title: FB4

source_name: Control (prenatally (G15) expossed to betamethasone) P14 female rat hypothalamic ARC nucleus Replicate 4


title: FS4

status: Public on Mar 06 2013

type: RNA

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

description:
FS_3-4.txt
Gene expression in hypothalamic ARC nuclei of prenatally betamethasone treated P14 male rat

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

molecule: total RNA

organism: Rattus norvegicus

source_name: Control (prenatally (G15) expossed to saline) P14 female rat hypothalamic ARC nucleus Replicate 4

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: On G15, some pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30; controls received vehicle (normal saline) instead. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males and four females.

tag: Sex

value: female

tag: strain

value: Sprague-Dawley

tag: tissue

value: hypothalamic ARC nuclei

tag: developmental stage


title: MB2

description:
MB_1-2.txt
Gene expression in hypothalamic ARC nuclei of prenatally betamethasone treated P14 male rat

source_name: Control (prenatally (G15) expossed to betamethasone) P14 male rat hypothalamic ARC nucleus Replicate 2

value: male


title: MB1

source_name: Control (prenatally (G15) expossed to betamethasone) P14 male rat hypothalamic ARC nucleus Replicate 1


title: hippocampus_normoxicControl_vehicleControl_1-Week_rep3

city: Cambridge

first: Joachim

last: Theilhaber

state: MA

address: 270 Albany Street

department: Translational Medicine

institute: Sanofi

description:
hippocampus of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 168h post-hypoxia/normoxic control condition.
Developmental baseline for hippocampal tissues.

hyb_protocol: Following fragmentation, cRNA were hybridized  on Affymetrix HT_Rat-Focus Array according to standard Affymetrix protocol. Chips were washed and stained in the  Affymetrix Fluidics Station 4500.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Probe set intensity values were summarized using the MAS5 algorithm implemented as a stand-alone command-line application. Linear scaling of samples using 75th percentile of MAS5 present probe-set intensities was used to normalize the gene expression profiles to each other.

label: biotin

source_name: hippocampus of P10 rat pup

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Post-natal day 10 (P10) Long-Evans rat pups raised in their original litters were used.

extract_protocol: Total RNA was extracted from homogenized hippocampi and cortices using Qiagen Rneasy kit.

treatment_protocol: The animals were subjected to 15 minute mild hypoxia (5% O2) or normoxic control sham event, and subsequently treated with NBQX or vehicle control through 4 repeated IP injections over a 48 h period. At the end of a specified time interval in the set {1h, 6h, 12h, 48h or 168h}, each animal was sacrificed and hippocampi and cortices isolated for gene expression profiling.

tag: compound

value: vehicleControl

tag: flagbothtissues

tag: hypoxia

value: normoxicControl

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier

tag: timetofirstszmin

value: hippocampus


title: FS2

description:
FS_1-2.txt
Gene expression in hypothalamic ARC nuclei of prenatally saline treated P14 female rat

source_name: Control (prenatally (G15) expossed to saline) P14 female rat hypothalamic ARC nucleus Replicate 2


title: DAC GB

city: Birmingham

first: sarah

last: leonard

address: Edgbaston

department: School of cancer sciences

country: United Kingdom

institute: University of Birmingham

description: RNA from xenograft bone marrow

hyb_protocol: Hybridization was performed by the Affymetrix service provider in the University of Birmingham

scan_protocol: Scanning was performed by the Affymetrix service provider in the University of Birmingham

data_processing: Data was quantile normalized. Differentially regulated genes were identified using Limma. Each drug treated sample was compared to the PBS control and the FC shown in an excel sheet.

organism: Homo sapiens

source_name: AML xenograft bone marrow treated with DAC

label_protocol: Samples were fragmented and labeled using the WT Labeling Kit (Affymetrix)

extract_protocol: RNA was extracted from the xenograft bone marrow using the Qiagen all prep kit

value: bone marrow

tag: disease

value: paediatric AML


title: hippocampus_normoxicControl_vehicleControl_1-Week_rep2


title: D/A RL

description: RNA from xenograft bone marrow

source_name: AML xenograft bone marrow treated with D/A


title: hippocampus_normoxicControl_vehicleControl_48-hour_rep5

description:
hippocampus of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 48h post-hypoxia/normoxic control condition.
Developmental baseline for hippocampal tissues.


title: hippocampus_normoxicControl_vehicleControl_1-Week_rep1


title: D/A GB

description: RNA from xenograft bone marrow


title: hippocampus_normoxicControl_vehicleControl_1-Week_rep4


title: hippocampus_normoxicControl_vehicleControl_48-hour_rep2


title: hippocampus_normoxicControl_vehicleControl_48-hour_rep3


title: hippocampus_normoxicControl_vehicleControl_12-Hour_rep4

description:
hippocampus of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 12h post-hypoxia/normoxic control condition.
Developmental baseline for hippocampal tissues.


title: hippocampus_normoxicControl_vehicleControl_48-hour_rep1


title: MS2

description:
MS_1-2.txt
Gene expression in hypothalamic ARC nuclei of prenatally saline treated P14 male rat

source_name: Control (prenatally (G15) expossed to saline) P14 male rat hypothalamic ARC nucleus Replicate 2


title: D+A RL

description: RNA from xenograft bone marrow

source_name: AML xenograft bone marrow treated with D+A


title: hippocampus_normoxicControl_vehicleControl_12-Hour_rep1


title: D/A RB

description: RNA from xenograft bone marrow


title: D+A GB

description: RNA from xenograft bone marrow


title: DAC RB

description: RNA from xenograft bone marrow


title: hippocampus_normoxicControl_vehicleControl_1-Week_rep5


title: hippocampus_normoxicControl_vehicleControl_48-hour_rep4


title: hippocampus_normoxicControl_vehicleControl_12-Hour_rep2


title: MS3

description:
MS_3-4.txt
Gene expression in hypothalamic ARC nuclei of prenatally saline treated P14 male rat

source_name: Control (prenatally (G15) expossed to saline) P14 male rat hypothalamic ARC nucleus Replicate 3


title: FS3

description:
FS_3-4.txt
Gene expression in hypothalamic ARC nuclei of prenatally saline treated P14 female rat

source_name: Control (prenatally (G15) expossed to saline) P14 female rat hypothalamic ARC nucleus Replicate 3


title: FS1

source_name: Control (prenatally (G15) expossed to saline) P14 female rat hypothalamic ARC nucleus Replicate 1


title: hippocampus_normoxicControl_vehicleControl_12-Hour_rep3


title: MS1

source_name: Control (prenatally (G15) expossed to saline) P14 male rat hypothalamic ARC nucleus Replicate 1


title: Ara-C RL

description: RNA from xenograft bone marrow

source_name: AML xenograft bone marrow treated with Ara-C


title: hippocampus_normoxicControl_vehicleControl_6-Hour_rep3

description:
hippocampus of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 6h post-hypoxia/normoxic control condition.
Developmental baseline for hippocampal tissues.


title: MS4

description:
MS_3-4.txt
Gene expression in hypothalamic ARC nuclei of prenatally saline treated P14 female rat

source_name: Control (prenatally (G15) expossed to saline) P14 male rat hypothalamic ARC nucleus Replicate 4


title: hippocampus_normoxicControl_vehicleControl_6-Hour_rep5


title: hippocampus_normoxicControl_vehicleControl_6-Hour_rep2


title: hippocampus_normoxicControl_vehicleControl_6-Hour_rep4


title: hippocampus_normoxicControl_vehicleControl_1-Hour_rep5

description:
hippocampus of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 1h post-hypoxia/normoxic control condition.
Developmental baseline for hippocampal tissues.


title: A/D RL

description: RNA from xenograft bone marrow

source_name: AML xenograft bone marrow treated with A/D


title: D+A RB

description: RNA from xenograft bone marrow


title: hippocampus_normoxicControl_vehicleControl_1-Hour_rep1


title: hippocampus_normoxicControl_vehicleControl_1-Hour_rep3


title: hippocampus_normoxicControl_vehicleControl_6-Hour_rep1


title: hippocampus_normoxicControl_vehicleControl_1-Hour_rep4


title: Ara-C RB

description: RNA from xenograft bone marrow


title: A/D GB

description: RNA from xenograft bone marrow


title: Ara-C GB

description: RNA from xenograft bone marrow


title: A/D RB

description: RNA from xenograft bone marrow


title: hippocampus_normoxicControl_vehicleControl_1-Hour_rep2


title: CLL91_T

status: Public on Mar 05 2013

city: Portland

first: Alexey

last: Danilov

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: Oregon Health and Science Univeristy

description:
SAMPLE 21
CLL cells from patient with CLL

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using quantile normalisation with BRB Array Tools

source_name: Human CLL cells

label_protocol: Reverse transcription using an oligo(dT) primer bearing a T7 promoter and the high yield ArrayScriptTM reverse transcriptase were used to make cDNA. The cDNA was made double-stranded and purified to use as a template for in vitro transcription with T7 RNA Polymerase and the included biotin-NTP mix

growth_protocol: Cells were cultured in RPMI with 15% FBS

extract_protocol: B-cells isolated using B-cell purification kit (Multenyi Biotech). RNA isolated using RNEasy kit (Qiagen)

treatment_protocol: MLN4924 1 microM

tag: disease state

value: CLL

tag: agent

tag: cell type

value: B-cells purified using negative selection


title: CLL50_T

description:
SAMPLE 18
CLL cells from patient with CLL

scan_protocol: Standard Illumina hybridization protocol


title: CLL41_T

description:
SAMPLE 19
CLL cells from patient with CLL


title: CLL71_T

description:
SAMPLE 12
CLL cells from patient with CLL


title: CLL108_T

description:
SAMPLE 17
CLL cells from patient with CLL


title: CLL117_T

description:
SAMPLE 15
CLL cells from patient with CLL


title: CLL41_C

description:
SAMPLE 8
CLL cells from patient with CLL

value: control


title: CLL93_T

description:
SAMPLE 22
CLL cells from patient with CLL


title: CLL173_T

description:
SAMPLE 16
CLL cells from patient with CLL


title: CLL116_T

description:
SAMPLE 14
CLL cells from patient with CLL


title: CLL115_T

description:
SAMPLE 13
CLL cells from patient with CLL


title: CLL50_C

description:
SAMPLE 7
CLL cells from patient with CLL


title: CLL114_T

description:
SAMPLE 20
CLL cells from patient with CLL


title: CLL93_C

description:
SAMPLE 11
CLL cells from patient with CLL


title: CLL91_C

description:
SAMPLE 10
CLL cells from patient with CLL


title: CLL108_C

description:
SAMPLE 6
CLL cells from patient with CLL


title: CLL173_C

description:
SAMPLE 5
CLL cells from patient with CLL


title: CLL114_C

description:
SAMPLE 9
CLL cells from patient with CLL


title: CLL71_C

description:
SAMPLE 1
CLL cells from patient with CLL


title: CLL116_C

description:
SAMPLE 3
CLL cells from patient with CLL


title: CLL117_C

description:
SAMPLE 4
CLL cells from patient with CLL


title: RM75_2054_Neg_Poly IC L_PBMC

city: New Haven

first: Ruth

middle: R

last: Montgomery

state: CT

address: 300 Cedar St.

department: Internal Medicine

institute: Yale University School of Medicine

description: PBMCs from HCV-negative patient, Poly IC L-treated

hyb_protocol: 1.5 µg of cRNA was combined with hybridization controls and hybridized to the array for 16 hours in a hybridization oven at 58°C. The chip was then washed and stained with streptavidin-Cy3.

scan_protocol: The array was scanned using the Illumina BeadArray reader.

data_processing: Microarray data from the validation cohort underwent quantile normalization using the lumi package in bioconductor [R version 2.13.2, Lumi version 2.4, Limma version 3.8.3].

source_name: PBMC

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.

extract_protocol: Total RNA from paired macrophage and PBMC samples from VL- and VL+ subjects was extracted using the RNeasy mini kit (Qiagen, CA).

tag: infection status

value: Neg

value: PBMC

tag: treatment

value: Poly IC L


title: CLL115_C

description:
SAMPLE 2
CLL cells from patient with CLL


title: RM77_3058_Pos_Mock_PBMC

description: PBMCs from HCV-positive patient, Mock-treated

value: Pos

value: Mock


title: RM76_3057_Pos_Poly IC L_PBMC

description: PBMCs from HCV-positive patient, Poly IC L-treated


title: RM70_2053_Neg_Mock_PBMC

description: PBMCs from HCV-negative patient, Mock-treated


title: RM69_2052_Neg_Mock_PBMC


title: RM79_3058_Pos_Poly IC L_PBMC


title: RM74_3057_Pos_Mock_PBMC


title: RM72_2053_Neg_Poly IC L_PBMC


title: RM78_3059_Pos_Mock_PBMC


title: RM71_2052_Neg_Poly IC L_PBMC


title: RM73_2054_Neg_Mock_PBMC


title: RM67_3055_Pos_Poly IC L_PBMC


title: RM65_3055_Pos_Mock_PBMC


title: RM66_3056_Pos_Mock_PBMC


title: RM68_3056_Pos_Poly IC L_PBMC


title: RM62_2051_Neg_Mock_PBMC


title: RM63_2050_Neg_Poly IC L_PBMC


title: RM64_2051_Neg_Poly IC L_PBMC


title: input vs Alx3 IP

type: genomic

city: Shinagawa

first: Atsushi

last: Yamada

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

country: Japan

institute: Showa University

description: FLAG-binding DNA analysis using Agilent Mouse promoter 1M microarray

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with CGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 1 minute with 37°C CGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: genomic DNA

organism: Mus musculus

source_name: input DNA

label_protocol: IP and input DNA was amplified using WGA kit(Sigma) as following manufacturer's instructions and then purified using Qiaquick PCR prep kit (Qiagen). 4 µg of amplified enriched DNA were labeled using Bioprime kit as following manufacturer's instructions

extract_protocol: Fixation of C2C12 cellsl using formaldehyde and fragmentation using sonication and then immunoprecipitation with FLAG-monoclonal antibody using EpiQuikTM Chromatin Immunoprecipitation Kit (Epigentek) as following manufacturer's instructions. Fixed C2C12 cells were immunoprecipitated using EpiQuikTM Chromatin Immunoprecipitation Kit (Epigentek) as following manufacturer's instructions. Input DNA was prepared the 1/100 volume of sonicated mouse cell sample.

treatment_protocol: C2C12 cells were treated with hBMP2 (300 ng/ml) for 96h.

tag: cell line

source_name: FLAG-IP DNA


title: RM80_3059_Pos_Poly IC L_PBMC


title: Patient V3 fibroblasts mock, biological rep4

city: Edinburgh

first: Paul

last: Dickinson

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

institute: University of Edinburgh

description: Gene expression data from patient V3 fibroblasts with a mock treatment for 10h.

hyb_protocol: Standard Affymetrix hybridization and wash procedure FS450_0002.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner G3000 7G using the AGCC software tool.

data_processing: R/Bioconductor using RMA normalization, non-specific expression level filter of 50 applied and empirical Bayes statistical test with Benjamini-Hochberg FDR adjustment performed.

source_name: Dermal fibroblasts from patient V3, mock

label_protocol: Standard Affymetrix labeling procedure.

growth_protocol: Patient (V:3) and control fibroblasts were cultured in DMEM containing 10% FCS in 24-well plates.

extract_protocol: Total cellular RNA was isolated using the QIAgen RNeasy Plus kit protocol.

treatment_protocol: Cells were either treated with 1,000 U/ml interferon-alpha for 10 hrs or given a mock treatment.

tag: genotype/variation

value: STAT2 deficient

value: primary dermal fibroblasts

value: mock


title: RM57_2014_Neg_Mock_PBMC


title: RM58_2047_Neg_Mock_PBMC


title: Patient V3 fibroblasts mock, biological rep2


title: RM59_2014_Neg_Poly IC L_PBMC


title: RM55_3053_Pos_Poly IC L_PBMC


title: RM53_3053_Pos_Mock_PBMC


title: Patient V3 fibroblasts IFNa, biological rep4

description: Gene expression data from patient V3 fibroblasts treated with 1,000U/ml interferon-alpha for 10h.

source_name: Dermal fibroblasts from patient V3, IFNa

value: interferon-alpha (IFNa)


title: RM54_3054_Pos_Mock_PBMC


title: RM56_3054_Pos_Poly IC L_PBMC


title: Patient V3 fibroblasts mock, biological rep3


title: Patient V3 fibroblasts mock, biological rep1


title: RM60_2047_Neg_Poly IC L_PBMC


title: Patient V3 fibroblasts IFNa, biological rep1


title: Control fibroblasts mock, biological rep4

description: Gene expression data from control fibroblasts with a mock treatment for 10h.

source_name: Dermal fibroblasts from control, mock

value: wild type


title: RM51_2049_Neg_Poly IC L_PBMC


title: Patient V3 fibroblasts IFNa, biological rep2


title: RM49_2049_Neg_Mock_PBMC


title: RM61_2050_Neg_Mock_PBMC


title: RM52_3052_Pos_Poly IC L_PBMC


title: RM50_3052_Pos_Mock_PBMC


title: Patient V3 fibroblasts IFNa, biological rep3


title: Control fibroblasts mock, biological rep3


title: Control fibroblasts mock, biological rep2


title: RM47_3050_Pos_Poly IC L_PBMC


title: PGK12.1ES_H4K16ac_genome tiling

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: NimbleGen genome tiling array 2007-07-27_MM8_TILE_ChIP_10_HX1 was used.

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates

source_name: H4K16ac ChIP DNA from mouse female PGK12.1 ES cells

label_protocol: Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection.

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody . Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.

treatment_protocol: No treatment

tag: genotype

value: Wild type XX

value: PGK12.1 ES

tag: strain

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

tag: chip antibody

source_name: ChIP input DNA

tag: sample type

value: input

tag: antibody


title: RM46_2048_Neg_Mock_PBMC


title: RM45_3050_Pos_Mock_PBMC


title: Sm1021 innoculated roots-40dpi-biological rep3

city: Minneapolis

first: Kevin

middle: A

last: Silverstein

state: MN

address: 599 Walter Library, 117 Pleasant St SE

department: Minnesota Supercomuting Institute

institute: Universtiy of Minnesota

description: Gene expression data from 40 dpi root segments excluding the root tip of  plants innoculated with Sm1021 WT rhizobia.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on to the AtMtDEFL custom Array. GeneChips were washed and stained using the MAUI 12-bay hybridization system.

scan_protocol: GeneChips were scanned using the MAUI 12-bay hybridization system.

data_processing: Microarray normalizations and initial analyses were performed in R using custom scripts that made use of Bioconductor routines. To implement the Stable-genes Based Quantile (SBQ) normalization (Sato et al., 2007), we first combined expression data from all 11 probes within a probe set into a single expression measure using the Bioconductor expression command, using RMA-style background correction and median polish probe summarization.  These summarized values were output from R and used as input to the SBQ perl script (Sato et al., 2007).For statistical analysis, SBQ normalized signal intensity values were Log2 transformed and statistical analysis was based on a t-test or ANOVA (P<0.05) with Benjamini and Hochberg false discovery rate multiple testing correction (Benjamini and Hochberg, 1995), and the corrected p values were designated as q values.

organism: Medicago truncatula

source_name: Medicago truncatula roots were innoculated with Sm1021 WT rhizobia, and nodulated roots were harvested after 40 days.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: plant age

value: 45 days

value: inoculated with Sinorhizobium meliloti Sm1021

tag: treatment-time

value: 40 days

tag: tissue

value: roots


title: RM44_3049_Pos_Poly IC L_PBMC

value: PBMC


title: RM48_2048_Neg_Poly IC L_PBMC

value: Neg

value: Poly IC L


title: Control fibroblasts IFNa, biological rep1

description: Gene expression data from control fibroblasts treated with 1,000U/ml interferon-alpha for 10h.

source_name: Dermal fibroblasts from control, IFNa


title: Control fibroblasts IFNa, biological rep2


title: Control fibroblasts mock, biological rep1


title: Control fibroblasts IFNa, biological rep3


title: PGK12.1ES_H2AZ_genome tiling

source_name: H2AZ ChIP DNA from mouse female PGK12.1 ES cells


title: PGK12.1ES_PolIIS2p_genome tiling

source_name: PolIIS2p ChIP DNA from mouse female PGK12.1 ES cells


title: PGK12.1ES_MOF_genome tiling

source_name: MOF ChIP DNA from mouse female PGK12.1 ES cells

value: MOF


title: Sm1021 innoculated roots-40dpi-biological rep1


title: PGK12.1ES_PolIIS5p_genome tiling

source_name: PolIIS5p ChIP DNA from mouse female PGK12.1 ES cells


title: nifH innoculated roots-14dpi-biological rep3

description: Gene expression data from 14 dpi root segments excluding the root tip of  plants innoculated with nifH rhizobia mutant.

source_name: Medicago truncatula roots were innoculated with nifH rhizobia mutant, and nodulated roots were harvested after 14 days.

value: 19 days

value: inoculated with nifH mutant

value: 14 days


title: RM43_2046_Neg_Poly IC L_PBMC


title: CD15ES_PolIIS5p_genome tiling

organism: Mus musculus x Mus spretus

source_name: PolIIS5p ChIP DNA from mouse female CD15 ES cells

value: CD15 ES

value: Derived from F1 blastcysts from a BL6 female crossed to a spretus male.


title: RM42_3049_Pos_Mock_PBMC

value: Pos

value: Mock


title: CD15ES_PolII_genome tiling

source_name: PolII ChIP DNA from mouse female CD15 ES cells

value: Wild type XX

value: PolII


title: Sm1021 innoculated roots-40dpi-biological rep2

value: 45 days


title: PGK12.1ES_H3K36me3_genome tiling

source_name: H3K36me3 ChIP DNA from mouse female PGK12.1 ES cells

value: PGK12.1 ES

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

value: input


title: RM38_3059_Pos_Mock_MACRO

description: Primary Monocyte-derived Macrophages from HCV-positive patient, Mock-treated

source_name: Monocyte-derived Macrophage

value: Monocyte-derived Macrophage


title: nifH innoculated roots-14dpi-biological rep2

value: roots


title: RM39_3058_Pos_Poly IC H_MACRO

description: Primary Monocyte-derived Macrophages from HCV-positive patient, Poly IC H-treated

value: Poly IC H


title: PGK12.1ES_H2AZac_genome tiling

source_name: H2AZac ChIP DNA from mouse female PGK12.1 ES cells


title: RM41_2046_Neg_Mock_PBMC

source_name: PBMC

value: Neg

value: PBMC


title: RM37_3058_Pos_Mock_MACRO


title: bacA innoculated roots-14dpi-biological rep2

description: Gene expression data from 14 dpi root segments excluding the root tip of  plants innoculated with bacA rhizobia mutant.

source_name: Medicago truncatula roots were innoculated with bacA rhizobia mutant, and nodulated roots were harvested after 14 days.

value: 19 days

value: inoculated with bacA mutant


title: bacA innoculated roots-14dpi-biological rep3

value: 14 days


title: nifH innoculated roots-14dpi-biological rep1

value: inoculated with nifH mutant


title: RM40_3059_Pos_Poly IC H_MACRO

value: Pos


title: Sm1021 innoculated roots-7dpi-biological rep3

description: Gene expression data from 7 dpi root segments excluding the root tip of  plants innoculated with Sm1021 WT rhizobia

source_name: Medicago truncatula roots were innoculated with Sm1021 WT rhizobia, and nodulated roots were harvested after 7 days

value: 12 days

value: inoculated with Sinorhizobium meliloti Sm1021

value: 7 days


title: Control fibroblasts IFNa, biological rep4

value: wild type

value: primary dermal fibroblasts

value: interferon-alpha (IFNa)


title: Sm1021 innoculated roots-7dpi-biological rep2


title: RM34_2054_Neg_Mock_MACRO

description: Primary Monocyte-derived Macrophages from HCV-negative patient, Mock-treated

value: Mock


title: RM36_2054_Neg_Poly IC H_MACRO

description: Primary Monocyte-derived Macrophages from HCV-negative patient, Poly IC H-treated

value: Monocyte-derived Macrophage


title: RM35_2053_Neg_Poly IC H_MACRO


title: RM32_3057_Pos_Poly IC H_MACRO


title: Sm1021 innoculated roots-7dpi-biological rep1

value: roots


title: Sm1021 innoculated roots-4dpi-biological rep3

description: Gene expression data from 4 dpi root segments excluding the root tip of  plants innoculated with Sm1021 WT rhizobia

source_name: Medicago truncatula roots were innoculated with Sm1021 WT rhizobia, and nodulated roots were harvested after 4 days

value: 9 days

value: 4 days


title: RM33_2053_Neg_Mock_MACRO

value: Neg


title: Sm1021 innoculated roots-4dpi-biological rep2


title: Sm1021 innoculated roots-4dpi-biological rep1


title: RM30_3057_Pos_Mock_MACRO


title: Sm1021 innoculated roots-3dpi-biological rep3

description: Gene expression data from 3 dpi root segments excluding the root tip of  plants innoculated with Sm1021 WT rhizobia

source_name: Medicago truncatula roots were innoculated with Sm1021 WT rhizobia, and nodulated roots were harvested after 3 days

value: 8 days

value: 3 days


title: Sm1021 innoculated roots-3dpi-biological rep2


title: Sm1021 innoculated roots-3dpi-biological rep1


title: exoY innoculated roots-14dpi-biological rep3

description: Gene expression data from 14 dpi root segments excluding the root tip of  plants innoculated with exoY rhizobia mutant.

source_name: Medicago truncatula roots were innoculated with exoY rhizobia mutant, and nodulated roots were harvested after 14 days.

value: 19 days

value: inoculated with exoY mutant

value: 14 days


title: RM28_2052_Neg_Poly IC H_MACRO

value: Poly IC H


title: CD15ES_PolII-S5p_promoter

description: 2.1M Promoter tiling array using NimbleGen platform. Mouse MM9 build.

value: Wild type XX

value: CD15 ES

value: Derived from F1 female blastcysts from a BL6 female crossed to a spretus male.

source_name: ChIP input DNA

value: input


title: RM31_3056_Pos_Poly IC H_MACRO

value: Pos


title: RM26_2052_Neg_Mock_MACRO

value: Mock


title: RM24_2051_Neg_Poly IC H_MACRO

value: Monocyte-derived Macrophage


title: nodC innoculated roots-14dpi-biological rep2

description: Gene expression data from 14 dpi root segments excluding the root tip of  plants innoculated with nodC rhizobia mutant.

source_name: Medicago truncatula roots were innoculated with nodC rhizobia mutant, and nodulated roots were harvested after 14 days.

value: inoculated with nodC mutant

value: roots


title: exoY innoculated roots-14dpi-biological rep2


title: RM23_2050_Neg_Poly IC H_MACRO


title: RM29_3056_Pos_Mock_MACRO


title: exoY innoculated roots-14dpi-biological rep1


title: RM22_2051_Neg_Mock_MACRO


title: RM20_2047_Neg_Poly IC H_MACRO


title: nodC innoculated roots-14dpi-biological rep3


title: PGK12.1ES_MOFRNAi_H2AZac_promoter

source_name: H2AZac ChIP DNA from mouse female PGK12.1 ES cells treated by MOF siRNAs

treatment_protocol: MOF siRNA treatment.

value: PGK12.1 ES

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

tag: sirna

value: MOF


title: nodC innoculated roots-14dpi-biological rep1


title: bacA innoculated roots-14dpi-biological rep1

value: inoculated with bacA mutant


title: Mock roots-40dpi-biological rep3

description: Gene expression data from 40 dpi root segments excluding the root tip of  plants mock innoculated with sterile water and used as control for Sinorhizobium meliloti Sm1021 innoculated roots.

source_name: Medicago truncatula roots were treated with sterile water and harvested from mock innoculated plants after 40 days.

value: 45 days

value: mock inoculated

value: 40 days


title: PGK12.1ES_Control RNAi_H2AZac_promoter

source_name: H2AZac ChIP DNA from mouse female PGK12.1 ES cells treated by negative control siRNAs

treatment_protocol: Control RNAi treatment

value: control


title: Mock roots-7dpi-biological rep3

description: Gene expression data from 7 dpi root segments excluding the root tip of  plants mock innoculated with sterile water and used as control for Sinorhizobium meliloti Sm1021 innoculated roots.

source_name: Medicago truncatula roots were treated with sterile water and harvested from mock innoculated plants after 7 days.

value: 12 days

value: 7 days


title: Mock roots-40dpi-biological rep2


title: Mock roots-40dpi-biological rep1


title: CD15ES_PolII_promoter

value: Wild type XX

value: CD15 ES

value: Derived from F1 female blastcysts from a BL6 female crossed to a spretus male.

value: PolII


title: RM21_2050_Neg_Mock_MACRO

value: Neg

value: Monocyte-derived Macrophage

value: Mock


title: Mock roots-7dpi-biological rep2

value: roots


title: Mock roots-4dpi-biological rep3 [mc4d_3.CEL]

description: Gene expression data from 4 dpi root segments excluding the root tip of  plants mock innoculated with sterile water and used as control for Sinorhizobium meliloti Sm1021 innoculated roots.

source_name: Medicago truncatula roots were treated with sterile water and harvested from mock innoculated plants after 4 days.

value: 9 days

value: 4 days


title: RM18_2047_Neg_Mock_MACRO


title: RM17_2014_Neg_Mock_MACRO


title: RM19_2014_Neg_Poly IC H_MACRO

value: Poly IC H


title: Mock roots-7dpi-biological rep1


title: Mock roots-4dpi-biological rep2 [mc4d_2.CEL]


title: CD15ES_MOF_promoter

source_name: MOF ChIP DNA from mouse female CD15 ES cells

value: MOF

value: input


title: Mock roots-4dpi-biological rep1 [mc4d_1.CEL]

value: mock inoculated


title: RM13_3053_Pos_Mock_MACRO

value: Pos


title: RM14_3054_Pos_Mock_MACRO


title: RM15_3053_Pos_Poly IC H_MACRO


title: RM16_3054_Pos_Poly IC H_MACRO


title: RM10_3052_Pos_Mock_MACRO


title: RM12_3052_Pos_Poly IC H_MACRO


title: RM11_2049_Neg_Poly IC H_MACRO


title: Mock roots-0dpi-biological rep3

description: Gene expression data from 0 dpi root segments excluding the root tip of  plants mock innoculated with sterile water and used as control for Sinorhizobium meliloti Sm1021 innoculated roots.

source_name: Medicago truncatula roots were treated with sterile water and harvested from mock innoculated plants after 0 days.

value: 5 days

value: 0 days


title: Mock roots-0dpi-biological rep2


title: Mock roots-0dpi-biological rep1


title: RM8_2048_Neg_Poly IC H_MACRO

source_name: Monocyte-derived Macrophage


title: RM7_2048_Neg_Mock_MACRO


title: RM5_3049_Pos_Poly IC H_MACRO


title: RM6_3050_Pos_Poly IC H_MACRO


title: RM2_2046_Neg_Poly IC H_MACRO


title: 67_ein2_elf18_2h_rep3

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

country: China

institute: Huazhong Agricultural University

hyb_protocol: GeneChips were washed and stained with Fluidics Script FS450-004 in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G. The data were analyzed with Affymetrix GeneChip Operating Software version 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

data_processing: The raw data (CELL files) were subjected to GCRMA.

label: Biotin

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA was prepared according to a standard Ambion protocol from 1 μg total RNA (MessageAmp II-Biotin Enhanced Kit; Ambion). After amplification and fragmentation, 12.5 μg of cRNA was hybridized for 16 h at 45°C on GeneChip ATH1-121501 Genome Array.

growth_protocol: Arabidopsis seedlings were grown on agar plates containing 0.5X MS and 25 mM sucrose for 5-6 days under 12h light/12h dark conditions, then transferred to liquid media with 0.5X MS and 25 mM sucrose for additional 5-6 days.

extract_protocol: Total RNA was isolated with RNeasy Mini kit supplied with RNase-Free DNase set (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Whole seedlings were treated with 1 µM elf18 or Pep2

tag: time


title: RM1_2046_Neg_Mock_MACRO


title: 65_ein2_elf18_2h_rep1


title: 64_WT_elf18_2h_rep3

value: Wild-type


title: RM9_2049_Neg_Mock_MACRO


title: 63_WT_elf18_2h_rep2


title: RM3_3049_Pos_Mock_MACRO


title: RM4_3050_Pos_Mock_MACRO


title: 66_ein2_elf18_2h_rep2


title: 59_bak1_pep2_10h_rep1


title: 60_bak1_pep2_10h_rep2


title: 57_p1p2_pep2_10h_rep2

source_name: Arabidopsis_pepr1 pepr2_pep2_10h

value: pepr1-1 Pepr2-3


title: 90 days of CeCl3 administration (0.5, 1, and 2 mg/kg body weight)

city: Suzhou

first: fashui

last: Hong

state: Jiangsu

address: Renai Road 199

institute: Medical College of Soochow University

hyb_protocol: Standard Illumina hybridization protocol. cRNA from each mouse was hybridized for 18 h at 55°C on Illumina MouseWG-6 v2.0 expression beadchip, containing 45, 200 probes (Illumina, Inc., San Diego, CA, USA), according to the manufacturer’s protocol.

scan_protocol: BeadSation Illumina scanning protocol [Illumina BeadArray Reader 500]

data_processing: The data were normalised using BeadStudio

source_name: Hippocampus, CeCl3-treated

label_protocol: Biotinylated cRNA were prepared with the Ambion  Amplification Kit for Illumina arrays. cRNA was generated and labeled using the one-cycle target labeling method.

growth_protocol: All experiments were conducted during the light phase, were approved by the Animal Experimental Committee of Soochow University (Grant 2111270) and were in accordance with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals (NIH Guidelines),and were housed in polypropylene cages with corncob bedding in a controlled-environment animal room (temperature, 24±1°C; relative humidity, 60±10%; photoperiod, 12 h light/dark cycle).

extract_protocol: Total RNA was isolated using the Ambion Illumina RNA Amplification Kit (cat no. 1755) according to the manufacturer’s protocol, and stored at −80°C. RNA amplification is the standard method for preparing RNA samples for array analysis (Kacharmina et al., 1999). Total RNA was then submitted to the Biostar Genechip Inc. (Shanghai, China) where RNA quality was analyzed using a BioAnalyzer.

treatment_protocol: Three hundred animals were randomly divided into four groups (75 mice/group): control group (treated with puriﬁed water) and three experimental groups (treated with 0.5, 1, and 2 mg/kg body weight [BW] CeCl3, respectively). With regard to the dose selection in this study, we identified the average intake of Ln (1.75-2.25 mg/day) in humans (Zhu et al. 1997). The mice were weighed and the CeCl3 solutions were administered intragastrically every day for 90 days. Symptoms and mortality were carefully observed and recorded every day for 90 days (death not observed).

value: ICR

tag: gender

value: male

tag: age

value: 4 weeks

value: cerium chloride-induced


title: 62_WT_elf18_2h_rep1


title: 90 days of control

source_name: Hippocampus, control

value: control


title: DLA _irradiated-2 Gy, biological rep 1

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

description: Gene expression data of daltons lymphoma ascites cells from irradiated mouse

hyb_protocol: The fragmented and labelled cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA.

source_name: Daltons lymphoma ascites from 2 Gy irradiated mice 48 h

label_protocol: 300 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (# 1101058).

growth_protocol: DLA-cell implantation in mice was performed by transplanting 1×10⁶ Daltons lymphoma ascites cells in peritoneal cavity of 4-5 months old male Swiss albino mice, weighed 25-30 g . The animals usually survive for 18-20 days after implantation.

extract_protocol: To isolate total RNA, DLA cells were harvested from peritoneal cavity of control and irradiated mice after 48 hours of irradiation. Extraction of total RNA was performed using Trizol (invitrogen) according to the manufacturer's instructions.

treatment_protocol: 8 days after the transplantation of DLA cells, total body of the treatment group of mice were exposed to 2 Gy of electron radiation.

value: Swiss

tag: cell type

value: Daltons lymphoma ascites cells in vivo

tag: stress

value: 2 Gy dose of electron radiation


title: 58_p1p2_pep2_10h_rep3

tag: treatment


title: DLA _irradiated-2 Gy, biological rep 2


title: RM27_3055_Pos_Poly IC H_MACRO

tag: infection status

value: Monocyte-derived Macrophage

value: Poly IC H


title: 61_bak1_pep2_10h_rep3


title: DLA _control, biological rep 1

description: Gene expression data of daltons lymphoma ascites cells from non-irradiated mouse

source_name: Daltons lymphoma ascites from unirradiated mice


title: 55_WT_pep2_10h_rep3


title: 56_p1p2_pep2_10h_rep1


title: 53_WT_pep2_10h_rep1


title: DLA _control, biological rep 2


title: 37_efr_elf18_10h_rep1


city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Primary node-negative infiltrating ductal breast carcinoma (E_06_T) sample

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.10) 'affy' in R.2.15.1

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved breast tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).


title: 38_efr_elf18_10h_rep2


title: 54_WT_pep2_10h_rep2


title: 36_ein2_elf18_10h_rep3


description: Primary node-negative infiltrating ductal breast carcinoma (E_07_T) sample


description: Primary node-negative infiltrating ductal breast carcinoma (E_02_B_mamaT) sample


description: Primary node-negative infiltrating ductal breast carcinoma (E_05_E_mamaT) sample


title: 39_efr_elf18_10h_rep3


description: Primary node-negative infiltrating ductal breast carcinoma (E_04_D_mamaT) sample


description: Primary node-positive infiltrating ductal breast carcinoma (D_6T) sample


title: 32_WT_elf18_10h_rep2


title: 31_WT_elf18_10h_rep1


description: Primary node-negative infiltrating ductal breast carcinoma (E_03_C_mamaT) sample


description: Primary node-positive infiltrating ductal breast carcinoma (D_57T) sample


title: 34_ein2_elf18_10h_rep1


description: Primary node-positive infiltrating ductal breast carcinoma (D_56T) sample


description: Primary node-positive infiltrating ductal breast carcinoma (D_54T) sample


title: 33_WT_elf18_10h_rep3


description: Primary node-negative infiltrating ductal breast carcinoma (E_01_A_mamaT) sample


description: Primary node-positive infiltrating ductal breast carcinoma (D_55T) sample


title: 26_bak1_pep2_2h_rep2


title: 35_ein2_elf18_10h_rep2


description: Primary node-positive infiltrating ductal breast carcinoma (D_4T) sample


title: 25_bak1_pep2_2h_rep1


description: Primary node-positive infiltrating ductal breast carcinoma (D_46T) sample


title: RM25_3055_Pos_Mock_MACRO

description: Primary Monocyte-derived Macrophages from HCV-positive patient, Mock-treated

value: Mock


title: 27_bak1_pep2_2h_rep3


description: Primary node-positive infiltrating ductal breast carcinoma (D_39T) sample


title: 24_p1p2_pep2_2h_rep3

source_name: Arabidopsis_pepr1 pepr2_pep2_2h


description: Primary node-positive infiltrating ductal breast carcinoma (D_2T) sample


title: 20_ein2_pep2_2h_rep2


title: 22_p1p2_pep2_2h_rep1


title: 21_ein2_pep2_2h_rep3


title: 18_WT_pep2_2h_rep3


title: 23_p1p2_pep2_2h_rep2


description: Primary node-positive infiltrating ductal breast carcinoma (D_27T) sample


title: 17_WT_pep2_2h_rep2


description: Primary node-positive infiltrating ductal breast carcinoma (D_26T) sample


title: 19_ein2_pep2_2h_rep1


description: Primary node-positive infiltrating ductal breast carcinoma (D_21T) sample


description: Primary node-positive infiltrating ductal breast carcinoma (D_23T) sample


title: 14_bak1_0h_rep2

value: untreated


title: 11_p1p2_0h_rep2

source_name: Arabidopsis_pepr1 pepr2_untreated


title: 12_p1p2_0h_rep3


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_54G) sample


title: 13_bak1_0h_rep1


description: Primary node-positive infiltrating ductal breast carcinoma (D_34T) sample


description: Primary node-positive infiltrating ductal breast carcinoma (D_28T) sample


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_46G) sample


title: GBM_neurosphere_4days_4

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

institute: University of Navarra/ Clínica Universidad de Navarra

description: reanalysis of GSM520526

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: Data analysis performed using R (2.15.0) and Bioconductor packages. The function rma of package affy (1.36.0) was used for normalization

source_name: Glioblastoma multiforme cells, neurospheres, 4 days

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: Tumor cells were resuspended in serum-free DMEM/F12 medium (Invitrogen, Carlsbad, CA) containing human recombinant EGF (20 ng/ml; Sigma, St. Louis, MO), bFGF (20 ng/ml; Sigma), B-27 (20 ml per ml of medium; Invitrogen) and heparin (2 mg/ml), and seeded at a density of 3x106 live cells/60-mm plate

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Glioblastoma neurospheres were differentiated in the presence of 10% fetal calf serum and in absence of B-27 supplement for 4days

value: Brain

tag: disease status

value: Glioblastoma multiforme

tag: patient

value: neurospheres


title: GBM_differentiation_4days_1

description: reanalysis of GSM520521

source_name: Glioblastoma multiforme cells, differentiation, 4 days

value: differentiated 4 days


title: GBM_neurosphere_4days_3


title: GBM_differentiation_4days_2

description: reanalysis of GSM520523


description: Primary node-positive infiltrating ductal breast carcinoma (D_25T) sample


description: Primary node-positive infiltrating ductal breast carcinoma (D_11T) sample


title: GBM_neurosphere_4days_1

description: reanalysis of GSM520522


title: 15_bak1_0h_rep3

tag: genotype


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_39G) sample


title: GBM_differentiation_4days_3


description: Primary node-positive infiltrating ductal breast carcinoma (D_19T) sample


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_56G) sample


title: 10_p1p2_0h_rep1

value: pepr1-1 Pepr2-3


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_6G) sample


title: GBM_neurosphere_4days_2

description: reanalysis of GSM520524


title: 09_efr_0h_rep3


title: GBM_differentiation_4days_4

description: reanalysis of GSM520525


title: C7_IL-10

city: Sacramento

first: Dennis

middle: Jay

last: Montoya

state: CA

address: 2700 Stockton Blvd #2354

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

hyb_protocol: Performed by UCLA Clinical Microarray Core on Affymetrix Human Genome U133 Plus 2.0 Array

data_processing: Dchip analysis and RMA normalization using DNA-Chip Analyzer (Build date: Feb 21 2010,  www.dchip.org)

label_protocol: Performed by UCLA Clinical Microarray Core using Ambion Labeling kit

extract_protocol: Trizol protocol for RNA isolation followed by purification of RNA by Qiagen Rneasy kit

treatment_protocol: Peripheral blood monuclear cells derived through Ficoll-Hypaque from the blood of healthy human donors (n=4).  Cells adhered to tissue culture treated 6-well plates for 2 hours in 1% Fetal Bovine Serum (FBS) RPMI and then stimulated by IL-10 (R&D Systems) 10ng/ml or media alone in 10% FBS RPMI for 24 hours at 37°C, 5% CO2.

value: Peripheral blood monuclear cells

tag: stimulated with

value: IL-10 (10ng/ml) for 24hr


title: D7_IL-10

scan_protocol: Performed by UCLA Clinical Microarray Core


title: C6_media

source_name: monocytes_media alone

value: media alone for 24hr


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_55G) sample


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_34G) sample


title: 08_efr_0h_rep2


title: A7_IL-10


title: 16_WT_pep2_2h_rep1

value: Wild-type


title: 05_ein2_0h_rep2


title: D6_media


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_2G) sample


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_28G) sample


title: A6_media


title: 06_ein2_0h_rep3


title: B6_media


title: B7_IL-10


title: Rhesus macaque-testicle-22 years 74 days old

city: Shanghai

first: Zhao

last: Guodong

address: Yueyang Road

institute: PICB

description:
miRNA sequencing raw reads from post-mortem testicle of a 8104 day old human individual
lib_14

data_processing:
Basecalls performed using CASAVA version 1.4
To remove the adapter sequence from the sequence reads, we firstly used DUST algorithm to remove reads with low complexity. For the remaining reads, we trimmed them by matching the adapter sequence to the 3’-end allowing 3 mismatches. We aligned the trimmed reads to rhesus macaque genome (rheMac2) by using the bowtie algorithm.
To make our analysis comparable with previous studies, we used the human miRNA annotations instead of rhesus macaque miRNA annotations. We firstly downloaded human miRNA annotations from miRBase (Release 12) and then used the reciprocal BLAST method to get the genomic location of human miRNA ortholog in the rhesus macaque genome. Sequencing reads mapped within the proximity of the mature miRNA were used to quantify miRNA expression. We used TPM (Transcript per Million) to quantify miRNA expression profile.
Genome_build: Mmul_051212
Processed_data_file_format_and_content: The tab-delimited .txt file (linked to the Series record) includes abundance measurements (TPM values) for each Sample.

organism: Macaca mulatta

source_name: Dissected rhesus macaque post-mortem testicle

extract_protocol:
Total RNA was isolated from the frozen testicle tissue using the Trizol (Invitrogen, USA) protocol with no modifications.
Library construction_protocol: Low molecular weight RNA was isolated, ligated to the adapters, amplified, and sequenced following the Small RNA preparation protocol (Illumina, USA) with no modifications.
Instrument model: Illumina Genome Analyzer.
Library strategy:  RNA-Seq (size fractionation)

treatment_protocol: Rhesus macaque samples were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The postnatal age of all samples range from 16 days to 26 years with 2 technical replicates. All subjects were healthy and died from a sudden death which has no relation with the tissue we used. No subjects suffered a prolonged agonal state.

value: male

value: testicle


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_27G) sample


title: DGM-01270

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: department of genetic medicine id

tag: smoking status

value: NS


title: HD3 Treg

city: Bethesda

first: Alan Lap-Yin

last: Pang

state: MD

address: 49 Convent Drive, Room 2C08, MSC 4429

department: NICHD/LCG/SDG

institute: National Institutes of Health

hyb_protocol: Follow the hybridization and washing protocol set up for GeneChip Human Genome U133 Plus 2.0 arrays from Affymetrix

scan_protocol: Image was acquired by GeneChip Scanner 3000 from Affymetrix

data_processing: Scaling and normalization factors were both set as 1

source_name: Regulatory T cells isolated from healthy donor

label_protocol: Follow the manufacturer's protocol of the Two-cycle target labeling and control reagents kit from Affymetrix

extract_protocol: Extraction by TRIzol reagent and RNeasy MinElute spin column

value: blood

tag: subject status

value: healthy donor


title: 03_WT_0h_rep3


title: 02_WT_0h_rep2


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_23G) sample


title: PCa1 Treg

source_name: Regulatory T cells isolated from metastatic castration-resistant prostate cancer patient


title: Rhesus macaque-testicle-6 years 165 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 2355 day old human individual
lib_13

value: 2355 days


title: HD1 Treg


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_19G) sample


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_26G) sample


title: HUVEC_IL-33_4hours_rep2

city: OSLO

first: Guttorm

last: Haraldsen

state: OSLO

address: Sognsvannsveien 20

department: Department for Pathology

country: Norway

institute: Oslo University Hospital

description:
IL-33stim_replicate2
1674120075_E

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data was pre-processed by Illumina’s BeadStudio software V2.

source_name: Confluent HUVEC, stimulated with IL-33 50ng/ml for 4 hours

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™-96 RNA Amplification Kit

growth_protocol: Pooled HUVEC from 10 donors were seeded 10.000 cells/cm2 and cultured for 4 days in MCDB 131 with 7.5% FBS, 10 ng/ml EGF, 1 ng/ml bFGF, 1μg/ml hydrocortisone, 50 μg/ml gentamicin, 250 ng/ml fungizone and 1% L-glutamine. Cells were maintained at 37°C in human 95% air/ 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to instructions of the manufacturer.

treatment_protocol: Stimulation for 4 hours with IL-1β 0.5 ng/ml or IL-33 50 ng/ml. Control cells were given fresh medium.

tag: protocol

value: HUVEC pool of 10 donors


title: PCa2 Treg

tag: tissue

value: metastatic castration-resistant prostate cancer patient


title: PCa3 Treg


title: Rhesus macaque-testicle-3 year 110 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 1205 day old human individual
lib_11

value: 1205 days


title: 04_ein2_0h_rep1

value: untreated


title: Rhesus macaque-testicle-4 year 27 days old_rep2

description:
miRNA sequencing raw reads from post-mortem testicle of a 1487 day old human individual
lib_12

value: 1487 days


title: HUVEC_medium_rep1

description:
control_replicate1
1674120075_D

source_name: Confluent HUVEC, given medium for 4 hours (control)

value: control


description: Lymph node metastasis from infiltrating ductal breast carcinoma (C_25G) sample


description: Lymph node metastasis from infiltrating ductal breast carcinoma (B_57G+) sample


title: Rhesus macaque-testicle-215 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 215 day old human individual
lib_09

value: 215 days


title: G63_14d

hyb_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array instruction manual using a Tecan HS 4800™ hybridization station (Tecan, Austria). Samples were hybridized onto miRNA miRCURY™ LNA Array version 5th Generation (Exiqon)

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al.) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm after removal of empty spots and controls

source_name: GBM neurospheres derived from a tumor sample of G63 patient upon 14 days of differentiation

label_protocol: 1000 ng of total RNA were labeled with miRCURY Hy3/Hy5 Power labeling kit (Exiqon) . Each individual sample was labeled with Hy3 and the common reference pool of all samples with Hy5.

extract_protocol: Total RNA from the GBM cell lines G52, G63, G59, GN1C and G97C, at the neurosphere state or after 4 or 14 days of differentiation, was extracted using mirVana miRNA Isolation Kit (Ambion) and analyzed with the 2100 Bioanalyzer (Agilent). All of the samples showed a RIN value of ≥ 8.0.

treatment_protocol: Glioblastoma neurospheres were differentiated in the presence of 10% fetal calf serum and in absence of B-27 supplement for 4 and 14 days

source_name: common reference: a pool of all samples

tag: reference

value: pool of all samples


title: G63_4d

source_name: GBM neurospheres derived from a tumor sample of G63 patient upon 4 days of differentiation


title: G52_14d

source_name: GBM neurospheres derived from a tumor sample of G52 patient upon 14 days of differentiation


title: G52_4d

source_name: GBM neurospheres derived from a tumor sample of G52 patient upon 4 days of differentiation


title: HUVEC_IL-1_4hours_rep2

description:
IL-1stim_replicate2
1674120075_F

source_name: Confluent HUVEC, stimulated with IL-1b 0.5ng/ml for 4 hours


title: Rhesus macaque-testicle-16 days old_rep2

description:
miRNA sequencing raw reads from post-mortem testicle of a 16 day old human individual
lib_08

value: 16 days


title: HD2 Treg


title: HUVEC_medium_rep2

description:
control_replicate2
1674120075_C


title: HUVEC_IL-1_4hours_rep1

description:
IL-1stim_replicate1
1674120075_A

value: stimulated with IL-1b 0.5ng/ml for 4 hours


title: 07_efr_0h_rep1

tag: time


title: Rhesus macaque-testicle-2 years 9 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 739 day old human individual
lib_10

tag: gender

value: 739 days


title: GN1C_14d

source_name: GBM neurospheres derived from a tumor sample of GN1C patient upon 14 days of differentiation


title: 01_WT_0h_rep1

value: Wild-type


title: G52_NS

source_name: GBM neurospheres derived from a tumor sample of G52 patient


title: G63_NS

source_name: GBM neurospheres derived from a tumor sample of G63 patient


title: GN1C_4d

source_name: GBM neurospheres derived from a tumor sample of GN1C patient upon 4 days of differentiation


title: GN1C_NS

source_name: GBM neurospheres derived from a tumor sample of GN1C patient


title: G97C_4d

source_name: GBM neurospheres derived from a tumor sample of G97C patient upon 4 days of differentiation


title: Rhesus macaque-testicle-7 years 15 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 2570 day old human individual
lib_06

source_name: Dissected rhesus macaque post-mortem testicle

value: male

tag: age

value: 2570 days

value: testicle


title: Unaffected lymp node (A_57G-)

description: Unaffected lymp node (A_57G-) sample

source_name: Unaffected lymp node (A_57G-)

value: Unaffected lymph node


title: Rhesus macaque-testicle-4 years 27 days old_rep1

description:
miRNA sequencing raw reads from post-mortem testicle of a 1487 day old human individual
lib_05


title: Rhesus macaque-testicle-3 years 40 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 1135 day old human individual
lib_04

value: 1135 days


title: G97C_14d

source_name: GBM neurospheres derived from a tumor sample of G97C patient upon 14 days of differentiation

tag: cell type


title: G97C_NS

source_name: GBM neurospheres derived from a tumor sample of G97C patient


title: G59_14d

source_name: GBM neurospheres derived from a tumor sample of G59 patient upon 14 days of differentiation


title: Rhesus macaque-testicle-1 years 106 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 471 day old human individual
lib_03

value: 471 days


title: Rhesus macaque-testicle-16 days old_rep1

description:
miRNA sequencing raw reads from post-mortem testicle of a 16 day old human individual
lib_01


title: Rhesus macaque-testicle-20 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 20 day old human individual
lib_02

value: 20 days


title: G59_NS

source_name: GBM neurospheres derived from a tumor sample of G59 patient


title: Unaffected lymp node (A_4G-)

description: Unaffected lymp node (A_4G-) sample

source_name: Unaffected lymp node (A_4G-)


description: Lymph node metastasis from infiltrating ductal breast carcinoma (B_4G+) sample


title: Unaffected lymp node (A_11G-)

description: Unaffected lymp node (A_11G-) sample

source_name: Unaffected lymp node (A_11G-)


title: M. sedula - Autotrophic Carbon Rich (ACR) vs Heterotrophic (HTR)

city: Raleigh

first: Aaron

last: Hawkins

state: North Carolina

address: 840 Main Campus Dr

department: Chemical and Biomolecular Engineering

institute: North Carolina State Universit

description: Scatterplots of signal intensities are reviewed to check for balance between channels.

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 3ml 10% SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95C in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42C to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42C with 2X SSC + 0.2% SDS; 1 wash cycle at RT with 0.5X SSC + 0.2% SDS; 1 wash cycles at RT with 0.5X SSC; final wash with 0.05X SCC.

scan_protocol: Images were aquired with a GenePix 4000B with automatic calculation of PMT gain.

data_processing: Signals for each channel were obtained using GenePix Pro v6.0 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once all slides are quantitated, data from all slides in loop were analyzed with JMP Genomics 3.1 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

organism: Metallosphaera sedula DSM 5348

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy3 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol: Cells was grown aerobically at 70°C in a shaking oil bath (90 rpm) under autotrophic conditions on DSMZ medium 88 at pH 2 with a headspace concentration of 33% H2, 8% CO2, 12% O2, balance N2. Cell growth was scaled up from 300 ml in sealed 1L bottles to 2 liters in a stirred bench-top glass fermentor (Applikon), also on DSMZ medium 88 (pH 2) at 70°C, with agitation at 250 rpm. Two separately regulated gas feeds were used such that flow rates were held constant for all conditions at 1 ml/min for the hydrogen/CO2 gas mixes (composition varied) and 100 ml/min for air (composition - 78% N2, 21% O2, 0.03% CO2).  For the autotrophic carbon rich (ACR) condition the feed was H2 (80%) and CO2 (20%).

extract_protocol: At harvest, cells were quickly chilled and then centrifuged at 6000 x g for 15 minutes at 4C. RNA was extracted using Trizol (Invitrogen) and purified using an RNeasy Mini Kit (Qiagen).

value: M. sedula DSMZ 5348 - whole cells

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy5 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol: Cells was grown aerobically at 70°C in a shaking oil bath (90 rpm) under heterotrophic conditions on DSMZ medium 88 supplemented with 0.1% tryptone at pH 2. Cell growth was scaled up from 300 ml in 1L bottles to 2 liters in a stirred bench-top glass fermentor (Applikon), also on DSMZ medium 88 with 0.1% tryptone (pH 2) at 70°C, with agitation at 250 rpm. Two separately regulated gas feeds were used such that flow rates were held constant for all conditions at 1 ml/min for the hydrogen/CO2 gas mixes (composition varied) and 100 ml/min for air (composition - 78% N2, 21% O2, 0.03% CO2). For the heterotrophic (HTR) condition the feed was N2 (80%) and CO2 (20%).


title: M. sedula - Autotrophic Carbon Limited (ACL) vs Heterotrophic (HTR)

growth_protocol: Cells was grown aerobically at 70°C in a shaking oil bath (90 rpm) under autotrophic conditions on DSMZ medium 88 at pH 2 with a headspace concentration of 33% H2, 8% CO2, 12% O2, balance N2. Cell growth was scaled up from 300 ml in sealed 1L bottles to 2 liters in a stirred bench-top glass fermentor (Applikon), also on DSMZ medium 88 (pH 2) at 70°C, with agitation at 250 rpm. Two separately regulated gas feeds were used such that flow rates were held constant for all conditions at 1 ml/min for the hydrogen/CO2 gas mixes (composition varied) and 100 ml/min for air (composition - 78% N2, 21% O2, 0.03% CO2).  For the autotrophic carbon-limited (ACL) condition the feed was H2 (80%) and N2 (20%).

growth_protocol: Cells was grown aerobically at 70°C in a shaking oil bath (90 rpm) under heterotrophic conditions on DSMZ medium 88 supplemented with 0.1% tryptone at pH 2. Cell growth was scaled up from 300 ml in 1L bottles to 2 liters in a stirred bench-top glass fermentor (Applikon), also on DSMZ medium 88 with 0.1% tryptone (pH 2) at 70°C, with agitation at 250 rpm. Two separately regulated gas feeds were used such that flow rates were held constant for all conditions at 1 ml/min for the hydrogen/CO2 gas mixes (composition varied) and 100 ml/min for air (composition - 78% N2, 21% O2, 0.03% CO2).  For the heterotrophic (HTR) condition the feed was N2 (80%) and CO2 (20%).


title: M. sedula - Autotrophic Carbon Limited (ACL) vs Autotrophic Carbon Rich (ACR)


title: E12.5 primordial germ cells, male, biological rep1

status: Public on Mar 04 2013

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

description: EA0964_04_E12.5M rep1

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization).

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

source_name: E12.5 male PGC

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay).

growth_protocol:
BDF1 female mice were mated with stella-EGFP transgenic males (B6/CBA mixed background), and embryos were collected at the indicated embryonic days.
Reference for stella-EGFP transgenic mice: Payer et al., 2006, Genesis 44: 75-83 (PMID 16437550).

extract_protocol: Total RNA was isolated with the Qiagen RNeasy Micro Kit according to the manufacturer's instructions. cDNA was synthesized and amplified as described in Kurimoto et al. 2006, NAR 34: e42, with minor modifications (initial PCR was performed with 12 cycles), from 5ng total RNA (equivalent to 500 cells). T7 promoters were added to the 3' end of the cDNAs with PCR. cDNA was then subjected to the labeling procedure.

treatment_protocol: Genital ridges were isolated in DMEM/0.1% BSA, and treated with 0.05% Trypsin-EDTA at 37C for 10min. PGCs were purified with FACS Aria II based on fluorescence of the stella-EGFP reporter.

tag: transgene

value: stella-EGFP

value: primordial germ cells (PGCs)

value: embryonic day 12.5


title: E13.5 primordial germ cells, female, biological rep2

description: EA0964_12_E13.5F rep2

source_name: E13.5 female PGC

tag: strain/background

value: mixed

value: embryonic day 13.5

value: female


title: Rhesus macaque-testicle-26 years 28 days old

description:
miRNA sequencing raw reads from post-mortem testicle of a 9518 day old human individual
lib_07

value: 9518 days


title: E13.5 primordial germ cells, male, biological rep1

description: EA0964_05_E13.5M rep1

source_name: E13.5 male PGC


title: E12.5 primordial germ cells, female, biological rep2

description: EA0964_10_E12.5F rep2

source_name: E12.5 female PGC


title: E9.5 primordial germ cells, biological rep2

source_name: E9.5 PGC

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Kit according to the manufacturer's instructions. cDNAs were amplified with a quantitative global PCR method (Kurimoto et al., 2006, Nucleic Acids Research) using 22-cycle PCR from 5ng total RNA (equivalent to 500 cells).

tag: strain

value: embryonic day 9.5


title: E12.5 primordial germ cells, female, biological rep1

description: EA0964_03_E12.5F rep1


title: G59_4d

source_name: GBM neurospheres derived from a tumor sample of G59 patient upon 4 days of differentiation

source_name: common reference: a pool of all samples

value: pool of all samples


title: E10.5 primordial germ cells, biological rep2

description: EA0964_07_E10.5 rep2

source_name: E10.5 PGC

value: embryonic day 10.5


title: E10.5 primordial germ cells, biological rep1

description: EA0964_01_E10.5 rep1


title: HUVEC_IL-33_4hours_rep1

description:
IL-33stim_replicate1
1674120075_B

hyb_protocol: Standard Illumina hybridization protocol

source_name: Confluent HUVEC, stimulated with IL-33 50ng/ml for 4 hours

value: HUVEC pool of 10 donors


title: E12.5 primordial germ cells, male, biological rep2

description: EA0964_09_E12.5M rep2

value: male


title: E11.5 primordial germ cells, biological rep1

description: EA0964_02_E11.5 rep1

source_name: E11.5 PGC

value: embryonic day 11.5


title: E9.5 primordial germ cells, biological rep1


title: E13.5 primordial germ cells, male, biological rep2

description: EA0964_11_E13.5M rep2


title: Normal_Trp53_NPOOL30

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

hyb_protocol: 825ng of Cy3-labelled aRNA samples were co-hybridised with 825ng of Cy5-labelled reference aRNA to Whole Mouse Genome (4x44K) arrays (Agilent, G4122F). Slides were washed according to the manufacturer's instructions.

scan_protocol: Agilent dual-laser scanner (P/N: G2505B). Feature extraction was performed using Agilent software (FE 9.5.3.1)

data_processing: We used the R (2.15.1) with the limma package (3.12.1) for normalization. Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and quantile normalized.

source_name: Mammary pooled normal

label_protocol: One round amplification and labelling for microarray hybridisation was carried out using the Amino Allyl MessageAmp II aRNA kit (Ambion P/N: AM1753). Universal Mouse reference RNA (Stratagene cat. 740100-41) was amplified and labelled in the same manner.

extract_protocol: RNA was extracted from mouse mammary tumors and normal mammary glands that had been snap-frozen immediately following animal necropsy. Tissues were powdered under liquid nitrogen, homogenised in Qiashredder columns and RNA isolated using the Qiagen Allprep kit (Qiagen).

value: Female

value: FVB

value: Normal

tag: parity

value: Nulliparous

tag: pathology

source_name: Stratagene universal mouse reference

value: Stratagene universal mouse reference


title: Tumor_MetTrp53_TA2244

source_name: Mammary tumor

value: Tumor

tag: genotype

value: Multiparous

value: Adenocarcinoma


title: Normal_WT_NPOOL14

value: Wild-Type


title: Tumor_MetTrp53_TA4716

value: Spindloid


title: Normal_MetTrp53_NPOOL15

source_name: Mammary normal


title: Tumor_MetTrp53_TA4328

value: Intermediate


title: Tumor_Trp53_TA3340


title: Tumor_Trp53_TA4375_3R


title: Tumor_Trp53_TA4719_23L


title: E13.5 primordial germ cells, female, biological rep1

description: EA0964_06_E13.5F rep1

value: mixed

value: stella-EGFP

value: primordial germ cells (PGCs)

value: embryonic day 13.5

value: female


title: Normal_WT_NPOOL32


title: Normal_MetTrp53_NPOOL31


title: WD44ES_MOF_promoter

description: 2.1M Promoter tiling array using NimbleGen platform. Mouse MM8 build.

source_name: MOF ChIP DNA from mouse male WD44 ES cells

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody . Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.

value: Wild type XY

tag: cell line

value: WD44 ES

value: Derived from male BL6 blastcysts

tag: chip antibody

value: MOF

source_name: ChIP input DNA

tag: sample type

value: input

tag: antibody


title: Tumor_Trp53_TA4504

value: Female

value: FVB

value: Stratagene universal mouse reference


title: Tumor_Trp53_TA3957

value: Tumor

value: Multiparous


title: Tumor_Met_T5156

value: MMTV-Met

value: Solid Nodular Carcinoma


title: Tumor_MetTrp53_TA646

value: Nulliparous

value: Spindloid


title: WD44ES_PolII-S5p_promoter

source_name: PolIIS5p ChIP DNA from mouse male WD44 ES cells


title: Tumor_MetTrp53_TA1221

value: Poorly Differentiated Adenocarcinoma


title: Tumor_Met_T6696


title: Normal_Met_N6030

value: Normal


title: Tumor_Met_T5482


title: Normal_MetTrp53_NA66


title: Tumor_MetTrp53_TA1034


title: PGK12.1ES_H4K16ac_promoter

source_name: H4K16ac ChIP DNA from mouse female PGK12.1 ES cells

value: Wild type XX

value: PGK12.1 ES

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.


title: Tumor_Met_T5033


title: Tumor_Met_T4425

value: Adenocarcinoma


title: Tumor_MetTrp53_TA66


title: Tumor_MetTrp53_TA1471


title: Tumor_MetTrp53_TA1129


title: Tumor_Met_T4695

value: Scirrhous Adenocarcinoma


title: PGK12.1ES_H2AZ_promoter

source_name: H2AZ ChIP DNA from mouse female PGK12.1 ES cells

value: input


title: Tumor_MetTrp53_TA65

value: Female


title: Tumor_Met_T6030

value: FVB


title: Normal_MetTrp53_NA1222

value: Stratagene universal mouse reference


title: Normal_Trp53_NPOOL16


title: Normal_MetTrp53_NA1471


title: Tumor_Met_T5154

value: Tumor

value: Adenosquamous


title: Normal_Met_N4425

value: MMTV-Met

value: Multiparous


title: PGK12.1ES_MOFRNAi_H4K16ac_promoter

source_name: H4K16ac ChIP DNA from mouse female PGK12.1 ES cells treated by MOF siRNAs

tag: sirna

value: MOF


title: Tumor_Trp53_TA4719_1L

tag: tissue

value: Spindloid


title: PGK12.1ES_H3K4me3_promoter

source_name: H3K4me3 ChIP DNA from mouse female PGK12.1 ES cells


title: PGK12.1ES_MOF promoter_replicate2

source_name: MOF ChIP DNA from mouse female PGK12.1 ES cells


title: E11.5 primordial germ cells, biological rep2

description: EA0964_08_E11.5 rep2

value: mixed

value: stella-EGFP

value: primordial germ cells (PGCs)

value: embryonic day 11.5


title: BC_luminal B_No.2_mRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were performed following the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: F635 Median column as Red signal. The raw Red signal data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals.The raw Red signal data intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. Detected signals for each gene were normalized by the global normalization method (the median of the detected signal intensity was adjusted to 30).

source_name: breast cancer tissue, luminal B

label_protocol: Amino Allyl aRNA was synthesized by the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). Cy dye coupling and fragmentation were performed following the protocol supplied by TORAY Industries, Inc.

extract_protocol: RNA samples were extracted from frozen tissue using the miRNeasy Mini Kit (Qiagen).

value: breast cancer

tag: subtype

value: luminal B

tag: estrogen receptor status

value: positive

value: female


title: BC_luminal B_No.3_mRNA

tag: gender


title: Tumor_MetTrp53_TA1004

value: Female

value: Nulliparous

tag: reference


title: PGK12.1ES_H3_promoter

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates

source_name: H3 ChIP DNA from mouse female PGK12.1 ES cells

label_protocol: Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.

value: Wild type XX

value: PGK12.1 ES

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

value: input


title: BC_luminal A_No.4_mRNA

source_name: breast cancer tissue, luminal A

value: luminal A


title: Tumor_MetTrp53_TA899

value: FVB

value: Tumor

value: Intermediate

value: Stratagene universal mouse reference


title: BC_luminal A_No.3_mRNA


title: PGK12.1ES_H3ac_promoter

source_name: H3ac ChIP DNA from mouse female PGK12.1 ES cells


title: Tumor_Trp53_TA4375_23R

value: Adenocarcinoma


title: Tumor_MetTrp53_TA2843

value: Spindloid


title: PGK12.1ES_MOFRNAi_PolIIS5p_promoter

source_name: PolIIS5p ChIP DNA from mouse female PGK12.1 ES cells treated by MOF siRNAs (Invitrogen).

value: MOF


title: E176_31_Leptin_1_A

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: cRNA, according to manufacturer's recommendations

data_processing: RMA; RMA preprocessed log2 expression values

source_name: PBMC

label_protocol: biotin, according to manufacturer's recommendations

extract_protocol: RNA was isolated from PBMCs using the manufacturer’s protocol for Trizol Reagent (Invitrogen, Grand Island, NY) and further purified using RNAeasy spin columns (Qiagen, Valencia, CA). RNA concentration and purity were determined from 260nm/280 nm absorbances. RNA integrity was determined using the Agilent 2100 BioChip (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Human PBMCs were isolated by stratifying of whole blood on Ficoll-Paque PREMIUM (GE Healthcare; Pscataway, NJ). Subjects were randomized in a 1:1 fashion to receive either metreleptin or placebo, for a period of 36 weeks in the form of a self-administered daily subcutaneous injection.

tag: sample

tag: treatment

value: Leptin

tag: weeks of treatment

tag: subject


title: E176_30_Placebo_2_A

scan_protocol: according to manufacturer's recommendations

value: Placebo


title: BC_luminal A_No.2_mRNA

value: breast cancer

value: positive

value: female


title: E176_31_Leptin_2_A


title: 21 hr-2

city: San Antonio

first: Keith

last: Ashcraft

state: TX

address: 8403 Floyd Curl Dr.

institute: UT Health Science Center San Antonio

description: replicate 2

data_processing: Raw data was analyzed using GenomeStudio v2011.1

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total RNA was extracted using Trizol

value: abdominal adipose tissue

tag: cell type

value: primary adipose stromal cells (ASCs)

tag: culture condition

value: 3d Collagen gel for 21 hrs


title: BC_luminal A_No.1_mRNA


title: E176_32_Leptin_3_A


title: 21 hr-3

description: replicate 3


title: Peripheral human B cells replicate 6

city: Davos Platz

first: Willem

last: van de Veen

address: Oberestrasse 22

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research

description: Biological replicate 6 of 6.

hyb_protocol: The labeled cDNAs were combined and hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4 x 44K. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using a DNA microarray scanner (Agilent Technologies).

data_processing: Preprocessing of the microarray data include normalization using the Lowess algorithm and incorporation of the Rosetta error model. The resulting ratios for each reporter between the signal intensities of the co-hybridized IL-10- and IL-10+ samples were transformed to logarithms to base 2 (log2 ratios). Individual signal detection- and ratio- p-values were calculated (Rosetta error model, Rosetta Inpharmatics, LLC) to evaluate the reliability of signal, and expression based on signal to background intensities of both co-hybridized samples per array. Expression differences for individual reporters between the IL-10- and IL-10+ sample groups were identified by one-group t-test followed by multiple testing correction (Benjamini & Hochberg) on the log2 ratio data and effect size (fold change). Candidate genes with differential expression were selected if they passed a corrected p-value ≤ 0.05 in the group-wise comparison. Genes were additionally filtered for detection p-value ≤ 0.01 in at least four out of six samples per channel, followed by selection of array data sets with ratio p-values ≤ 0.01 in all six replicate experiments.

source_name: CD19+IL-10+ cells

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling in a Klenow Fragment reaction.

growth_protocol: Human B cells were isolated from peripheral blood by magnetic activated cell sorting (using B cell isolation kit II, Miltenyi Biotec) and cultured for 3 days with 1 µM CpG2006 (Microsynth).

extract_protocol: Cell lysates were prepared in Superamp lysis buffer (Miltenyi Biotec) and mRNA isolation, cDNA synthesis and amplification was performed by Miltenyi Biotec

treatment_protocol: IL-10-secreting B cells were labeled using a cytokine secretion assay (Miltenyi Biotect) and IL-10-secreting and non-IL-10-secreting cells were sorted by flow cytometry (FACS Aria II, BD Biosciences).

tag: health status

value: Normal Healthy donor

value: Male

value: human peripheral b lymphocytes

tag: cell subset

value: IL-10-secreting B cells

source_name: CD19+IL-10- cells

value: non-IL-10-secreting B cells


title: SC-1

description: replicate 1

value: 2d culture


title: Peripheral human B cells replicate 5

description: Biological replicate 5 of 6.


title: SC-2

description: replicate 2


title: E176_30_Placebo_1_A


title: E176_29_Placebo_3_A


title: E176_31_Leptin_2_B


title: SC-3

description: replicate 3


title: E176_31_Leptin_1_B


title: E176_31_Leptin_4_A


title: E176_32_Leptin_1_A


title: Peripheral human B cells replicate 4

description: Biological replicate 4 of 6.

value: Female


title: E176_30_Placebo_4_A


title: PGK12.1ES_MOF promoter_replicate1

city: Seattle

first: Xinxian

last: Deng

address: 1959 NE Pacific St.

institute: University of Washington

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

tag: genotype

value: Wild type XX

tag: cell line

value: PGK12.1 ES

tag: strain

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

tag: chip antibody

value: input


title: Tumor_Trp53_TA3571

source_name: Mammary tumor

value: FVB

tag: tissue

value: Tumor

tag: parity

value: Nulliparous

tag: pathology

value: Spindloid

source_name: Stratagene universal mouse reference

value: Stratagene universal mouse reference


title: Peripheral human B cells replicate 3

description: Biological replicate 3 of 6.

tag: gender


title: E176_20_Leptin_2_A

value: Leptin


title: E176_31_Leptin_3_A


title: E176_32_Leptin_2_A


title: E176_32_Leptin_3_B


title: E176_30_Placebo_2_B

value: Placebo


title: E176_20_Leptin_3_A


title: Peripheral human B cells replicate 1

description: Biological replicate 1 of 6.

value: Normal Healthy donor

value: Male


title: Tumor_Met_T4425

hyb_protocol: miRNA was hybridized to Agilent 8x60K miRNA Oligo Microarrays (G4872A-038112). Arrays were washed as directed by the manufacturer.

scan_protocol: Agilent dual laser scanner (P/N: G2505B). Feature extraction was carried out using Agilent software (FE 10.7.3).

data_processing: Raw Cy3 intensities were background corrected using the RMA background correction algorithm. Data was log2 transformed and quantile normalized.

label_protocol: Labeling was carried out with the miRNA Complete Labeling and Hyb Kit and microRNA Spike-in kit (both Agilent).

extract_protocol: RNA was extracted from mouse mammary tumors and normal mammary glands that had been snap-frozen immediately following animal necropsy. Tissues were powdered under liquid nitrogen, homogenised in Qiashredder columns and RNA isolated using the miRNeasy Mini Kit (Qiagen).

value: MMTV-Met

value: Multiparous

value: Adenocarcinoma


title: E176_29_Placebo_2_A


title: E176_09_Leptin_4_A


title: E176_31_Leptin_4_B


title: E176_30_Placebo_3_A


title: E176_30_Placebo_4_B


title: Tumor_MetTrp53_TA1005

value: Female

tag: reference


title: E176_29_Placebo_4_A

tag: sample


title: E176_32_Leptin_1_B

tag: treatment


title: E176_27_Leptin_2_A

tag: weeks of treatment


title: Peripheral human B cells replicate 2

description: Biological replicate 2 of 6.

value: human peripheral b lymphocytes

value: IL-10-secreting B cells

value: non-IL-10-secreting B cells


title: E176_27_Leptin_3_A

tag: subject


title: E176_29_Placebo_3_B


title: E176_09_Leptin_1_A


title: Tumor_MetTrp53_TA1005


title: Tumor_Trp53_TA4719_1L


title: Tumor_MetTrp53_TA1471


title: E176_29_Placebo_1_A


title: E176_15_Leptin_4_A


title: E176_09_Leptin_3_A


title: E176_30_Placebo_1_B


title: E176_15_Leptin_3_A


title: BC_luminal B_No.4_mRNA

value: breast cancer

tag: subtype

value: luminal B

tag: estrogen receptor status

value: positive

value: female


title: E176_15_Leptin_2_A


title: E176_31_Leptin_3_B


title: Tumor_Met_TA1349

value: FVB

value: Tumor

value: Solid Nodular Carcinoma


title: E176_15_Leptin_1_A

value: Leptin


title: E176_17_Placebo_2_A

value: Placebo


title: E176_32_Leptin_2_B


title: Tumor_Met_T4695

value: Scirrhous Adenocarcinoma


title: E176_17_Placebo_4_A


title: E176_17_Placebo_3_A


title: E176_12_Placebo_4_A


title: E176_30_Placebo_3_B


title: E176_17_Placebo_1_A


title: Tumor_Trp53_TA4504

value: Spindloid


title: E176_12_Placebo_3_A


title: E176_20_Leptin_1_A


title: E176_12_Placebo_2_A


title: E176_20_Leptin_3_B


title: E176_12_Placebo_1_A


title: Tumor_MetTrp53_TA1221

value: Nulliparous

value: Poorly Differentiated Adenocarcinoma


title: E176_29_Placebo_4_B


title: E176_20_Leptin_2_B


title: Tumor_Trp53_TA3957

value: Female

value: Multiparous

value: Intermediate


title: BC_luminal B_No.1_mRNA


title: Normal_WT_NPOOL_NP

source_name: Pooled normal mammary tissue

value: Normal

value: Wild-Type


title: E176_14_Leptin_2_A


title: Tumor_MetTrp53_TA899


title: E176_29_Placebo_2_B


title: E176_14_Leptin_1_A


title: Tumor_Met_T5154

value: MMTV-Met

value: Adenosquamous


title: E176_14_Leptin_3_A


title: E176_11_Leptin_2_A


title: E176_09_Leptin_4_B


title: E176_09_Leptin_3_B


title: E176_11_Leptin_1_A


title: E176_09_Placebo_1_A


title: E176_09_Placebo_2_A


title: E176_27_Leptin_3_B


title: E176_07_Placebo_4_A


title: E176_27_Leptin_2_B


title: E176_11_Leptin_3_A


title: E176_08_Placebo_2_A


title: E176_08_Placebo_1_A


title: Tumor_MetTrp53_TA1034


title: E176_05_Placebo_4_A


title: E176_09_Leptin_1_B


title: E176_07_Placebo_2_A


title: Tumor_Met_T6030


title: E176_07_Placebo_3_A


title: E176_05_Placebo_3_A


title: E176_15_Leptin_4_B


title: Tumor_MetTrp53_TA66


title: E176_07_Placebo_1_A


title: 21 hr-1

description: replicate 1

value: female

value: abdominal adipose tissue

tag: cell type

value: primary adipose stromal cells (ASCs)

tag: culture condition

value: 3d Collagen gel for 21 hrs


title: Tumor_Trp53_TA3340

value: FVB

value: Tumor

tag: genotype


title: Tumor_Trp53_TA4719_23L

value: Adenocarcinoma


title: Tumor_Met_T5482

value: Spindloid


title: Tumor_MetTrp53_TA1129

value: Nulliparous


title: E176_04_Leptin_4_A

value: Leptin


title: E176_15_Leptin_2_B


title: Tumor_Trp53_TA4375_3R

value: Female

value: Poorly Differentiated Adenocarcinoma


title: E176_29_Placebo_1_B

value: Placebo


title: E176_05_Placebo_2_A


title: E176_15_Leptin_1_B


title: E176_01_Leptin_4_A


title: E176_15_Leptin_3_B


title: E176_04_Leptin_2_A


title: BC_luminal B_No.3_miRNA

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR Labeling Kit (Exiqon, Vedbaek, Denmark).

value: breast cancer

value: luminal B

value: positive


title: E176_17_Placebo_4_B


title: BC_luminal B_No.4_miRNA


title: E176_17_Placebo_1_B


title: E176_01_Leptin_3_A


title: Tumor_Trp53_TA4375_23R


title: E176_20_Leptin_1_B


title: Tumor_Met_T5156

value: MMTV-Met

value: Multiparous

value: Solid Nodular Carcinoma


title: Tumor_MetTrp53_TA2244


title: Normal_WT_NPOOL_MP

value: Normal

value: Wild-Type


title: E176_04_Leptin_3_A


title: BC_luminal B_No.1_miRNA

value: female


title: E176_12_Placebo_4_B


title: E176_17_Placebo_2_B


title: BC_luminal A_No.4_miRNA

value: luminal A


title: Tumor_Trp53_TA3571

value: FVB

value: Tumor


title: BC_luminal B_No.2_miRNA


title: E176_12_Placebo_2_B


title: E176_12_Placebo_3_B


title: E176_17_Placebo_3_B


title: E176_12_Placebo_1_B


title: BC_luminal A_No.3_miRNA


title: BC_luminal A_No.2_miRNA


title: BC_luminal A_No.1_miRNA


title: E176_14_Leptin_3_B


title: E176_14_Leptin_1_B


title: E176_14_Leptin_2_B


title: E176_09_Placebo_2_B


title: Normal_MetTrp53_MFP2

hyb_protocol: 2ug of sample and reference DNA were hybridised to Agilent 44K whole mouse genome CGH arrays (Agilent, G4414A). Samples were prepared using the direct method according to the manufacturer’s protocol, to which minor changes were incorporated.   Hybridization took place in a rotisserie oven for 72 hours, set to 65C and rotation speed of 20rpm.  The washing and scanning of the slides took place in an ozone free area to prevent the degradation of the  Cy5 dye.  In turn, the slides were washed according to the wash procedure B.

scan_protocol: Scanned on an Agilent High-Resolution C scanner. Feature extraction was performed using Agilent software (FE 9.5.3.1).

data_processing: Raw Cy5 and Cy3 intensities were background corrected using the Edwards log linear interpolation background correction algorithm. Data was transformed to log2 ratios and a weighted median subtraction was used to normalize within Arrays.  Duplicate probes were averaged and all probes were then reordered by genomic position.  The dataset was segmented using a Circular Binary Segmentation (CBS) algorithm.  Probes corresponding to the Met transgene were removed based on the peak observed in the MMTV-Met;Trp53fl/+ MFP sample

source_name: Mammary normal

label_protocol: DNA was prepared for array hybridisation using the Agilent Genomic DNA Enzymatic Labeling kit and labelled with Cy-5.   Cy3-labelled genomic DNA extracted from mouse spleen was used as a reference.

extract_protocol: Genomic DNA was isolated from snap frozen tissue pieces using the Qiagen Allprep kit (as described for RNA isolation).

source_name: Normal Splenic DNA

value: Normal Splenic DNA


title: E176_11_Leptin_2_B

value: Leptin


title: Normal_MetTrp53_MFP3

value: Female


title: Tumor_Trp53_A4504.4R

value: Spindloid


title: Tumor_Trp53_A4719.1L


title: Tumor_Trp53_A3571


title: Tumor_Trp53_A3340

value: Other


title: Tumor_MetTrp53_A1005


title: Tumor_Trp53_A4375.3R

value: Poorly Differentiated Adenocarcinoma


title: Tumor_Trp53_A3957


title: Normal_MetTrp53_A66.MFP


title: Tumor_MetTrp53_A1034


title: E176_11_Leptin_3_B


title: Tumor_MetTrp53_A65


title: Tumor_Trp53_A4375_2.3R


title: Normal_MFP1


title: Tumor_Trp53_A4719.2.3L


title: Tumor_MetTrp53_A1129