis seedling with HS treatment, under light condition

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

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

growth_protocol: Arabidopsis (Arabidopsis thaliana) plants of ecotype Col-0 were used for all experiments. Sterilized seeds were grown in Murashige & Skoog solid medium within glass plates. After a 72 h vernalization at 4℃ in dark condition, plats were transferred to the growth camber (ambient temperature of 23℃, relative humidity of approximately 70%, and a photoperiod of 16 h light approximately 100 μmol m-2s-1 alternating with 8 h darkness).

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

treatment_protocol: for HS groups, the treatment was 37℃ for 30min

tag: cultivar

value: 15-day-old seedlings


title: light-hs, rep2

description:
B2= light-hs-rep2
Gene expression data from Arabidopsis seedling with HS treatment, under light condition

value: 14-day-old seedlings


title: dark-control,rep1

description:
B1= dark-control-rep1
Gene expression data fromeArabidopsis seedling without HS treatment, under dark condition

value: 16-day-old seedlings


title: light-hs, rep1

description:
B1= light-hs-rep1
Gene expression data from Arabidopsis seedling with HS treatment, under light condition

value: 13-day-old seedlings


title: dark-control,rep2

description:
B2= dark-control-rep2
Gene expression data fromeArabidopsis seedling without HS treatment, under dark condition

value: 17-day-old seedlings


title: dark-control,rep3

description:
B3= dark-control-rep3
Gene expression data fromeArabidopsis seedling without HS treatment, under dark condition

value: 18-day-old seedlings


title: Sorghum leaf_control_R16_rep1


title: light-control,rep2

description:
A2= light-control-rep2
Gene expression data frome Arabidopsis seedling without HS treatment, under light condition

value: 11-day-old seedlings


title: dark-hs,rep3

description:
A3= dark-hs-rep3
Gene expression data from Arabidopsis seedling with HS treatment, under dark condition

value: 21-day-old seedlings


title: light-control, rep1

description:
A1= light-control-rep1
Gene expression data frome Arabidopsis seedling without HS treatment, under light condition

value: 10-day-old seedlings


title: Breast tumor 500

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

description: 5542829016_G: GP500

hyb_protocol: 750 ng of labeled cRNA were applied to Illimuna whole-genome gene expression HumanRef-8 v2 BeadChips for an overnight hybridization at 58°C.

scan_protocol: Signal is developed with streptavidin-Cy3 and the BeadChip is scanned with the Illumina BeadArray Reader.

data_processing: Image data were processed by GenomeStudio software using background subtraction and quantile normalization. Methods to adjust the normalized intensity values see MAQC Consortium’s description [PMID: 16964229]. Log2 expression ratio of a normalized intensity value to the average signal in all samples for each transcript was calculated.

source_name: Human primary breast tumor

label_protocol: 200 ng of total RNA were converted to cDNA, followed by an in vitro transcription amplification step to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX).

extract_protocol: RNA was extracted from fine needle aspirates of tumors with QIAGEN RNAeasy Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: margin (cm)

tag: tumor type

value: IDC

tag: tumor size (cm)

tag: tumor grade

tag: ln positive (total)

tag: lvi

value: Yes

tag: eic

value: Positive

value: Negative

tag: cmtc

tag: recurrence

value: no

tag: recurrence free time (months)

tag: location of recurrence

tag: used in the 284bc dataset?

value: yes

tag: rin


title: dark-hs,rep1

description:
A1= dark-hs-rep1
Gene expression data from Arabidopsis seedling with HS treatment, under dark condition

tag: developmental stage

value: 19-day-old seedlings


title: Breast tumor 494

description: 5542829016_A: GP494

tag: age

value: DCIS

tag: er

tag: pr


title: Breast tumor 501

description: 5542829016_H: GP501

tag: margin (cm)

value: No


title: Breast tumor 498

description: 5542829016_E: GP498

tag: tumor type


title: dark-hs,rep2

description:
A2= dark-hs-rep2
Gene expression data from Arabidopsis seedling with HS treatment, under dark condition

tag: cultivar

value: 20-day-old seedlings


title: Breast tumor 499

description: 5542829016_F: GP499

tag: tumor size (cm)

tag: tumor grade


title: Breast tumor 487

description: 5542829005_B: GP487

tag: ln positive (total)

tag: lvi


title: Breast tumor 495

description: 5542829016_B: GP495

tag: eic

tag: cmtc


title: Breast tumor 488

description: 5542829005_C: GP488

tag: recurrence

tag: recurrence free time (months)


title: Breast tumor 497

description: 5542829016_D: GP497

tag: location of recurrence

tag: used in the 284bc dataset?


title: Breast tumor 493

description: 5542829005_H: GP493

tag: rin


title: Breast tumor 492

description: 5542829005_G: GP492

tag: age


title: Breast tumor 489

description: 5542829005_D: GP489

tag: er


title: Breast tumor 490

description: 5542829005_E: GP490

tag: pr

value: local


title: Slide 345472

description: Sample 2

tag: genotype/variation

value: LacT mutant

value: Wild-type


title: PAPI11 [SNP]

description: Hybridised to SNP6

tag: subtype

value: Invasive papillary carcinoma

tag: grade

value: ER+

value: HER-


title: Breast tumor 496

description: 5542829016_C: GP496

tag: margin (cm)

tag: tumor type

tag: tumor size (cm)


title: PAPI13 [SNP]

description: Hybridised to SNP6

value: Encapsulated papillary carcinoma


title: Breast tumor 484

description: 5392306060_G: GP484

value: IDC

tag: tumor grade

tag: ln positive (total)

tag: lvi


title: Breast tumor 485

description: 5392306060_H: GP485

tag: eic

tag: cmtc

tag: recurrence


title: Breast tumor 481

description: 5392306060_D: GP481

tag: recurrence free time (months)

tag: location of recurrence

tag: used in the 284bc dataset?


title: Breast tumor 491

description: 5542829005_F: GP491

tag: age

value: Yes

tag: er

tag: rin


title: Imatinib 24h/Control 24h biological replica 1 technical replica 1

description:
Imatinib 24h/Control 24h 1
ch1: Non-treated paired adult worms (24h) biological replica 1 - technical replica 1_Cy3
ch2: Imatinib-treated paired adult worms (24h) biological replica 1- technical replica 1 _Cy5

source_name: Control 24h 1_ Cy3

tag: developmental stage

value: adult

tag: agent

value: Non-treated

tag: time

source_name: Imatinib 24h 1_Cy5

value: Imatinib-treated


title: Breast tumor 486

description: 5542829005_A: GP486

tag: margin (cm)

tag: tumor type

value: Positive

tag: pr

value: Negative

value: no

value: yes


title: Breast tumor 482

description: 5392306060_E: GP482

tag: tumor size (cm)

tag: tumor grade

tag: ln positive (total)

value: No


title: Breast tumor 483

description: 5392306060_F: GP483

tag: lvi

tag: eic

tag: cmtc


title: PAPI15 [SNP]

description: Hybridised to SNP6

tag: subtype

value: Solid papillary carcinoma

tag: grade

value: PR+


title: Breast tumor 480

description: 5392306060_C: GP480

tag: age

tag: recurrence

tag: recurrence free time (months)

tag: location of recurrence

tag: used in the 284bc dataset?


title: Breast tumor 475

description: 5392306058_F: GP475

tag: er

tag: rin


title: Breast tumor 476

description: 5392306058_G: GP476

tag: margin (cm)

tag: tumor type

value: DCIS


title: Breast tumor 467

description: 5371062058_E: GP467

tag: tumor size (cm)

tag: pr


title: Breast tumor 479

description: 5392306060_B: GP479

tag: tumor grade

tag: ln positive (total)


title: Breast tumor 470

description: 5371062058_H: GP470

tag: lvi

tag: eic


title: light-control, rep3

description:
A3= light-control-rep3
Gene expression data frome Arabidopsis seedling without HS treatment, under light condition

tag: cultivar

tag: developmental stage

value: 12-day-old seedlings


title: Breast tumor 471

description: 5392306058_A: GP471

tag: age

tag: cmtc


title: Breast tumor 478

description: 5392306060_A: GP478

tag: recurrence

tag: recurrence free time (months)


title: Breast tumor 472

description: 5392306058_B: GP472

tag: location of recurrence

tag: used in the 284bc dataset?


title: Breast tumor 465

description: 5371062058_C: GP465

tag: er

tag: rin


title: Breast tumor 466

description: 5371062058_D: GP466

tag: margin (cm)

tag: tumor type


title: Breast tumor 473

description: 5392306058_D: GP473

tag: tumor size (cm)

tag: pr


title: Breast tumor 477

description: 5392306058_H: GP477

tag: tumor grade

tag: ln positive (total)


title: Breast tumor 468

description: 5371062058_F: GP468

tag: lvi

tag: eic


title: Breast tumor 461

description: 5371062047_G: GP461


title: Breast tumor 463

description: 5371062058_A: GP463

value: local


title: Breast tumor 462

description: 5371062047_H: GP462


title: Breast tumor 469

description: 5371062058_G: GP469


title: Breast tumor 474

description: 5392306058_E: GP474


title: Breast tumor 464

description: 5371062058_B: GP464


title: Breast tumor 460

description: 5371062047_F: GP460


title: Breast tumor 456

description: 5371062047_A: GP456


title: Breast tumor 455

description: 5392306053_H: GP455


title: Breast tumor 457

description: 5371062047_C: GP457


title: Breast tumor 459

description: 5371062047_E: GP459


title: Breast tumor 450

description: 5392306053_C: GP450

value: ILC


title: Breast tumor 454

description: 5392306053_G: GP454


title: Breast tumor 451

description: 5392306053_D: GP451


title: Breast tumor 449

description: 5392306053_B: GP449


title: Breast tumor 446

description: 5392306052_G: GP446


title: Breast tumor 440

description: 5392306052_A: GP440


title: Breast tumor 444

description: 5392306052_E: GP444


title: Breast tumor 452

description: 5392306053_E: GP452

value: DCIS/IDC


title: Breast tumor 435

description: 5392306045_D: GP435

value: IDC


title: Breast tumor 448

description: 5392306053_A: GP448

value: IMC


title: Breast tumor 458

description: 5371062047_D: GP458


title: Breast tumor 447

description: 5392306052_H: GP447


title: Breast tumor 436

description: 5392306045_E: GP436


title: Breast tumor 433

description: 5392306045_B: GP433

value: Yes


title: Breast tumor 453

description: 5392306053_F: GP453


title: Breast tumor 441

description: 5392306052_B: GP441

value: IDC/DCIS


title: Breast tumor 439

description: 5392306045_H: GP439

value: axillary


title: Breast tumor 430

description: 5392306038_G: GP430

value: Positive


title: Breast tumor 437

description: 5392306045_F: GP437


title: Breast tumor 431

description: 5392306038_H: GP431

value: Negative


title: Breast tumor 443

description: 5392306052_D: GP443

value: no


title: Breast tumor 432

description: 5392306045_A: GP432

value: yes


title: Breast tumor 442

description: 5392306052_C: GP442

value: No


title: Breast tumor 426

description: 5392306038_C: GP426


title: Breast tumor 445

description: 5392306052_F: GP445


title: Breast tumor 434

description: 5392306045_C: GP434


title: Breast tumor 428

description: 5392306038_E: GP428


title: Breast tumor 438

description: 5392306045_G: GP438


title: Breast tumor 427

description: 5392306038_D: GP427


title: Breast tumor 429

description: 5392306038_F: GP429


title: Breast tumor 424

description: 5392306038_A: GP424


title: Breast tumor 422

description: 4936527026_G: GP422


title: Breast tumor 417

description: 4936527026_A: GP417


title: Breast tumor 420

description: 4936527026_E: GP420


title: Breast tumor 421

description: 4936527026_F: GP421


title: Breast tumor 418

description: 4936527026_B: GP418


title: Breast tumor 412

description: 4936527003_C: GP412


title: Breast tumor 415

description: 4936527003_F: GP415


title: Breast tumor 425

description: 5392306038_B: GP425


title: Breast tumor 414

description: 4936527003_E: GP414


title: Breast tumor 423

description: 4936527026_H: GP423


title: Breast tumor 410

description: 4936527003_A: GP410


title: Breast tumor 413

description: 4936527003_D: GP413


title: Breast tumor 405

description: 5083888057_D: GP405


title: Breast tumor 407

description: 5083888057_F: GP407


title: Breast tumor 408

description: 5083888057_G: GP408


title: Breast tumor 406

description: 5083888057_E: GP406


title: Breast tumor 419

description: 4936527026_C: GP419


title: Breast tumor 404

description: 5083888057_C: GP404


title: Breast tumor 401

description: 5083888056_H: GP401


title: Breast tumor 402

description: 5083888057_A: GP402


title: Breast tumor 416

description: 4936527003_G: GP416


title: Breast tumor 400

description: 5083888056_G: GP400


title: Breast tumor 403

description: 5083888057_B: GP403


title: Breast tumor 409

description: 5083888057_H: GP409


title: Breast tumor 411

description: 4936527003_B: GP411


title: Breast tumor 399

description: 5083888056_F: GP399


title: Breast tumor 397

description: 5083888056_D: GP397


title: Breast tumor 396

description: 5083888056_C: GP396


title: Breast tumor 398

description: 5083888056_E: GP398


title: Breast tumor 395

description: 5083888056_B: GP395


title: Breast tumor 388

description: 5083888055_C: GP388


title: Breast tumor 390

description: 5083888055_E: GP390


title: Breast tumor 392

description: 5083888055_G: GP392


title: Breast tumor 394

description: 5083888056_A: GP394


title: Breast tumor 393

description: 5083888055_H: GP393


title: Breast tumor 386

description: 5083888055_A: GP386


title: Breast tumor 387

description: 5083888055_B: GP387


title: Breast tumor 389

description: 5083888055_D: GP389


title: Breast tumor 377

description: 5083888049_H: GP377


title: Breast tumor 385

description: 5083888051_H: GP385


title: Breast tumor 376

description: 5083888049_F: GP376


title: Breast tumor 383

description: 5083888051_F: GP383


title: Breast tumor 374

description: 5083888049_D: GP374


title: Breast tumor 381

description: 5083888051_D: GP381


title: Breast tumor 379

description: 5083888051_B: GP379


title: Breast tumor 372

description: 5083888049_B: GP372


title: Breast tumor 384

description: 5083888051_G: GP384


title: Breast tumor 382

description: 5083888051_E: GP382


title: Breast tumor 391

description: 5083888055_F: GP391


title: Breast tumor 380

description: 5083888051_C: GP380


title: Breast tumor 371

description: 5083888049_A: GP371


title: Breast tumor 370

description: 5083888043_H: GP370


title: Breast tumor 375

description: 5083888049_E: GP375


title: Breast tumor 369

description: 5083888043_G: GP369


title: Breast tumor 378

description: 5083888051_A: GP378


title: Breast tumor 368

description: 5083888043_F: GP368


title: Breast tumor 373

description: 5083888049_C: GP373


title: Breast tumor 361

description: 4921106027_C: GP361


title: Breast tumor 358

description: 4921106025_H: GP358


title: Breast tumor 357

description: 4921106025_F: GP357


title: Breast tumor 356

description: 4921106025_E: GP356


title: Breast tumor 365

description: 5083888043_C: GP365


title: Breast tumor 366

description: 5083888043_D: GP366


title: Breast tumor 367

description: 5083888043_E: GP367

value: bone


title: Breast tumor 363

description: 5083888043_A: GP363


title: Breast tumor 355

description: 4921106025_C: GP355


title: Breast tumor 360

description: 4921106027_B: GP360


title: Breast tumor 364

description: 5083888043_B: GP364


title: Breast tumor 359

description: 4921106027_A: GP359


title: Breast tumor 353

description: 4921106025_A: GP353


title: Breast tumor 351

description: 4921106020_G: GP351


title: Breast tumor 362

description: 4921106027_D: GP362


title: Breast tumor 350

description: 4921106020_F: GP350


title: Breast tumor 344

description: 4921106019_G: GP344


title: Breast tumor 341

description: 4921106019_D: GP341


title: Breast tumor 352

description: 4921106020_H: GP352


title: Breast tumor 354

description: 4921106025_B: GP354


title: Breast tumor 346

description: 4921106020_A: GP346


title: Breast tumor 348

description: 4921106020_D: GP348


title: Breast tumor 345

description: 4921106019_H: GP345


title: Breast tumor 347

description: 4921106020_B: GP347


title: Breast tumor 343

description: 4921106019_F: GP343


title: Breast tumor 340

description: 4921106019_C: GP340


title: Breast tumor 339

description: 4921106019_B: GP339


title: Breast tumor 349

description: 4921106020_E: GP349


title: Breast tumor 336

description: 4921106008_F: GP336


title: Breast tumor 327

description: 4921085012_E: GP327


title: Breast tumor 328

description: 4921085012_F: GP328


title: Breast tumor 334

description: 4921106008_D: GP334


title: Breast tumor 335

description: 4921106008_E: GP335


title: Breast tumor 331

description: 4921106008_A: GP331


title: Breast tumor 329

description: 4921085012_G: GP329


title: Breast tumor 330

description: 4921085012_H: GP330


title: Breast tumor 332

description: 4921106008_B: GP332


title: Breast tumor 326

description: 4921085012_D: GP326


title: Breast tumor 338

description: 4921106019_A: GP338


title: Breast tumor 337

description: 4921106008_G: GP337


title: Breast tumor 325

description: 4921085012_C: GP325


title: Breast tumor 324

description: 4921085012_B: GP324


title: Breast tumor 323

description: 4921085012_A: GP323


title: Breast tumor 321

description: 4807266013_E: GP321


title: Breast tumor 312

description: 4849554045_C: GP312


title: Breast tumor 333

description: 4921106008_C: GP333


title: Breast tumor 318

description: 4807266013_B: GP318


title: Breast tumor 316

description: 4849554045_G: GP316

value: brain


title: Breast tumor 322

description: 4807266013_F: GP322


title: Breast tumor 319

description: 4807266013_C: GP319


title: Breast tumor 342

description: 4921106019_E: GP342


title: Breast tumor 320

description: 4807266013_D: GP320


title: Breast tumor 315

description: 4849554045_F: GP315


title: Breast tumor 311

description: 4849554045_B: GP311


title: Breast tumor 317

description: 4849554045_H: GP317


title: Breast tumor 313

description: 4849554045_D: GP313


title: Breast tumor 314

description: 4849554045_E: GP314

value: ADH


title: Breast tumor 307

description: 4849554044_F: GP307


title: Breast tumor 309

description: 4849554044_H: GP309


title: Breast tumor 310

description: 4849554045_A: GP310


title: Breast tumor 306

description: 4849554044_E: GP306


title: Breast tumor 308

description: 4849554044_G: GP308


title: Breast tumor 301

description: 4849554043_G: GP301


title: Breast tumor 299

description: 4849554043_E: GP299


title: Breast tumor 303

description: 4849554044_A: GP303


title: Breast tumor 305

description: 4849554044_C: GP305


title: Breast tumor 302

description: 4849554043_H: GP302


title: Breast tumor 304

description: 4849554044_B: GP304


title: 2nd Pb_rep1

city: Shanghai

first: Tian

address: 138 Yi Xue Yuan Road

institute: Fudan University

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the InnoScan 710 scanner.

data_processing: The data processing was performed using Bluefuse Multi  v3.2 (11184),algorithm  Cytochip  v2. Smoothing:  backbone=3,  Disease=3.

source_name: Oocyte

label_protocol: A Bluegnome SureRef Pack was used for sample labeling.

extract_protocol: Genomic DNA was extracted from each sample and amplified by SurePlex Kit of Bluegnome, DNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: cell type

value: 2nd polar body


title: Spindle_rep1

value: spindle


title: 1st Pb_rep1

value: 1st polar body


title: female pronucleus_rep1

value: female pronucleus


title: Heavy_LPS1h_rep2

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

description:
H4
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing four or more ribosomes per mRNA. Out of the pooled fractions, 0.3% of the volume was used.

hyb_protocol: Hybridization was performed according to the GeneChip WT Terminal Labeling and Hybridization User Manual, using a Hybridization Oven 640 and the Fluidiq Station 450 for washing and staining.

scan_protocol: Scanning was performed with a Genechip scanner 3000 7G.

data_processing: Probe sequences of pm probes were retrieved using the Bioconductor packages oligo (version 1.22.0) and pd.mogene.1.0.st.v1. Probes were mapped to the mouse RefSeq transcriptome as downloaded from the UCSC Genome Browser mm10 refGene table on February 5, 2013. Probes that match transcripts of more than one gene (as defined by a common gene symbol) were excluded. For mapping and further processing of probe information, the Bioconductor packages seqinr and Biostrings and in-house developed Perl scripts were used. Expression values were obtained and summarized at the gene level with the basicRMA() function of the oligo package and the target genes as probe set names. Index, target gene and probe sequence of all pm probes in the analysis are provided in the file mogene10st_annotation.csv.  The different fractions (cytoplasmic, free, 40S-associated, light and heavy) were pre-processed as groups. To obtain the proportion of each mRNA (without distinction of isoforms) in a specific pool, expression values (not log2-transformed) were corrected for the relative volume of the pool that was used for labeling. For further analysis, only protein-coding genes with at least four specific probes and log2 expression values above 4 in the cytoplasmic samples of treated and untreated cells were included.

source_name: RAW264.7 cells, RNA with heavy polysomes, 1 h LPS

label_protocol: Labeling was performed according to the GeneChip WT Terminal Labeling and Hybridization User Manual, using random hexamers to avoid any bias due to poly-A tail length.

growth_protocol: RAW264.7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (PAA Laboratories), 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in 5% CO2.

extract_protocol: RNA was extracted with Phenol-Chloroform-Isoamylalcohol (PCI, 25:24:1) and precipitated with Isopropanol.

treatment_protocol: RAW264.7 cells were treated with LPS (100 ng/ml, Sigma, L2630, E. coli serotype O111:B4) for 1 h.

value: RAW264.7 macrophages

tag: agent

value: LPS

tag: rna fraction

value: heavy


title: Heavy_ctrl_rep3

description:
H5
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing four or more ribosomes per mRNA. Out of the pooled fractions, 0.5% of the volume was used.

source_name: RAW264.7 cells, RNA with heavy polysomes, untreated

value: untreated


title: Breast tumor 297

description: 4849554043_C: GP297

tag: age

value: IDC

value: Yes

tag: cmtc

tag: recurrence


title: Heavy_ctrl_rep2

description:
H3
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing four or more ribosomes per mRNA. Out of the pooled fractions, 0.4% of the volume was used.


title: Ligh_LPS1h_rep3

description:
L6
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing monosomes, disomes and trisomes. Out of the pooled fractions, 1.4% of the volume was used.

source_name: RAW264.7 cells, RNA with monosomes and light polysomes, 1 h LPS

value: light


title: Breast tumor 298

description: 4849554043_D: GP298

value: Positive

value: Negative

value: no

tag: recurrence free time (months)

tag: location of recurrence

tag: used in the 284bc dataset?


title: Heavy_LPS1h_rep3

description:
H6
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing four or more ribosomes per mRNA. Out of the pooled fractions, 0.5% of the volume was used.


title: Breast tumor 296

description: 4849554043_A: GP296

tag: margin (cm)

value: IMC

value: No

tag: er

value: yes

tag: rin


title: Breast tumor 293

description: 4849554003_F: GP293

tag: tumor type

tag: tumor size (cm)

tag: pr


title: Ligh_ctrl_rep3

description:
L5
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing monosomes, disomes and trisomes. Out of the pooled fractions, 1.7% of the volume was used.

source_name: RAW264.7 cells, RNA with monosomes and light polysomes, untreated


title: Heavy_ctrl_rep1

description:
H1
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing four or more ribosomes per mRNA. Out of the pooled fractions, 0.4% of the volume was used.


title: Ligh_ctrl_rep2

description:
L3
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing monosomes, disomes and trisomes. Out of the pooled fractions, 1.4% of the volume was used.


title: Heavy_LPS1h_rep1

description:
H2
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing four or more ribosomes per mRNA. Out of the pooled fractions, 0.3% of the volume was used.


title: Ligh_LPS1h_rep2

description:
L4
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing monosomes, disomes and trisomes. Out of the pooled fractions, 1.2% of the volume was used.


title: Breast tumor 292

description: 4849554003_E: GP292

tag: tumor grade

tag: ln positive (total)

tag: lvi


title: Breast tumor 294

description: 4849554003_G: GP294

tag: eic


title: Breast tumor 295

description: 4849554003_H: GP295


title: 40S_LPS1h_rep2

description:
S4
After sucrose density gradient centrifugation, 40S-associated RNA was isolated from the fractions containing the 40S peak. Out of the pooled fractions, 3.4% of the volume was used.

source_name: RAW264.7 cells, 40S-associated RNA, 1 h LPS

tag: cell type

tag: agent

tag: rna fraction


title: Ligh_LPS1h_rep1

description:
L2
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing monosomes, disomes and trisomes. Out of the pooled fractions, 1.1% of the volume was used.


title: Breast tumor 300

description: 4849554043_F: GP300

tag: age

tag: cmtc

tag: recurrence


title: Breast tumor 291

description: 4849554003_D: GP291

tag: recurrence free time (months)

tag: location of recurrence

tag: used in the 284bc dataset?


title: 40S_ctrl_rep2

description:
S3
After sucrose density gradient centrifugation, 40S-associated RNA was isolated from the fractions containing the 40S peak. Out of the pooled fractions, 3.3% of the volume was used.

source_name: RAW264.7 cells, 40S-associated RNA, untreated


title: 40S_LPS1h_rep1

description:
S2
After sucrose density gradient centrifugation, 40S-associated RNA was isolated from the fractions containing the 40S peak. Out of the pooled fractions, 3.1% of the volume was used.


title: 40S_ctrl_rep1

description:
S1
After sucrose density gradient centrifugation, 40S-associated RNA was isolated from the fractions containing the 40S peak. Out of the pooled fractions, 2.4% of the volume was used.


title: Breast tumor 290

description: 4849554003_C: GP290

tag: margin (cm)

tag: er

tag: rin


title: Free_LPS1h_rep3

description:
F6
After sucrose density gradient centrifugation, free RNA was isolated from the fractions above the 40S peak. Out of the pooled fractions, 13.8% of the volume was used.

source_name: RAW264.7 cells, free RNA, 1 h LPS

value: free


title: 40S_LPS1h_rep3

description:
S6
After sucrose density gradient centrifugation, 40S-associated RNA was isolated from the fractions containing the 40S peak. Out of the pooled fractions, 4.6% of the volume was used.


title: 40S_ctrl_rep3

description:
S5
After sucrose density gradient centrifugation, 40S-associated RNA was isolated from the fractions containing the 40S peak. Out of the pooled fractions, 5.0% of the volume was used.


title: Light_ctrl_rep1

description:
L1
After sucrose density gradient centrifugation, ligth RNA was isolated from the fractions containing monosomes, disomes and trisomes. Out of the pooled fractions, 0.7% of the volume was used.


title: Breast tumor 287

description: 4849554002_H: GP287

tag: tumor type

tag: tumor size (cm)

tag: pr


title: Free_LPS1h_rep2

description:
F4
After sucrose density gradient centrifugation, free RNA was isolated from the fractions above the 40S peak. Out of the pooled fractions, 9.4% of the volume was used.


title: Free_ctrl_rep1

description:
F1
After sucrose density gradient centrifugation, free RNA was isolated from the fractions above the 40S peak. Out of the pooled fractions, 12.5% of the volume was used.

source_name: RAW264.7 cells, free RNA, untreated


title: Free_ctrl_rep3

description:
F5
After sucrose density gradient centrifugation, free RNA was isolated from the fractions above the 40S peak. Out of the pooled fractions, 16.7% of the volume was used.


title: Breast tumor 286

description: 4849554002_G: GP286

tag: tumor grade

tag: ln positive (total)

tag: lvi


title: Free_ctrl_rep2

description:
F3
After sucrose density gradient centrifugation, free RNA was isolated from the fractions above the 40S peak. Out of the pooled fractions, 13.5% of the volume was used.

tag: cell type

tag: agent


title: Cytoplasmic_LPS1h_rep3

description:
C6
Cytoplasmic RNA was isolated after removal of nuclei by centrifugation.

source_name: RAW264.7 cells, cytoplasmic RNA, 1 h LPS

tag: rna fraction

value: cytoplasmic


title: Free_LPS1h_rep1

description:
F2
After sucrose density gradient centrifugation, free RNA was isolated from the fractions above the 40S peak. Out of the pooled fractions, 12.5% of the volume was used.


title: Cytoplasmic_LPS1h_rep2

description:
C4
Cytoplasmic RNA was isolated after removal of nuclei by centrifugation.


title: Breast tumor 285

description: 4849554002_F: GP285

tag: age

tag: eic

tag: cmtc


title: Breast tumor 289

description: 4849554003_B: GP289

tag: recurrence

tag: recurrence free time (months)

tag: location of recurrence


title: Breast tumor 284

description: 4849554002_E: GP284

tag: margin (cm)

tag: er

tag: used in the 284bc dataset?


title: Cytoplasmic_LPS1h_rep1

description:
C2
Cytoplasmic RNA was isolated after removal of nuclei by centrifugation.


title: Cytoplasmic_ctrl_rep1

description:
C1
Cytoplasmic RNA was isolated after removal of nuclei by centrifugation.

source_name: RAW264.7 cells, cytoplasmic RNA, untreated


title: Cytoplasmic_ctrl_rep3

description:
C5
Cytoplasmic RNA was isolated after removal of nuclei by centrifugation.


title: Breast tumor 288

description: 4849554003_A: GP288

tag: tumor type

tag: tumor size (cm)

tag: rin


title: Breast tumor 283

description: 4849554002_D: GP283

value: ILC

tag: tumor grade

tag: ln positive (total)

tag: pr


title: Cytoplasmic_ctrl_rep2

description:
C3
Cytoplasmic RNA was isolated after removal of nuclei by centrifugation.

tag: cell type

tag: agent


title: Breast tumor 282

description: 4849554002_C: GP282

tag: age

tag: lvi


title: Breast tumor 280

description: 4849554002_A: GP280

tag: eic

tag: cmtc


title: Breast tumor 279

description: 4849554001_H: GP279

tag: recurrence

tag: recurrence free time (months)


title: Breast tumor 281

description: 4849554002_B: GP281

tag: margin (cm)

tag: location of recurrence

value: liver


title: Breast tumor 277

description: 4849554001_E: GP277

tag: er

tag: used in the 284bc dataset?


title: Breast tumor 276

description: 4849554001_D: GP276

tag: tumor type

tag: tumor size (cm)


title: M4685

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University

description: SAMPLE 14

hyb_protocol: Standard NimbleGen protocol (http://www.nimblegen.com/support/dna-microarray-support.html); briefly, test and control samples were hybridized on the 385K tiled array,containing one probe every ~5.8kb (GPL11620).

scan_protocol: Standard NimbleGen protocol (http://www.nimblegen.com/support/dna-microarray-support.html); briefly, data was scanned using the NimbleGen MS 200 Microarray Scanner and the MS 200 Data Collection Software.

data_processing: Standard NimbleGen protocol (http://www.nimblegen.com/support/dna-microarray-support.html); briefly, NimbleScan software was used to generate raw data (.pair files); spatial correction, normalization between Cy3 and Cy5 inherent differences, window averaging and CGH-segMNT Analysis were applied (.gff files).

source_name: thymic lymphoma_Rb1ΔL/+; Trp53-/-

label_protocol: Standard NimbleGen protocol (http://www.nimblegen.com/support/dna-microarray-support.html); briefly, test and control samples were labelled with Cy3 and Cy5 respectively by a Klenow reaction using Cy3 and Cy5 Random Nonomers.

extract_protocol: DNA was extracted as per the protocol entitled Preparation of Genomic DNA from Mammalian Tissue; Current Protocols in Molecular Biology (1998); Unit 2.2, Sections 2.2.1-2.2.3.

tag: strain background

value: Mixed 129/B6

tag: gender

value: Male

tag: genotype/variation

tag: tissue/cell type

value: Thymic Lymphoma

source_name: pooled male ctrl DNA_wild type

value: wild type


title: Breast tumor 274

description: 4849554001_B: GP274

value: IDC

tag: tumor grade

tag: ln positive (total)

tag: pr

tag: rin


title: Breast tumor 275

description: 4849554001_C: GP275

tag: age

tag: lvi

tag: eic

tag: cmtc


title: Breast tumor 278

description: 4849554001_G: GP278

tag: margin (cm)

value: Yes

tag: recurrence

tag: recurrence free time (months)

tag: location of recurrence


title: Cy5-miR-182-3p_Cy3-20CL

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.

scan_protocol: Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version A.7.5.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Feature Extraction Software (version A.7.5.1).

source_name: miR-182-3p-transfection in SK-LC-7

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: cell line

value: mixture of 20 cell ines


title: Cy5-NC_Cy3-20CL

source_name: NC-transfection in SK-LC-7

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.


title: M6577

description: SAMPLE 13

tag: strain background


title: lung_87

first: Patrick

last: Grossmann

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Canacer Institute

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

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

data_processing: Raw CEL files were normalized by RMA algorithm as implemented in the justRMA function in Bioconductor/R with default parameters.

source_name: Right Middle Lobe

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

tag: gender

value: M

tag: histology

value: 871. Squamous Cell Carcinoma, Papillary


title: Breast tumor 273

description: 4849554001_A: GP273

source_name: Human primary breast tumor

tag: tumor type

tag: tumor size (cm)

tag: er

value: Positive

value: Negative

value: no

tag: used in the 284bc dataset?


title: lung_89

source_name: Left Upper Lobe

value: F

value: 869. Squamous Cell Carcinoma, NOS


title: lung_85

source_name: Right Upper Lobe

value: 57. Adenocarcinoma, Acinar Type


title: lung_88

value: 723. Non-Small Cell, Pleomorphic Type


title: Cy5-miR-30d_Cy3-20CL

source_name: miR-30d-transfection in SK-LC-7


title: Breast tumor 271

description: 4801489039_G: GP271

tag: tumor grade

tag: ln positive (total)

value: No

tag: pr

value: yes

tag: rin


title: lung_81

value: 105. Adenocarcinoma, NOS


title: Breast tumor 270

description: 4801489039_F: GP270

tag: age

tag: lvi

tag: eic

tag: cmtc


title: lung_86


title: 2-Control

description: SAMPLE 8

value: Mixed 129/B6

value: Male

tag: genotype/variation

tag: tissue/cell type

value: Liver

source_name: pooled female ctrl DNA_wild type

value: Female


title: RNA mix 5 of nomarl lungs

source_name: Normal lung

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: tissue type

value: Normal lung

tag: cell line

value: mixture of 20 cell ines


title: M5221

description: SAMPLE 2

tag: strain background

tag: gender

value: Thymic Lymphoma

value: wild type


title: F4689

description: SAMPLE 10


title: Cy5-miR-195_Cy3-20CL

source_name: miR-195-transfection in SK-LC-7


title: lung_84

tag: histology


title: F4688

description: SAMPLE 9


title: lung_82

value: M


title: F6958

description: SAMPLE 6


title: M6590

description: SAMPLE 12


title: lung_80

value: 60. Adenocarcinoma, Bronchiolo-alveolar Features


title: lung_83

value: F


title: Control

description: SAMPLE 1


title: F5683

description: SAMPLE 7


title: F6504

description: SAMPLE 3


title: M4858

description: SAMPLE 11


title: M5651

description: SAMPLE 4


title: M6927

description: SAMPLE 5


title: lung_79

value: 869. Squamous Cell Carcinoma, NOS


title: RNA mix 3 of nomarl lungs


title: lung_77


title: Breast tumor 272

description: 4801489039_H: GP272

tag: margin (cm)

tag: tumor type

value: IDC

tag: tumor size (cm)

value: Yes

tag: er

value: Positive

value: Negative

tag: recurrence

tag: recurrence free time (months)

tag: location of recurrence

value: bone


title: Breast tumor 268

description: 4801489039_D: GP268

tag: age

tag: tumor grade

tag: ln positive (total)

tag: lvi

value: No

tag: pr

value: no

tag: used in the 284bc dataset?

value: yes

tag: rin


title: lung_73

source_name: Left Lower Lobe


title: lung_72

value: 105. Adenocarcinoma, NOS


title: lung_76


title: lung_78


title: Breast tumor 267

description: 4801489039_C: GP267

tag: eic

tag: cmtc


title: Breast tumor 265

description: 4801489039_A: GP265


title: RNA mix 2 of nomarl lungs

tag: tissue type

value: Normal lung

tag: histology

tag: cell line


title: Squamous cell carcinoma 035

source_name: Primary lung tumor

value: Primary lung tumor

value: SQ

value: mixture of 20 cell ines


title: RNA mix 1 of nomarl lungs


title: Squamous cell carcinoma 033


title: Breast tumor 266

description: 4801489039_B: GP266

tag: margin (cm)

tag: tumor type

tag: tumor size (cm)


title: Breast tumor 269

description: 4801489039_E: GP269

tag: er

tag: recurrence

tag: recurrence free time (months)


title: lung_74

tag: gender


title: lung_71


title: Squamous cell carcinoma 032


title: lung_69


title: lung_68

value: M


title: lung_70

source_name: Right Lower Lobe


title: lung_75

value: 52. Adenocarcinoma With Papillary Features


title: lung_67

value: 709. Non-Small Cell


title: Breast tumor 264

description: 4801489038_H: GP264

tag: age

tag: tumor grade

tag: ln positive (total)

tag: location of recurrence


title: Breast tumor 263

description: 4801489038_G: GP263

tag: lvi

tag: pr

value: brain

tag: used in the 284bc dataset?

tag: rin


title: Breast tumor 262

description: 4801489038_F: GP262

value: IDC

tag: eic

tag: cmtc


title: Breast tumor 259

description: 4801489038_C: GP259

tag: margin (cm)

value: Yes


title: lung_60

value: F

tag: histology

value: 250. Carcinoma, Large Cell, Neuroendocrine


title: lung_59


title: lung_65

value: 870. Squamous Cell Carcinoma, Other (Specify)endobronchial


title: lung_64

value: 869. Squamous Cell Carcinoma, NOS


title: Breast tumor 261

description: 4801489038_E: GP261

tag: tumor type

tag: tumor size (cm)

value: No

value: Positive

value: Negative

value: no


title: Squamous cell carcinoma 028

tag: tissue type

value: Primary lung tumor

tag: cell line


title: Squamous cell carcinoma 029

value: SQ


title: lung_62

tag: gender

value: 105. Adenocarcinoma, NOS


title: lung_63

value: M


title: lung_57


title: Squamous cell carcinoma 025

value: mixture of 20 cell ines


title: Squamous cell carcinoma 030


title: lung_61


title: Breast tumor 260

description: 4801489038_D: GP260

tag: age

tag: er

tag: recurrence

tag: recurrence free time (months)


title: Squamous cell carcinoma 026


title: Breast tumor 258

description: 4801489038_B: GP258

tag: tumor grade

tag: ln positive (total)

tag: lvi

tag: location of recurrence


title: lung_56


title: lung_58

value: 709. Non-Small Cell


title: lung_54


title: Squamous cell carcinoma 024


title: Breast tumor 257

description: 4801489038_A: GP257

tag: eic

tag: pr

tag: used in the 284bc dataset?

value: yes

tag: rin


title: lung_55

tag: histology


title: lung_53


title: Squamous cell carcinoma 023


title: lung_66

value: 60. Adenocarcinoma, Bronchiolo-alveolar Features


title: Breast tumor 255

description: 4801489012_G: GP255

tag: margin (cm)

tag: tumor type

value: IDC

tag: tumor size (cm)

tag: cmtc


title: Breast tumor 256

description: 4801489012_H: GP256

tag: age


title: Squamous cell carcinoma 020

tag: tissue type

tag: cell line


title: Breast tumor 254

description: 4801489012_F: GP254

tag: er

tag: recurrence

tag: recurrence free time (months)


title: lung_49

tag: gender

value: F


title: lung_50


title: lung_42

value: 52. Adenocarcinoma With Papillary Features


title: lung_46


title: Squamous cell carcinoma 018


title: Squamous cell carcinoma 021


title: Squamous cell carcinoma 019


title: lung_44

value: 109. Adenocarcinoma, Papillary, NOS


title: lung_47

value: 869. Squamous Cell Carcinoma, NOS


title: lung_48


title: Breast tumor 253

description: 4801489012_E: GP253

tag: tumor grade

tag: ln positive (total)

tag: lvi

value: No

tag: location of recurrence


title: Squamous cell carcinoma 022


title: lung_52


title: lung_51


title: Squamous cell carcinoma 017


title: lung_45


title: Breast tumor 250

description: 4801489012_B: GP250

tag: eic

value: Positive

tag: pr

tag: used in the 284bc dataset?

tag: rin


title: lung_40

tag: histology


title: Breast tumor 251

description: 4801489012_C: GP251

tag: margin (cm)

tag: tumor type

tag: tumor size (cm)

value: Negative

tag: cmtc


title: lung_41


title: lung_37


title: Breast tumor 249

description: 4801489012_A: GP249

tag: age

tag: er

value: no


title: Breast tumor 247

description: 4801489011_G: GP247

value: Yes

tag: recurrence

tag: recurrence free time (months)


title: Squamous cell carcinoma 015

tag: tissue type

value: Primary lung tumor

value: SQ

tag: cell line


title: lung_35

tag: gender

value: M


title: lung_39

value: 105. Adenocarcinoma, NOS


title: lung_34


title: lung_38


title: Squamous cell carcinoma 016

value: mixture of 20 cell ines


title: Squamous cell carcinoma 013


title: Squamous cell carcinoma 014


title: lung_36


title: lung_33

value: 49. Adenocarcinoma With Mucinous Features


title: Squamous cell carcinoma 010


title: Breast tumor 248

description: 4801489011_H: GP248

tag: tumor grade

tag: ln positive (total)

tag: lvi

tag: location of recurrence

value: yes


title: Breast tumor 246

description: 4801489011_F: GP246

value: IDC

tag: eic

tag: pr

tag: used in the 284bc dataset?

tag: rin


title: Breast tumor 245

description: 4801489011_E: GP245

tag: margin (cm)

tag: tumor type

tag: tumor size (cm)


title: lung_28

value: F

tag: histology


title: lung_30


title: lung_31


title: lung_29

value: 57. Adenocarcinoma, Acinar Type


title: lung_32

value: 870. Squamous Cell Carcinoma, Other (Specify) with adeno features


title: Squamous cell carcinoma 011


title: Squamous cell carcinoma 009


title: Breast tumor 244

description: 4801489011_D: GP244

tag: age

tag: er

tag: cmtc

tag: recurrence


title: Squamous cell carcinoma 008

tag: tissue type

tag: cell line


title: lung_27

tag: gender

value: 869. Squamous Cell Carcinoma, NOS


title: lung_25

value: 109. Adenocarcinoma, Papillary, NOS


title: Breast tumor 241

description: 4801489011_A: GP241

tag: tumor grade

tag: ln positive (total)

tag: lvi

value: Positive

tag: recurrence free time (months)


title: Squamous cell carcinoma 031


title: lung_43


title: Breast tumor 240

description: 4801489010_H: GP240

value: DCIS

tag: eic

tag: pr

tag: location of recurrence

tag: used in the 284bc dataset?


title: Breast tumor 239

description: 4801489010_G: GP239

tag: margin (cm)

tag: tumor type

tag: tumor size (cm)

value: Negative

value: local

tag: rin


title: Breast tumor 243

description: 4801489011_C: GP243

tag: age

value: Yes

value: No

tag: er

tag: cmtc

value: no


title: lung_20

value: M

tag: histology


title: lung_17

tag: gender

value: 105. Adenocarcinoma, NOS


title: lung_22


title: Breast tumor 242

description: 4801489011_B: GP242

tag: tumor grade

tag: recurrence


title: lung_26


title: lung_18


title: lung_24


title: lung_19

value: 709. Non-Small Cell


title: Large cell neuroendocrine carcinoma 002

tag: tissue type

value: Primary lung tumor

value: LCNEC

tag: cell line

value: mixture of 20 cell ines


title: lung_21


title: lung_23


title: Squamous cell carcinoma 007

value: SQ


title: lung_16


title: Squamous cell carcinoma 006


title: Breast tumor 238

description: 4801489010_F: GP238

tag: ln positive (total)

tag: lvi

tag: eic

tag: recurrence free time (months)


title: lung_14


title: Large cell neuroendocrine carcinoma 001


title: lung_15

value: 94. Adenocarcinoma, Mucinous With Bronchiolo-alveolar Features


title: Breast tumor 252

description: 4801489012_D: GP252

tag: margin (cm)

value: IDC

tag: pr

tag: location of recurrence

tag: used in the 284bc dataset?

value: yes


title: Squamous cell carcinoma 004


title: Breast tumor 237

description: 4801489010_E: GP237

tag: age

tag: tumor type

tag: tumor size (cm)

value: Positive

tag: rin


title: lung_10

tag: gender

tag: histology

value: 836. Solid Type And Acinar


title: Breast tumor 236

description: 4801489010_D: GP236

tag: tumor grade

tag: er

value: Negative

tag: cmtc

tag: recurrence

value: bone, marrow


title: Breast tumor 235

description: 4801489010_C: GP235

tag: ln positive (total)

tag: lvi


title: Large cell carcinoma 018

tag: tissue type

value: LA

tag: cell line


title: lung_9


title: lung_11

value: 869. Squamous Cell Carcinoma, NOS


title: Breast tumor 234

description: 4801489010_B: GP234

tag: margin (cm)

value: Yes

tag: eic

value: No

tag: pr

value: no

tag: recurrence free time (months)


title: Breast tumor 232

description: 4801489005_H: GP232

tag: age

tag: tumor type

tag: location of recurrence

tag: used in the 284bc dataset?


title: Large cell carcinoma 016

tag: histology


title: Breast tumor 231

description: 4801489005_G: GP231

value: DCIS/IDC

tag: tumor size (cm)

tag: tumor grade

tag: rin


title: lung_12

tag: gender

value: M


title: lung_13

value: F

value: 90. Adenocarcinoma, Mixed


title: Large cell carcinoma 013

value: Primary lung tumor

value: mixture of 20 cell ines


title: Large cell carcinoma 017


title: Breast tumor 233

description: 4801489010_A: GP233

value: IDC

tag: ln positive (total)

tag: er

tag: cmtc

tag: recurrence


title: Large cell carcinoma 012

tag: tissue type

tag: cell line


title: lung_7


title: lung_8

value: 105. Adenocarcinoma, NOS


title: Large cell carcinoma 011


title: Large cell carcinoma 009


title: lung_6


title: lung_5


title: lung_4

value: 756. Papillary Type AND 60. Adenocarcinoma, Bronchiolo-alveolar Features


title: Large cell carcinoma 010


title: RNA mix 3 of nomal lungs

hyb_protocol: see miRNA Labeling and Microarray Hybricization Protocol Version 0.1 (Agilent Technologies)

scan_protocol: Cy3-sample RNA were generated and hybridized to a Human miRNA Microarray and scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software.

data_processing: Raw data was normalized by a 75 percentile shift.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I.

value: Normal lung


title: Breast tumor 230

description: 4801489005_F: GP230

tag: margin (cm)

tag: lvi

tag: eic

value: Positive

tag: pr

value: Negative

value: yes


title: Breast tumor 229

description: 4801489005_E: GP229

tag: age

tag: tumor type

tag: recurrence free time (months)

tag: location of recurrence


title: RNA mix 4 of nomal lungs

label_protocol: see miRNA Labeling and Microarray Hybricization Protocol Version 0.1 (Agilent Technologies)

tag: histology


title: RNA mix 5 of nomal lungs


title: Large cell carcinoma 015

value: LA


title: lung_2

value: 109. Adenocarcinoma, Papillary, NOS


title: RNA mix 1 of nomal lungs


title: lung_1

value: 869. Squamous Cell Carcinoma, NOS


title: Squamous cell carcinoma 035

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma

value: SQ


title: RNA mix 2 of nomal lungs


title: Breast tumor 226

description: 4482545111_H: GP226

tag: tumor size (cm)

tag: tumor grade

value: No

value: no

tag: used in the 284bc dataset?

tag: rin


title: Squamous cell carcinoma 032


title: Breast tumor 225

description: 4482545111_G: GP225

value: DCIS/IDC

tag: ln positive (total)

tag: er

tag: cmtc


title: Large cell carcinoma 006

tag: tissue type

value: Primary lung tumor

tag: cell line


title: Breast tumor 228

description: 4801489005_D: GP228

tag: margin (cm)

tag: lvi

value: Yes

tag: recurrence


title: Breast tumor 227

description: 4801489005_C: GP227

tag: age

value: IDC

tag: eic

tag: pr

value: lung


title: Large cell carcinoma 008

value: mixture of 20 cell ines


title: Large cell carcinoma 004


title: lung_3

tag: gender

value: M

value: 709. Non-Small Cell


title: Breast tumor 222

description: 4482545111_D: GP222

tag: tumor type

value: Positive

tag: recurrence free time (months)

tag: location of recurrence


title: Large cell carcinoma 005

tag: histology


title: Breast tumor 223

description: 4482545111_E: GP223

tag: tumor size (cm)

tag: tumor grade

value: Negative

tag: used in the 284bc dataset?

value: yes

tag: rin


title: Breast tumor 224

description: 4482545111_F: GP224

tag: ln positive (total)

tag: er

tag: cmtc


title: Breast tumor 221

description: 4482545111_C: GP221

tag: margin (cm)

tag: lvi


title: Squamous cell carcinoma 030

tag: tissue type


title: adenosquamous carcinoma 004

value: AS

tag: cell line


title: Squamous cell carcinoma 029


title: Breast tumor 220

description: 4482545111_B: GP220

tag: age

tag: eic

tag: pr

tag: recurrence

value: osseous, pulmonary, liver


title: Squamous cell carcinoma 033

value: Squamous cell carcinoma


title: Large cell carcinoma 007

value: LA


title: Squamous cell carcinoma 028

value: SQ


title: Squamous cell carcinoma 026


title: Large cell carcinoma 001


title: Squamous cell carcinoma 031


title: Squamous cell carcinoma 022


title: Breast tumor 219

description: 4482545111_A: GP219

tag: tumor type

value: No

value: no

tag: recurrence free time (months)

tag: location of recurrence


title: Squamous cell carcinoma 023

tag: histology


title: adenosquamous carcinoma 001

value: Primary lung tumor


title: Squamous cell carcinoma 021


title: Squamous cell carcinoma 018


title: Squamous cell carcinoma 020


title: Squamous cell carcinoma 019


title: Breast tumor 218

description: 4482545010_H: GP218

tag: tumor size (cm)

tag: tumor grade

tag: used in the 284bc dataset?


title: Squamous cell carcinoma 016


title: Squamous cell carcinoma 017


title: Squamous cell carcinoma 015


title: Squamous cell carcinoma 014


title: adenosquamous carcinoma 002


title: Squamous cell carcinoma 012


title: Breast tumor 217

description: 4482545010_G: GP217

tag: ln positive (total)

tag: er

tag: rin


title: Breast tumor 216

description: 4482545010_F: GP216

tag: margin (cm)

tag: lvi

tag: cmtc

value: axillary


title: BMPC ZBTB20 TRAP_3

city: Saint Louis

first: Yinan

state: Missouri

address: 660 South Euclid Avenue

department: Immunology and Pathology

institute: Washington University in St. Louis

hyb_protocol: Hybridization to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix) was performed by the Genome Technology Access Center core facility at Washington University in St. Louis

scan_protocol: Scanning and image acquisition were performed by the Genome Technology Access Center core facility at Washington University in St. Louis

data_processing: 8 CEL files were imported into ArrayStar (DNASTAR) for analysis. Data was normalized with RMA algorithm. Genes with greater than a 2-fold difference in mean expression between the two genotypes were selected.

source_name: Zbtb20-deficient bone marrow B220low/-CD138+ cells

label_protocol: cDNA synthesis and amplification was performed with Ovation Pico WTA system V2 (NuGEN), 5ug of amplified cDNA per sample was labelled with Encore Biotin Module (NuGEN).

growth_protocol: Chimeras were generated using Zbtb20-sufficient or Zbtb20-deficient E14.5 fetal livers. Donor cells were harvested from chimeras after 3-4 months following reconstitution.

extract_protocol: Total RNA was extracted from RLT-lyzed cells with the RNeasy Micro Kit (Qiagen).

treatment_protocol: Bones were crushed with pestle and mortar and marrow was separated from bone bits through a density gradient polysucrose solution. Bone marrow cells were stained with antibodies specific to B220, CD138, CD45.2 (donor) for purification via MACS and FACS. FACS-purified B220low/-CD138 cells were lyzed immediately with RLT buffer (Qiagen).

tag: cell type

value: bone marrow B220low/-CD138+ cells

tag: source

value: Zbtb20-deficient E14.5 fetal livers


title: BMPC ZBTB20 WT_4

source_name: Zbtb20-sufficient bone marrow B220low/-CD138+ cells

value: Zbtb20-sufficient E14.5 fetal livers


title: Squamous cell carcinoma 013

tag: tissue type


title: Squamous cell carcinoma 009


title: Squamous cell carcinoma 008


title: Squamous cell carcinoma 006


title: BMPC ZBTB20 WT_3


title: Squamous cell carcinoma 007


title: Squamous cell carcinoma 010


title: Squamous cell carcinoma 011


title: Breast tumor 214

description: 4482545010_D: GP214

tag: age

value: IDC

tag: eic

tag: pr

tag: recurrence


title: BMPC ZBTB20 WT_2


title: Breast tumor 213

description: 4482545010_C: GP213

tag: tumor type

tag: recurrence free time (months)

tag: location of recurrence


title: Breast tumor 212

description: 4482545010_B: GP212

value: DCIS/IDC

tag: tumor size (cm)

tag: tumor grade

tag: used in the 284bc dataset?


title: Breast tumor 211

description: 4418463227_H: GP211

tag: ln positive (total)

tag: er

value: Positive

tag: rin


title: BMPC ZBTB20 WT_1


title: Squamous cell carcinoma 004

tag: histology


title: Large cell neuroendocrine carcinoma 002

source_name: Large cell neuroendocrine carcinoma

value: Large cell neuroendocrine carcinoma

value: LCNEC


title: BMPC ZBTB20 TRAP_2

tag: cell type


title: Large cell carcinoma 018

source_name: Large cell carcinoma

value: Large cell carcinoma


title: Breast tumor 210

description: 4418463227_G: GP210

tag: margin (cm)

tag: lvi

tag: cmtc

value: yes


title: Large cell neuroendocrine carcinoma 001

tag: tissue type


title: BMPC ZBTB20 TRAP_1

tag: source


title: Large cell carcinoma 017


title: Large cell carcinoma 016


title: Breast tumor 215

description: 4482545010_E: GP215

tag: age

tag: eic

tag: pr

value: Negative

tag: recurrence

value: liver, bone


title: Large cell carcinoma 011

value: LA


title: Large cell carcinoma 013


title: Large cell carcinoma 012


title: Breast tumor 208

description: 4418463227_E: GP208

tag: tumor type

tag: tumor size (cm)

value: No

value: Yes

tag: recurrence free time (months)

tag: location of recurrence


title: Large cell carcinoma 010


title: Breast tumor 207

description: 4418463227_D: GP207

tag: tumor grade

tag: ln positive (total)

tag: er

value: no

tag: used in the 284bc dataset?


title: Breast tumor 209

description: 4418463227_F: GP209

tag: margin (cm)

value: FEA

tag: rin


title: All live sorted spinal cord cells, age E17.5 biological rep. 1

city: San Francisco

first: David

last: Rowitch

state: CA

address: 35 Medical Center Way, RMB 932D

department: Institute for Regenerative Medicine

institute: University of California-San Francisco

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
data preprocessed in R using Bioconductor suite- oligo package/RMA algorithm used to background correct, normalize, and summarize. Two types of analyses then performed: 1)  Limma package/treat algorithm used to assess differential expression, 2) Gene coexpression modules determined as described in Molofsky et al, Glia (2013) 61:1518
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.na30.mm9.probeset.csv

source_name: Aldh1L1-GFP flow sorted  spinal cord

label_protocol: purified RNA was amplified and biotin labeled (WT ovation, NuGen)

growth_protocol: mouse spinal cords from Aldh1l1-GFP transgenic mice on a swiss-webster background, various ages

extract_protocol: RNA was trizol purified with glycogen as a carrier molecule, DNAse digested, and further purified on an RNAeasy mini column (Qiagen)

treatment_protocol: papain dissociated and flow sorted on a BD facs aria II to isolate astrocytes (aldh1l1-GFP positive) and non-astrocytes (Aldh1l1-GFP negative),

tag: genetic background

value: Swiss-Webster

tag: cell type

value: whole spinal cord


title: Large cell carcinoma 009

tag: tissue type

tag: histology


title: Breast tumor 206

description: 4418463227_C: GP206

tag: age

tag: lvi

tag: eic

tag: cmtc


title: All live sorted spinal cord cells, age E18.5 biological rep. 3


title: All live sorted spinal cord cells, age E17.5 biological rep. 2


title: Breast tumor 205

description: 4418463227_B: GP205

tag: tumor type

tag: tumor size (cm)

tag: pr

tag: recurrence


title: Aldh1l1-GFP positive cells, age E17.5 biological rep. 2

value: Aldh1l1-GFP positive cells


title: Aldh1l1-GFP positive cells, age E17.5 biological rep. 1