title: ST-00007370_S-001045570_5988071015_F


title: ST-00007370_S-001045562_5988071015_E

status: Public on Jul 08 2016

type: RNA

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Yale University School of Medicine

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: VSN normalized, background corrected

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood sample from human subject

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: occupation

value: Pick-up and Delivery Driver


title: ST-00007187_S-001045567_5988071015_B


title: ST-00073501_S-001045572_5988071008_I


title: ST-00073501_S-001045596_5988071008_J


title: ST-00042016_S-001045556_5988071008_F


title: ST-00042016_S-001045400_5988071008_E


title: ST-00007190_S-001045559_5988071008_B


title: ST-01000527_S-001045366_5988071004_J

value: Dockworker


title: ST-01000527_S-001045324_5988071004_I


title: ST-00007191_S-001045560_5988071004_B

value: Officeworker


title: ST-00007190_S-001045403_5988071008_A


title: ST-01000527_S-001045377_5988071004_K


title: ST-00073501_S-001045284_5988071008_H


title: ST-00008299_S-001045583_5988071008_D


title: ST-00034503_S-001045346_5988071004_D


title: ST-00034503_S-001045415_5988071004_E


title: ST-00007191_S-001045401_5988071004_A


title: ST-00073496_S-001045279_5988071010_I


title: ST-00042016_S-001045589_5988071008_G


title: ST-00038875_S-001045294_5988071010_G


title: ST-00073496_S-001045295_5988071010_K


title: ST-00007188_S-001045588_5988071010_C


title: ST-00038875_S-001045289_5988071010_F


title: ST-00007188_S-001045402_5988071010_B


title: ST-00073496_S-001045283_5988071010_J


title: ST-00007188_S-001045398_5988071010_A


title: ST-00007195_S-001045580_5988071010_E


title: ST-00051647_S-001045519_5988071016_K


title: ST-00080354_S-001045331_5988071016_A


title: ST-00007190_S-001045591_5988071008_C


title: ST-00073497_S-001045296_5988071003_D


title: ST-00051647_S-001045287_5988071016_J


title: ST-00073497_S-001045280_5988071003_C


title: ST-00080359_S-001045546_5988071024_G


title: ST-00007191_S-001045563_5988071004_C


title: ST-01000523_S-001045364_5988071022_K


title: ST-00007195_S-001045577_5988071010_D


title: ST-00036801_S-001045326_5988071024_A


title: ST-00039170_S-001045404_5988071024_B


title: 384h sample, replicate 2

city: Rovereto

first: Mario

last: Lauria

state: TN

address: Piazza Manifattura 1

country: Italy

institute: COSBI

description: 384h sample, replicate 2

hyb_protocol: The RNA labeling and microarray hybridization was performed according to the manufacturer’s recommendations.

scan_protocol: Beadchips were scanned using Illumina BeadScan image data acquisition software.

data_processing: The raw SampleProbeProfile file was processed in R using the 'beadarray' package, and other packages from the Bioconductor project. The 'VSN' package was employed for calibration and variance stabilization of the data. Probe sequences were annotated with four quality categories ('Perfect', 'Good', 'Bad' and 'No match') using 'illuminaHumanv4.db', and those classified as either 'Bad' or 'No match' were removed. The remaining probes were re-annotated using the same tool ('illuminaHumanv4.db').

source_name: SBGS cells

growth_protocol: Human Simpson-Golabi-Behmel syndrome (SGBS) preadipocytes were used in this study and cultured as described previously25. Briefly, the SGBS preadipocytes cells were cultured at 37°C in a humidified incubator maintaining a 5% CO2 atmosphere. The growth medium consisted of DMEM:F12 (1:1) (GIBCO, Life technologies, Grand Island, NY),  33 mM biotin, and 17 mM pantothenate containing 10% fetal bovine serum (Hyclone, Logan, UT) and 1% penicillin-streptomycin (GIBCO, Life technologies).

extract_protocol: Cells were harvested in triplicates for each specific time points including 0, 6, 48, 96, 192 and 384 hours, following the initiation of differentiation to examine the time-dependent changes in mRNA transcripts. During harvesting, the medium was aspirated and the cells were harvested using Lysis/Binding Solution (Ambion®, Life Technologies). Total RNA was isolated from the harvested cells using the RNAqueous® Total RNA Isolation Kit (Ambion®, Life Technologies Inc., Carlsbad, CA) as per the manufacturer’s recommendations. The quality of the RNA isolated was examined using Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA).  RIN numbers of >9 were obtained in each case. The quantity of RNA was measured using the NanoDrop 8000 (Thermo Scientific Wilmington, DE) and the 260/280 ratios obtained were between 1.8 and 2.1.

treatment_protocol: For this study, SGBS preadipocytes were plated at 1x10^5 cells per well of a 6 well plate. The cells were grown to confluence and induced to differentiate into adipocytes one day post confluence by addition of a serum-free differentiation medium. The differentiation medium consisted of DMEM:F12 (1:1) (obtained by mixing Dulbecco′s Modified Eagle′s Medium without glucose (SIGMA) and Hams F12 nutrient mixture  containing 10 mM glucose (SIGMA) in a 1:1 ratio) to which 25 nM dexamethasone, 500 μM 3-isobutyl-1-methylxanthine, 2 μM rosiglitazone, 0.01 mg/ml human transferrin, 2 × 10−8 M insulin,10−7 M cortisol, 0.2 nM T3, 33 mM biotin, and 17 mM pantothenate was added. The cells were maintained in differentiation medium for 4 days after which the medium was changed to a serum-free adipogenic medium consisting of DMEM:F12 (1:1) with 0.01 mg/ml human transferrin, 2 × 10−8 M insulin, 10−7 M cortisol, 0.2 nM T3, 33 mM biotin, and 17 mM pantothenate. The adipogenic medium was essentially similar to the differentiation medium but without 3-Isobutyl-1-methylxanthine (IBMX), dexamethasone and rosiglitazone. Medium was renewed every two days from the initiation of differentiation.

tag: cell type

tag: time point


title: 384h sample, replicate 3

description: 384h sample, replicate 3

label_protocol: The RNA labeling and microarray hybridization was performed according to the manufacturer’s recommendations.

value: Simpson-Golabi-Behmel syndrome (SGBS) preadipocytes


title: ST-00051647_S-001045281_5988071016_I


title: ST-01000523_S-001045354_5988071022_J


title: ST-00038875_S-001045420_5988071010_H


title: 192h sample, replicate 3

description: 192h sample, replicate 3


title: 384h sample, replicate 1

description: 384h sample, replicate 1


title: ST-01000523_S-001045332_5988071022_I


title: ST-01000529_S-001045378_5988071029_I


title: ST-01000529_S-001045310_5988071029_G


title: 192h sample, replicate 2

description: 192h sample, replicate 2


title: ST-00039170_S-001045524_5988071024_C


title: ST-00080359_S-001045328_5988071024_E


title: 96h sample, replicate 3

description: 96h sample, replicate 3


title: ST-01000510_S-001045315_5988071022_G


title: ST-01000510_S-001045305_5988071022_F


title: ST-01000529_S-001045368_5988071029_H


title: 96h sample, replicate 4

description: 96h sample, replicate 4


title: 192h sample, replicate 1

description: 192h sample, replicate 1


title: 96h sample, replicate 1

description: 96h sample, replicate 1


title: ST-00073501_S-001048866_5988071029_K


title: ST-01000510_S-001045359_5988071022_H


title: 48h sample, replicate 2

description: 48h sample, replicate 2


title: 48h sample, replicate 3

description: 48h sample, replicate 3


title: 6h sample, replicate 9

description: 6h sample, replicate 9


title: 48h sample, replicate 1

description: 48h sample, replicate 1


title: 6h sample, replicate 2

description: 6h sample, replicate 2


title: 6h sample, replicate 8

description: 6h sample, replicate 8


title: 6h sample, replicate 3

description: 6h sample, replicate 3


title: 96h sample, replicate 2

description: 96h sample, replicate 2


title: 6h sample, replicate 1

description: 6h sample, replicate 1


title: 6h sample, replicate 7

description: 6h sample, replicate 7


title: 0h sample, replicate 3

description: 0h sample, replicate 3


title: 6h sample, replicate 6

description: 6h sample, replicate 6


title: 6h sample, replicate 5

description: 6h sample, replicate 5


title: 0h sample, replicate 2

description: 0h sample, replicate 2


title: HuR-E18A

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
SAMPLE 9
E18 mouse cortex was dissected, homogenized and immunoprecipitated with anti-HuR.  RNA was prepared for an Affymetrix Mouse Exon microarray.

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.extended.mps

label: biotin

organism: Mus musculus

source_name: E18 mouse cortex_anti-HuR

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

extract_protocol: Immunoprecipitated RNA was prepared by Trizol extraction.

tag: strain background

value: HuR fl/fl (C57BL/6J) crossed to Emx1-Cre (B6.129S2)

tag: age

tag: immunoprecipitation antibody

value: Rabbit anti-HuR, pAb

tag: antibody vendor

value: MBL International

tag: antibody cat#

tag: group

tag: tissue

value: fetal neocortex


title: IgG-E18A

description:
SAMPLE 11
E18 mouse cortex was dissected, homogenized and immunoprecipitated with IgG as negative control.  RNA was prepared for an Affymetrix Mouse Exon microarray.

source_name: E18 mouse cortex_IgG as negative control

tag: immunoprecipitation

value: IgG


title: Balbc_p53null_2374R_transplant_ADP_CGH

type: genomic

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: samples obtained from Chuck Perou Lab

hyb_protocol: described in Herschkowitz et al., 2012, PNAS, 109:2778-2783

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

molecule: genomic DNA

source_name: FVB DNA Reference

extract_protocol: Genomic DNA isolated using a Qiagen Blood and Tissue Kit

value: FVB DNA Reference

source_name: BALB/c p53null mammary transplant line: 2374R

value: BALB/c p53null mammary transplant line:2374R

tag: sample type

value: Mammary tumor DNA

value: mammary tumor


title: HuR-E17

description:
SAMPLE 7
E17 mouse cortex was dissected, homogenized and immunoprecipitated with anti-HuR.  RNA was prepared for an Affymetrix Mouse Exon microarray.

source_name: E17 mouse cortex_anti-HuR


title: 0h sample, replicate 1

description: 0h sample, replicate 1


title: 6h sample, replicate 4

description: 6h sample, replicate 4


title: IgG-E17

description:
SAMPLE 8
E17 mouse cortex was dissected, homogenized and immunoprecipitated with IgG as negative control.  RNA was prepared for an Affymetrix Mouse Exon microarray.

source_name: E17 mouse cortex_IgG as negative control


title: 384h sample, replicate 4

description: 384h sample, replicate 4


title: HuR-E18B

description:
SAMPLE 10
E18 mouse cortex was dissected, homogenized and immunoprecipitated with anti-HuR.  RNA was prepared for an Affymetrix Mouse Exon microarray.


title: IgG-E13B

description:
SAMPLE 6
E13 mouse cortex was dissected, homogenized and immunoprecipitated with IgG as negative control.  RNA was prepared for an Affymetrix Mouse Exon microarray.

source_name: E13 mouse cortex_IgG as negative control


title: Balbc_p53null_2374L_transplant_YA_CGH

description: samples obtained from Chuck Perou Lab

label_protocol: described in Herschkowitz et al., 2012, PNAS, 109:2778-2783

source_name: BALB/c p53null mammary transplant line: 2374L

value: BALB/c p53null mammary transplant line:2374L


title: ST-00035859_S-001045539_5988071016_B


title: ST-00039170_S-001045525_5988071024_D


title: Balbc_p53null_2245R_transplant_YA_CGH

description: samples obtained from Chuck Perou Lab

source_name: BALB/c p53null mammary transplant line: 2245R

value: BALB/c p53null mammary transplant line:2245R


title: Balbc_p53null_2350R_transplant_YA_CGH

description: samples obtained from Chuck Perou Lab

source_name: BALB/c p53null mammary transplant line: 2350R

value: BALB/c p53null mammary transplant line:2350R


title: HuR-E11B

description:
SAMPLE 2
E11 mouse cortex was dissected, homogenized and immunoprecipitated with anti-HuR.  RNA was prepared for an Affymetrix Mouse Exon microarray.

source_name: E11 mouse cortex_anti-HuR


title: Liver_WTEGFP_3

city: Bethesda

first: Richard

middle: Lee

last: Gieseck

state: MD

address: 4 Memorial Drive

department: NIAID

institute: NIH

description:
Mmic-9704007026-C
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Samples were normalized to 500 based on median and then coverted to log2 scale using NIH mAdb platform. Subsequent statistical analyses were performed in TM4 Mev Suite.

source_name: Whole Liver WT

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: The RNA was extracted using Trizol reagent and cleaned up using a Qiagen Rneasy miniprep kit.

treatment_protocol: Mice were given hydrodynamic delivery of either an EGFP or IL-13 mammalian overexpression plasmid and sacrificed after one week.

value: Liver

tag: genotype

value: wild type


title: Liver_Cre+EGFP_3

description:
Mmic-9704007026-A
replicate 3

source_name: Whole Liver Alb-Cre+

value: Alb-Cre+


title: HuR-E11A

description:
SAMPLE 1
E11 mouse cortex was dissected, homogenized and immunoprecipitated with anti-HuR.  RNA was prepared for an Affymetrix Mouse Exon microarray.


title: Liver_WTEGFP_4

description:
Mmic-9704007026-D
replicate 4


title: Liver_Cre+EGFP_2

description:
Mmic-9704007019-B
replicate 2


title: Liver_WTIL-13_2

description:
Mmic-9704007019-H
replicate 4


title: Liver_Cre+IL-13_3

description:
Mmic-9704007026-E
replicate 3


title: Liver_Cre+IL-13_1

description:
Mmic-9704007019-E
replicate 1


title: Liver_WTEGFP_2

description:
Mmic-9704007019-D
replicate 2


title: Liver_WTIL-13_3

description:
Mmic-9704007026-G
replicate 3


title: Liver_WTIL-13_1

description:
Mmic-9704007019-G
replicate 3


title: Liver_WTEGFP_1

description:
Mmic-9704007019-C
replicate 1


title: mgb_mir_mod_4

city: Columbus

first: Susan

last: Ingraham

address: 700 Childrens Drive

institute: Nationwide Children's Hospital

description: microRNA expression in obstructed kidney

hyb_protocol: Cyanine 3-pCP labeled miRNA was generated from 100 ng of total RNA.  Labeled miRNA was purified using spin columns, and completely dried with vacuum concentrator for ~1 hour at 45°C.  Samples were resuspended in 17ul of nuclease-free water and hybridized on Aglient Sureprint miRNA arrays in Hybe oven for 20 hours at 55°C, rotating 20 RPM.  Arrays were washed according to manufacturer’s instructions and scanned using Agilent DNA Mircroarray Scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x16 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1(Agilent) using default parameters (protocol miRNA_107_Sep 09 and Grid: 021828_D_F_20091031) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Whole kidney RNA, mgb-/- mouse 4

label_protocol: Cyanine 3-pCP labeled miRNA was prepared from 100ng of total RNA using the miRNA Complete Labeling and Hyb kit (Agilent) according to the manufacturer's instructions, followed by Micro Bio_Spin 6 column purification (Bio-Rad).

extract_protocol: Total RNA including the small RNA fraction was isolated from snap-frozen kidney samples (3.5-4 weeks old, WT and mgb -/- males) using Qiagen TissueLyser II and Ambion MiRVana Kit according to the supplier protocols. Quantity and integrity of RNA samples were measured using NanoDrop ND-1000 UV-Vis Spectrophotometer and Agilent 2100 Biozanalyzer Lab-On-A-Chip Agilent 6000 Series II chip, respectively

value: kidney

tag: gender

value: male

tag: genotype/variation

value: mgb-/-


title: 293T replication timing

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray (SurePrint G3 Human CGH Microarray Kit, 4x180K, AGILENT Technologies, genome reference Hg18) that covers the whole genome with one probe every 13 Kb (11 KB in RefSeq sequences).

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.

source_name: nascent DNA  from early S-phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification was conducted (WGA, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Each cells grown in culture condition defined by ATCC

extract_protocol: cells were incubated with BrdU (50µM) for one hour, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) as described by Hiratani et al 2008. To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

tag: cell line

source_name: nascent DNA  from late S-phase


title: mgb_mir_mod_3

source_name: Whole kidney RNA, mgb-/- mouse 3


title: RKO replication timing

value: RKO


title: Liver_Cre+IL-13_2

description:
Mmic-9704007019-F
replicate 2


title: HeLa replication timing

value: HeLa


title: Liver_Cre+EGFP_1

description:
Mmic-9704007019-A
replicate 1


title: HCT116 infected with lentivirus sh-RAP1-4#,biological rep1

city: Chicago

first: Yongyong

last: Yang

state: IL

address: 303 E Superior ST

department: Department of Urology

institute: Northwestern University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 640 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

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

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Raw data were normalized with the RMA algorithm by Gene Spring Software 12.5 (Agilent technologies, Santa Clara, CA, US).

source_name: HCT116_lentivirus sh-RAP1-4#_72 hr

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

growth_protocol: HCT116  cells were infected with lentivirus sh-negative-control and lentivirus sh-RAP1-4# for 72 hr, separately.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: HCT116  cells (1x10^5/well of 6-well plate) were infected with lentivirus sh-negative-control and lentivirus sh-RAP1-4# at an MOI of 20 for 72 hr, separately.

value: colorectal cancer cell

tag: infected with

value: lentivirus sh-RAP1-4# for 72 hr


title: Sox2- cells, biological rep4

city: Toronto

first: John

middle: E

last: Dick

state: Ontario

address: University Health Network, Princess Margaret Cancer Research Tower, E Tower, 8th floor, 8-301

department: Molecular Genetics

country: Canada

institute: University of Toronto

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized to the Affymetrix Mouse Gene 2.0 ST (GPL16570) array using the FS450_0002 protocol

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

data_processing: CHP files were generated by Expression Console (v.1.2.0.20) using Affymetrix default analysis settings and Robust Multi-array average (RMA) as normalization method. Partec was used for to analyze CEL files using RMA normalization for prinicple component analysis, discovery of differentially expressed genes by one-way ANOVA and hierarchical clustering.

source_name: Sox2- Patched1+/- medulloblastoma cells

label_protocol: cDNA were prepared from 0.1ug RNA with the Ambion WT Gene Expression kit.

growth_protocol: Mice were housed according to CCAC standards at Sickkids Laboratory for Animal Services. Patched1+/-; Sox2eGFP mice were administered 3Gy ionizing radiation at birth to induce medulloblastoma formation.

extract_protocol: Sorted cells were resuspended in 333uL Trizol and frozen at -80C. On the day of sample preparation, 3 samples, each representing one tumour, per biological replicate (GFP+ or GFP-) were pooled and RNA extracted using the ZymoReagent Easy-Zol column purification kit

treatment_protocol: Upon exhibiting signs of a brain tumour, animals were sacrificed using CO2 asphixiation and tumours microdissected in PBS. Tumours were dissociated to single cells using gentle pipetting followed by straining through a 70um then 40um cell strainer. Cell suspensions were depleted of CD45 and Ter119+ cells and Sox2 GFP+ and Sox2 GFP- cells were isolated by FACS on a Beckman Coulter MoFlo 9 colour cell sorter.

value: Patched1+/- CD1; Sox2eGFP B6 parents

value: >70 days

value: medulloblastoma cells

tag: cell subpopulation

value: Sox2-eGFP- cells


title: mgb_mir_mod_2

source_name: Whole kidney RNA, mgb-/- mouse 2


title: Sox2- cells, biological rep3

tag: cell type


title: mgb_mir_WT_4

description: microRNA expression in normal kidney

source_name: Whole kidney RNA, WT mouse 4

value: mgb+/+


title: Balbc_p53null_2397L_transplant_YA_CGH

description: samples obtained from Chuck Perou Lab

source_name: FVB DNA Reference

value: FVB DNA Reference

source_name: BALB/c p53null mammary transplant line: 2397L

value: BALB/c p53null mammary transplant line:2397L

value: Mammary tumor DNA

value: mammary tumor


title: U2OS replication timing


title: mgb_mir_WT_1

description: microRNA expression in normal kidney

source_name: Whole kidney RNA, WT mouse 1


title: mgb_mir_WT_2

description: microRNA expression in normal kidney

source_name: Whole kidney RNA, WT mouse 2


title: mgb_mir_WT_3

description: microRNA expression in normal kidney

source_name: Whole kidney RNA, WT mouse 3


title: Sox2+ cells, biological rep4

source_name: Sox2+ Patched1+/- medulloblastoma cells

value: Sox2-eGFP+ cells


title: Sox2+ cells, biological rep3


title: Sox2+ cells, biological rep2


title: Sox2+ cells, biological rep1


title: IBC-BC216UT1

status: Public on Jul 07 2016

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

description: Gene expression profile of human whole invasive breast cancer.

hyb_protocol: RNA was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4851A) according to manufacturer's instructions.

scan_protocol: Feature extraction was performed using Agilent Feature Extraction software.

data_processing: Individual arrays were background-corrected with the RMA algorithm, log2 transformed, and subsequently quantile normalized.

source_name: Invasive breast cancer (IBC)

label_protocol: Total RNA was amplified and labeled using Low RNA Input Quick Amp Labeling Kit (Agilent Technologies, USA). The procedure was followed by the protocol for One-Color Microarray-Based Gene Expression Analysis, Low Input Qucik Amp Labeling, Version 6.5 (Agilent Technologies, USA).

extract_protocol: Tumor tissues were homogenized using TRIzol Reagent (Invitrogen, Life Technologies, USA), and purified with RNeasy mini columns (Qiagen, Netherlands). The quality of RNA was assessed using NanoDrop ND-1000 Spectrophotometer, version 3.7.1 (NanoDrop Technologies, Thermo Fisher Scientific Inc, USA).

tag: tissue type

value: Invasive breast cancer (IBC)

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

value: Basal

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence event

tag: recurrence location

tag: recurrence type

tag: follow-up time


title: IBC-BC371UT1

tag: tissue type


title: IBC-BC136UT1

tag: er (ihc)


title: IBC-BC408UT1

tag: pr (ihc)


title: IBC-BC99UT1

tag: her2 (ihc)

value: LumA


title: Mouse embroyo fibroblasts

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description: Gene expression data from mouse fibroblasts

hyb_protocol: Following fragmentation, 4.2 ug of cDNA were hybridized for 16 hr at 45C on Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Partek® Genomics SuiteTM.  Expression values were RMA normalized, and fold-change values were then calculated using least-squares mean between samples.

source_name: Fibroblast cells from E13.5 mouse embroyo

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (wt_sensetarget_label_manual).

growth_protocol: Cells were cultured in induced medium for 25 days and transfer into MEF medium.

extract_protocol: Total RNA was performed  using Rneasy minikit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Cells were treated by compound cocktail ( VCSTO) for 25 days

tag: cell morphology

value: MEFs


title: HCT116 infected with lentivirus sh-negative-control,biological rep1

tag: cell line

tag: cell type

tag: infected with

value: lentivirus sh-negative-control for 72 hr


title: IBC-BC423UT1

tag: grade (combined)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

value: LumB


title: IBC-BC278UT1

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence event


title: IBC-BC166UT1

tag: tissue type

tag: er (ihc)

tag: recurrence location

tag: recurrence type

tag: follow-up time


title: IBC-BC263UT4

tag: pr (ihc)

tag: her2 (ihc)


title: IBC-BC191UT1

tag: grade (combined)


title: IBC-BC398UT1

tag: grade (elston)


title: IBC-BC94UT1

tag: grade (eortc)

value: Normal


title: Induced astrocytes

description: Gene expression data from induce astrocytes

source_name: MEFs treated by compounds

tag: cell morphology

value: astrocyte


title: Primary astrocytes

description: Gene expression data from primary astrocytes

source_name: Astrocyts from p2 mouse cortex


title: IBC-BC373UT1

tag: lymph node

tag: age (years)


title: IBC-BC226UT1

tag: size (mm)

tag: death event


title: IBC-BC329UT1

tag: iPSilateral event

tag: dmfs event


title: IgG-E13A

description:
SAMPLE 5
E13 mouse cortex was dissected, homogenized and immunoprecipitated with IgG as negative control.  RNA was prepared for an Affymetrix Mouse Exon microarray.

source_name: E13 mouse cortex_IgG as negative control

tag: strain background

value: HuR fl/fl (C57BL/6J) crossed to Emx1-Cre (B6.129S2)

tag: age

tag: immunoprecipitation

value: IgG

tag: group

tag: tissue

value: fetal neocortex


title: K562 replication timing

source_name: nascent DNA  from early S-phase

tag: cell line

source_name: nascent DNA  from late S-phase


title: IBC-BC201UT4

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: recurrence event

tag: recurrence location

tag: recurrence type

tag: follow-up time


title: IBC-BC340UT1

tag: grade (combined)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

tag: death event


title: IBC-BC152UT1

tag: iPSilateral event

tag: dmfs event


title: IBC-BC179UT1

tag: tissue type


title: HuR-E13A

description:
SAMPLE 3
E13 mouse cortex was dissected, homogenized and immunoprecipitated with anti-HuR.  RNA was prepared for an Affymetrix Mouse Exon microarray.

source_name: E13 mouse cortex_anti-HuR

tag: strain background

tag: age

tag: immunoprecipitation antibody

value: Rabbit anti-HuR, pAb

tag: antibody vendor

value: MBL International

tag: antibody cat#

tag: group

tag: tissue


title: Liver_Cre+EGFP_4

description:
Mmic-9704007026-B
replicate 4

source_name: Whole Liver Alb-Cre+

value: Liver

tag: genotype

value: Alb-Cre+


title: IBC-BC274UT1

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: recurrence event

tag: recurrence location

tag: recurrence type

tag: follow-up time


title: IBC-BC392UT1

tag: tissue type

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: dmfs event


title: IBC-BC400UT1

tag: er (ihc)


title: IBC-BC285UT1

tag: pr (ihc)


title: IBC-BC317UT1

tag: her2 (ihc)


title: IBC-BC153UT1

tag: grade (combined)


title: IBC-BC97UT1

tag: grade (elston)


title: IBC-BC182UT1

tag: recurrence event


title: IBC-BC280UT1

tag: recurrence location


title: IBC-BC187UT1

tag: recurrence type


title: IBC-BC410UT1

tag: follow-up time


title: DCIS-BC206UT5

description: Gene expression profile of human whole ductal carcinoma in situ.

source_name: Ductal carcinoma in situ (DCIS)

tag: tissue type

value: Ductal carcinoma in situ (DCIS)


title: IBC-BC145UT1

tag: grade (eortc)


title: DCIS-BC146UT1

description: Gene expression profile of human whole invasive breast cancer. This sample was flagged as possibly poor technical quality, and was not included in our analyses.

tag: lymph node


title: IBC-BC407UT1

tag: age (years)


title: DCIS-FW08_423_rep1

description: miRNA profile of human whole ductal carcinoma in situ.

hyb_protocol: RNA was hybridized to Human miRNA Microarray Release 16.0, 8x60K (G4872A-031181) according to manufacturer's instructions.

scan_protocol: Feature extraction was performed using Agilent Scanner G2565A and Feature Extraction software version 10.7.3.1.

data_processing: Data was normalized using the GeneSpring version 12 software environment provided by Agilent. Probe spots were either marked as detected with errors lower than 3 times the signal, or if flagged were given a value of 0.1. Probe spots for the same miRNA were summed, individual arrays were log2 transformed, and subsequently 90th percentile normalized.

label_protocol: 200ng RNA was used as input for labeling according to manufacturer's protocol.

tag: size (mm)

tag: source

value: Uppsala


title: Normal-AmbionCTRL_rep4

description: miRNA profile of human whole normal breast tissue control.

source_name: Normal breast tissue

value: Normal breast tissue

tag: death event

tag: iPSilateral event


title: DCIS-FW08_429_rep1

tag: er (ihc)

tag: dmfs event


title: DCIS-FW06_57_rep1

description: miRNA profile of human whole invasive breast cancer.

value: Invasive breast cancer (IBC)

tag: pr (ihc)

tag: her2 (ihc)

value: Oslo


title: Normal_AmbionCTRL_rep3

tag: grade (combined)

tag: grade (elston)


title: DCIS-FW06_24

tag: recurrence event

tag: recurrence location


title: DCIS-BC163UT1

value: LumA

tag: recurrence type

tag: follow-up time


title: DCIS-BC87RT5

tag: tissue type

tag: grade (eortc)


title: DCIS-BC150UT4

tag: lymph node

tag: age (years)


title: IBC-BRC_288

tag: size (mm)

tag: source

value: Trondheim


title: Adipocyte_RTV_DMSO

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

hyb_protocol: 11 μg of aRNA were hybridised onto the Affymetrix Mouse Genome 430 2.0 Array Kit (Affymetrix, High Wycombe, UK).

scan_protocol: Arrays were scanned in GCS3000 7G scanner as according to manufacturer's protocol (Affymetrix) to generate DAT and CEL files.

data_processing: CEL files were processed using Expression Console software to apply background correction, probeset summarisation and normalisation using the RMA-sketch algorithm.

label: Biotin

source_name: 3T3-L1 adipocytes; treated for 5 days

label_protocol: Total RNA was pooled from 4 replicate experiments and approx 500ng was converted to cDNA using Ambion MessageAmp Premier kit (Invitrogen Life Technologies). The cDNA was then used in an in-vitro transcription (IVT) reaction to synthesise biotin-modified amplified RNA (aRNA) according to the manufacturer’s protocol. Biotinylated aRNA was fragmented prior to hybridisation using the 5X Array Fragmentation Buffer supplied with the MessageAmp™ Kit.

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM-F12, supplemented with 10% FBS, 8 μg/ml pantothenate, 8 μg/ml biotin, 200 mM glutamine, 10,000 U/ml penicillin, 10 μg/l streptomycin and 10 mg/l MycoKill AB mycoplasma antibiotic at 37°C with 5% CO2. Pre-adipocytes were grown to near confluence for 5 days and a further two days to initiate growth arrest. Pre-adipocytes were induced to differentiate using an adipogenic cocktail of 1 μg/ml insulin, 0.5 mM 3-isobutyl-1-methylxanthine and 0.25 μmol/l dexamethasone for two days.

extract_protocol: Total RNA was extracted from adipocytes after 5 days of exposure to antiretroviral drug or control using the RNeasy Mini Kit according to manufacturer’s instructions (Qiagen, Manchester, UK). Briefly, cells were lysed and homogenised using a highly denaturing guanidine-thiocyanate-containing buffer. Ethanol was added to provide appropriate binding conditions and the sample was then applied to an RNeasy Mini spin column. Total RNA binds to the membrane and contaminants were efficiently washed away. RNA was eluted in 50 μl nuclease-free water. Total RNA (1 μg) was extracted from adipocytes after 5 days of exposure to antiretroviral drug or control using the RNeasy Mini Kit (Qiagen) as per manufacturer’s instructions. RNA was quantified using the NanoDrop® 1000 3.7.1

treatment_protocol: Subsequently, media were removed and replaced with adipogenic media supplemented with 1 μg/ml insulin and near Cmax concentrations of 20 μM RTV or 1μM TDF (VWR, Lutterworth, UK) or vehicle control ethanol (0.1% v/v), or RTV+c9,t11-CLA (100μM), t10,c12-CLA (100μM) or DMSO (0.1% v/v) control for  5 days. Media were changed every second day thereafter until the adipocytes were fully differentiated after the 5 days. Cells were exposed to treatments for a total of five days.

tag: cell line

tag: cell type

value: adipocytes

tag: treatment

value: Ritonavir+DMSO


title: DCIS-BC262UT1

tag: er (ihc)

tag: pr (ihc)

value: LumB

tag: death event

tag: iPSilateral event

tag: dmfs event


title: DCIS-FW08_419(2)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: recurrence event

tag: recurrence location


title: DCIS-BC225UT1

tag: tissue type

tag: grade (eortc)

tag: lymph node

value: Normal

tag: recurrence type

tag: follow-up time


title: Adipocyte_RTV_t10c12

tag: cell line

tag: cell type


title: DCIS-FW08_413

tag: er (ihc)

tag: age (years)

tag: size (mm)

value: Ipsi inv

value: Invasive

tag: source


title: DCIS-BC218UT4

tag: pr (ihc)

tag: death event

tag: iPSilateral event

tag: dmfs event


title: DCIS-FW06_7

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: recurrence event


title: IBC-BRC_239

tag: tissue type

tag: grade (eortc)

tag: lymph node

tag: recurrence location


title: Adipocyte_RTV_c9t11

tag: cell line

tag: cell type

tag: treatment


title: DCIS-CMB_349

tag: er (ihc)

tag: age (years)

tag: size (mm)

tag: recurrence type

tag: follow-up time

value: Akershus


title: DCIS-BC314UT1

tag: pr (ihc)

tag: death event

tag: iPSilateral event

tag: dmfs event


title: IBC-BRC_72

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: recurrence event

tag: source


title: HuR-E13B

description:
SAMPLE 4
E13 mouse cortex was dissected, homogenized and immunoprecipitated with anti-HuR.  RNA was prepared for an Affymetrix Mouse Exon microarray.

tag: strain background

value: HuR fl/fl (C57BL/6J) crossed to Emx1-Cre (B6.129S2)

tag: age

tag: immunoprecipitation antibody

value: Rabbit anti-HuR, pAb

tag: antibody vendor

value: MBL International

tag: antibody cat#

tag: group

tag: tissue

value: fetal neocortex


title: Adipocyte_TDF

tag: cell line

tag: cell type

tag: treatment

value: Tenofovir


title: Normal-AmbionCTRL_rep3

description: Gene expression profile of human whole normal breast tissue control.

tag: tissue type

value: Normal breast tissue

tag: er (ihc)

tag: pr (ihc)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: recurrence location

tag: recurrence type

tag: follow-up time

value: Ambion Human Breast Total RNA


title: DCIS-FW06_42

value: Ductal carcinoma in situ (DCIS)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: dmfs event

tag: recurrence event

tag: source

value: Oslo


title: IBC-FW06_56

tag: tissue type

value: Invasive breast cancer (IBC)

tag: er (ihc)

value: LumA

value: contralateral in situ then contra invasive

value: Mixed


title: IBC-BRC_28_rep2

tag: pr (ihc)

tag: grade (eortc)

value: Normal

value: Trondheim


title: DCIS-CMB_273

tag: lymph node

tag: age (years)


title: DCIS_FW08_423_rep2

tag: size (mm)

tag: death event

value: Uppsala


title: IBC-BC266UT1

value: LumB

tag: iPSilateral event

tag: recurrence location


title: DCIS-FW06_6

tag: recurrence type

tag: follow-up time


title: DCIS-FW08_418

tag: her2 (ihc)

tag: grade (combined)


title: DCIS-CMB_215

tag: grade (elston)

value: Basal

tag: dmfs event

value: Akershus


title: IBC-BRC_202

tag: recurrence event

tag: source


title: Sox2- cells, biological rep2

source_name: Sox2- Patched1+/- medulloblastoma cells

tag: genotype/variation

value: Patched1+/- CD1; Sox2eGFP B6 parents

tag: age

value: >70 days

tag: cell type

value: medulloblastoma cells

tag: cell subpopulation

value: Sox2-eGFP- cells


title: Sox2- cells, biological rep1


title: DCIS-BRC_777

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: grade (eortc)

tag: lymph node

tag: age (years)


title: DCIS-BRC_98

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: recurrence location

tag: recurrence type

tag: follow-up time


title: DCIS-CMB_291

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: dmfs event

tag: recurrence event

tag: source


title: Adipocyte_RTV

tag: cell line

tag: cell type

value: adipocytes

tag: treatment

value: Ritonavir


title: DCIS-FW08_407

tag: tissue type

value: Ductal carcinoma in situ (DCIS)

tag: er (ihc)

tag: pr (ihc)

tag: grade (eortc)

tag: lymph node


title: DCIS-CMB_273

tag: age (years)

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: recurrence location


title: DCIS-FW08_420

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: recurrence type

tag: follow-up time


title: IBC-BRC_128

value: Invasive breast cancer (IBC)

tag: dmfs event

tag: recurrence event

tag: source


title: IBC-BRC_766

tag: tissue type

tag: er (ihc)


title: Mouse Leukemic Spleen Male 21

city: Tampa

first: Michael

middle: B.

last: Mann

state: Florida

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: H. Lee Moffitt Cancer Center and Research Institute

description: Log base 2 expression value derived via RMA normalization in R

hyb_protocol: Samples were hybridized with GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) and scanned at the University of Otago Genomics & Bioinformatics Facility Microarray Core.

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

data_processing: Raw data were processeded in R (version 2.15, www.r-project.org) using the rma function of the affy package (quantile normalization, no background correction). Subsequent data analysis and statistical evaluations were performed with customized R scripts (version 2.15, http://www.r-project.org/).

label_protocol: RNA was labelled using a Affymetrix 3' IVT Express kit Cat # 901229 using 100ng of total RNA for each sample. Labelling was preformed according to manufacturer's instructions

growth_protocol: Flash Frozen tissues were collected at necropsy and stored at -80ºC until RNA isolation was performed.

extract_protocol: RNA was extracted using a NORGEN Bioteck Animal Tissue RNA Purification kit Cat #25700 according to manufacturer's instructions

tag: tumorid

tag: genotype

tag: Sex

value: M

tag: age

tag: tissue

value: Spleen, tumor

tag: diagnosis

value: Myeloid Leukemia, Undifferentiated

tag: disease stage

value: terminal

tag: biomaterial collected by

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA

value: Y


title: IBC-BC281UT1

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

value: LumA

tag: death event

tag: iPSilateral event

tag: recurrence location


title: DCIS-BRC_773

tag: tissue type

tag: er (ihc)

tag: grade (elston)

value: Basal

tag: dmfs event

tag: recurrence event

tag: recurrence type

tag: follow-up time

tag: source

value: Trondheim


title: IBC-BRC_14

tag: pr (ihc)

tag: her2 (ihc)


title: IBC-BRC_183

tag: grade (combined)

tag: grade (eortc)

value: Normal


title: Mouse Leukemic Spleen Male 20

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: Normal-AmbionCTRL_rep2

tag: tissue type

value: Normal breast tissue

tag: er (ihc)

tag: grade (elston)

tag: lymph node

tag: age (years)

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence location


title: DCIS-FW06_1

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (eortc)

value: LumB

tag: recurrence event

tag: recurrence type

tag: follow-up time

tag: source

value: Oslo


title: Mouse Leukemic Spleen Female 23

tag: tumorid

tag: genotype

tag: Sex

value: F

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: Mouse Leukemic Spleen Male 22


title: DCIS-FW06_42

tag: tissue type

tag: er (ihc)

tag: grade (elston)

tag: lymph node

tag: age (years)

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence location


title: Mouse Leukemic Spleen Female 24

tag: tumorid

tag: genotype


title: IBC-BRC_28

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (eortc)

tag: recurrence event

tag: recurrence type

tag: follow-up time

tag: source


title: DCIS-CMB_195

tag: tissue type

tag: er (ihc)

tag: grade (elston)

tag: lymph node

value: Akershus


title: Adipocyte_ETH

tag: cell line

tag: cell type

value: adipocytes

tag: treatment

value: Ethanol


title: IBC-BRC_246

value: Invasive breast cancer (IBC)

tag: age (years)

tag: size (mm)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence location


title: MRC5 replication timing


title: DCIS-CMB_17

value: Ductal carcinoma in situ (DCIS)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (eortc)

tag: recurrence event


title: IBC-BRC_239

tag: tissue type

tag: er (ihc)

tag: recurrence type

tag: follow-up time

tag: source


title: DCIS-FW08_440

tag: grade (elston)

tag: lymph node

value: Uppsala


title: DCIS-FW08_421

tag: age (years)

tag: size (mm)


title: Mouse Leukemic Spleen Male 17

tag: tumorid

tag: genotype

tag: Sex

value: M

tag: age

tag: tissue

value: Spleen, tumor

tag: diagnosis

value: Myeloid Leukemia, Undifferentiated

tag: disease stage

value: terminal

tag: biomaterial collected by


title: DCIS-FW08_440

tag: tissue type

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (eortc)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence event

tag: recurrence location


title: Mouse Leukemic Spleen Male 18

tag: tumorid

tag: genotype

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA

value: Y


title: DCIS-BRC_54

tag: er (ihc)

tag: grade (elston)

tag: lymph node

tag: age (years)

tag: size (mm)

value: Basal

tag: recurrence type

tag: follow-up time

tag: source

value: Trondheim


title: Mouse Leukemic Spleen Male 19

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: IBC-BC96UT1

tag: tissue type

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (eortc)

value: LumB

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence event

tag: recurrence location


title: DCIS-BRC_19

tag: er (ihc)

tag: grade (elston)

tag: lymph node

tag: age (years)

tag: size (mm)

value: LumA

tag: recurrence type

tag: follow-up time

tag: source


title: DCIS-FW06_23

tag: tissue type

tag: pr (ihc)

value: Oslo


title: DCIS-FW08_429

tag: her2 (ihc)

tag: grade (combined)


title: Mouse Leukemic Spleen Female 22

tag: tumorid

tag: genotype

tag: Sex

value: F

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: DCIS-CMB_338

tag: er (ihc)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: recurrence event

tag: recurrence location

value: Akershus


title: DCIS-FW08_432

tag: tissue type

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: size (mm)

tag: recurrence type

tag: follow-up time

tag: source


title: IBC-FW06_57

tag: er (ihc)

tag: grade (elston)


title: DCIS-FW08_423

tag: grade (eortc)

tag: lymph node


title: IBC-BRC_180

tag: age (years)

tag: death event


title: IBC-BRC_183

value: Normal

tag: iPSilateral event

tag: dmfs event


title: Mouse Leukemic Spleen Female 21

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: DCIS-CMB_45

tag: tissue type

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: size (mm)

tag: recurrence event

tag: recurrence location

tag: recurrence type

tag: follow-up time

tag: source


title: IBC-FW06_25

value: Invasive breast cancer (IBC)

tag: er (ihc)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event

value: Ipsilateral invasive

value: Invasive


title: Mouse Leukemic Spleen Male 16

tag: tumorid

tag: genotype

tag: Sex

value: M

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: DCIS-CMB_195

tag: tissue type

value: Ductal carcinoma in situ (DCIS)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: size (mm)

tag: recurrence event

tag: recurrence location

tag: recurrence type

tag: follow-up time

tag: source


title: DCIS-BRC_779

tag: er (ihc)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event


title: Mouse Leukemic Spleen Male 15

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

value: Spleen, tumor

tag: diagnosis

value: Myeloid Leukemia, Undifferentiated

tag: disease stage

tag: biomaterial collected by


title: IBC-FW06_68

tag: tissue type

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: size (mm)

tag: recurrence event

tag: recurrence location

value: Skin and brain

tag: recurrence type

tag: follow-up time

tag: source


title: IBC-BRC_246

tag: er (ihc)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event


title: DCIS-BRC_54

tag: tissue type

tag: pr (ihc)


title: Mouse Leukemic Spleen Female 20

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

value: terminal

tag: biomaterial collected by

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA

value: Y


title: DCIS-FW08_430

tag: er (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: size (mm)

tag: recurrence event

tag: recurrence location

value: Ipsi situ

tag: recurrence type

value: Non-Invasive

tag: follow-up time

tag: source

value: Uppsala


title: IBC-BRC_153

tag: tissue type

tag: pr (ihc)

tag: grade (eortc)

tag: lymph node

tag: age (years)

value: LumA

tag: death event

tag: iPSilateral event

tag: dmfs event

value: Trondheim


title: DCIS-FW06_24

tag: er (ihc)

tag: her2 (ihc)

value: Oslo


title: DCIS-FW06_2

tag: grade (combined)

tag: grade (elston)


title: IBC-FW06_12

value: Invasive breast cancer (IBC)

tag: size (mm)

tag: recurrence event


title: DCIS-FW06_5

description: miRNA profile of human whole ductal carcinoma in situ. This sample was flagged as possibly poor technical quality, and was not included in our analyses.

tag: recurrence location

value: contra invasive then liver +skeleton

tag: recurrence type


title: Mouse Leukemic Spleen Male 13

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: Mouse Leukemic Spleen Male 14


title: DCIS-FW06_6

tag: tissue type

tag: pr (ihc)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: DCIS-CMB_17

tag: er (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: size (mm)

value: LumB

tag: recurrence event

tag: recurrence location

tag: recurrence type

value: Akershus


title: IBC-FW06_26

tag: tissue type

tag: pr (ihc)


title: DCIS-FW06_41

value: Ductal carcinoma in situ (DCIS)

tag: grade (eortc)

tag: lymph node


title: Mouse Leukemic Spleen Female 19

tag: tumorid

tag: genotype

tag: Sex

value: F

tag: age

tag: tissue

value: Spleen, tumor

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: DCIS-FW08_432

tag: er (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: age (years)

value: Basal

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: Mouse Leukemic Spleen Male 12

tag: tumorid

tag: genotype

value: M

value: Myeloid Leukemia, Undifferentiated

value: terminal

value: N


title: IBC-BRC_190

tag: tissue type

tag: pr (ihc)

tag: grade (eortc)

tag: lymph node

tag: size (mm)

value: Normal

tag: recurrence event

tag: recurrence location

tag: recurrence type


title: DCIS-BRC_19

tag: er (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)


title: IBC-BRC_190

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event


title: IBC-FW06_26

tag: follow-up time

tag: source


title: Mouse Leukemic Spleen Female 18

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA

value: Y


title: IBC-BRC_153

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (eortc)

tag: lymph node

tag: size (mm)

value: LumA

tag: recurrence event

tag: recurrence location

tag: recurrence type

value: Trondheim


title: DCIS-FW06_8

tag: grade (combined)

tag: grade (elston)

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source

value: Oslo


title: Mouse Leukemic Spleen Female 17

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: DCIS-FW08_418

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (eortc)

tag: lymph node

tag: size (mm)

tag: recurrence event

tag: recurrence location

tag: recurrence type

value: Uppsala


title: Mouse Leukemic Spleen Female 25

tag: tumorid

tag: genotype


title: Mouse Leukemic Spleen Female 16

tag: Sex

tag: age


title: Mouse Leukemic Spleen Male 11

tag: tissue

tag: diagnosis


title: DCIS-BRC_98

tag: grade (combined)

tag: grade (elston)

tag: age (years)

tag: death event

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: DCIS-FW08_430

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (eortc)

tag: lymph node

tag: size (mm)

tag: recurrence event

value: Ipsi situ

value: Non-Invasive


title: IBC-BRC_202

value: Invasive breast cancer (IBC)

value: LumB

tag: recurrence location

tag: recurrence type


title: Normal-AmbionCTRL_rep1

value: Normal breast tissue

tag: grade (combined)

tag: grade (elston)

value: Ambion Human Breast Total RNA


title: IBC-BRC_198

tag: age (years)

tag: death event


title: Mouse Leukemic Spleen Female 15

tag: tumorid

tag: genotype

tag: Sex

value: F

tag: age

tag: tissue

value: Spleen, tumor

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: DCIS-FW08_419(2)

tag: tissue type

value: Ductal carcinoma in situ (DCIS)

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (eortc)

tag: lymph node

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: IBC-FW06_12

tag: grade (combined)

tag: grade (elston)

tag: age (years)

tag: size (mm)

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type


title: Mouse Leukemic Spleen Female 14

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

value: Myeloid Leukemia, Undifferentiated

tag: disease stage

value: terminal

tag: biomaterial collected by

value: N


title: Mouse Leukemic Spleen Male 10

value: M

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA


title: IBC-FW06_68

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (eortc)

tag: lymph node

tag: iPSilateral event

tag: dmfs event

value: Skin and brain

value: Invasive

tag: follow-up time

tag: source


title: DCIS-FW06_23

tag: grade (combined)

tag: grade (elston)

tag: age (years)

tag: size (mm)

value: LumA

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type

value: Oslo


title: DCIS-CMB_354

tag: tissue type

tag: er (ihc)

value: Akershus


title: DCIS-FW08_400

tag: pr (ihc)

tag: her2 (ihc)

value: Normal

value: Uppsala


title: DCIS-BRC_773

tag: grade (eortc)

tag: lymph node

value: Basal

value: Trondheim


title: LLC1 5x2Gy irradiation replicate 1

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description: Biological replicate 1 of 3. Total RNA isolated from LLC1 cells irradiated with fractionated 5x2 Gy X-ray dose.

hyb_protocol: 100 ng of RNA labeled with Cy3 dye was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Mouse miRNA Expression 8x15k Oligonucleotide Microarrays (Agilent Technologies) for 20 hours at 55°C in rotating hybridization oven.

scan_protocol: Microarrays were scanned using SureScan Microarray Scanner (Agilent Technologies)

data_processing: Image analysis was performed using Feature Extraction v10.7.3.1 (Agilent Technologies). Raw probe value normalization: Experimental Samples were Scaled to mean of All Samples

source_name: LLC1 cells irradiated with 5x2Gy

label_protocol: miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies) according to manufacturer’s instructuctions. In brief, 100 ng of total RNA were defosforilated and directly labeled with Cy3. Samples were dried out and resuspended in Hi-RPM Hybridization Buffer (Agilent Technologies), containing GE Blocking Agent (Agilent, USA), denaturated by heating 5 min in 100°C.

growth_protocol: LLC1 cells were cultured in DMEM cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2nM glutamine (Gibco), 100 UI/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA enrich in small noncoding RNAs was isolated from harvested cells using mirVana miRNA Isolation Kit (Ambion) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

tag: treatment

value: fractionated dose of 5x2Gy

tag: cell line


title: DCIS-FW08_421

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: LLC1 5x2Gy irradiation replicate 2

description: Biological replicate 2 of 3. Total RNA isolated from LLC1 cells irradiated with fractionated 5x2 Gy X-ray dose.


title: Mouse Leukemic Spleen Female 13

tag: tumorid

tag: genotype

tag: Sex

value: F

tag: age

tag: tissue

value: Spleen, tumor

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: Mouse Leukemic Spleen Male 9

value: Myeloid Leukemia, Undifferentiated


title: LLC1 10Gy irradiation replicate 3

description: Biological replicate 3 of 3. Total RNA isolated from LLC1 cells irradiated with single 10 Gy X-ray dose.

source_name: LLC1 cells irradiated with 10Gy

value: single dose of 10Gy


title: LLC1 10Gy irradiation replicate 2

description: Biological replicate 2 of 3. Total RNA isolated from LLC1 cells irradiated with single 10 Gy X-ray dose.


title: DCIS-CMB_354

tag: tissue type

value: Ductal carcinoma in situ (DCIS)

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: age (years)

tag: size (mm)

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type


title: LLC1 5x2Gy irradiation replicate 3

description: Biological replicate 3 of 3. Total RNA isolated from LLC1 cells irradiated with fractionated 5x2 Gy X-ray dose.

tag: treatment

tag: cell line


title: LLC1 10Gy irradiation replicate 1

description: Biological replicate 1 of 3. Total RNA isolated from LLC1 cells irradiated with single 10 Gy X-ray dose.


title: LLC1 2Gy irradiation replicate 3

description: Biological replicate 3 of 3. Total RNA isolated from LLC1 cells irradiated with single 2 Gy X-ray dose.

source_name: LLC1 cells irradiated with 2Gy

value: single dose of 2Gy


title: LLC1 control replicate 3

description: Biological replicate 3 of 3. Total RNA isolated from untreated LLC1 cells.

source_name: Untreated LLC1 cells

value: Control


title: LLC1 2Gy irradiation replicate 1

description: Biological replicate 1 of 3. Total RNA isolated from LLC1 cells irradiated with single 2 Gy X-ray dose.


title: DCIS-FW06_41

tag: grade (eortc)

tag: lymph node

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: LLC1 2Gy irradiation replicate 2

description: Biological replicate 2 of 3. Total RNA isolated from LLC1 cells irradiated with single 2 Gy X-ray dose.


title: LLC1 control replicate 2

description: Biological replicate 2 of 3. Total RNA isolated from untreated LLC1 cells.


title: IBC-BRC_128

source_name: Invasive breast cancer (IBC)

tag: tissue type

value: Invasive breast cancer (IBC)

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

value: LumB


title: IBC-BRC_14

tag: grade (combined)

tag: grade (elston)

tag: age (years)

tag: size (mm)


title: DCIS-FW06_7

description: miRNA profile of human whole ductal carcinoma in situ.

value: LumA

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type


title: Normal-AmbionCTRL_rep1

description: miRNA profile of human whole normal breast tissue control.

value: Normal breast tissue

tag: grade (eortc)

tag: lymph node


title: Mouse Leukemic Spleen Female 12

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

value: terminal

tag: biomaterial collected by

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA

value: N


title: Mouse Leukemic Spleen Female 11

value: Y


title: DCIS-BRC_779

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source

value: Trondheim


title: Mouse Leukemic Spleen Male 7

tag: tumorid

tag: genotype

value: M


title: Mouse Leukemic Spleen Male 8

tag: Sex

tag: age


title: Mouse Leukemic Spleen Female 10

value: F

tag: tissue

tag: diagnosis


title: Mouse Leukemic Spleen Female 9

value: Spleen, tumor

tag: disease stage

tag: biomaterial collected by


title: Mouse Leukemic Spleen Male 6

value: Myeloid Leukemia, Undifferentiated


title: Mouse Leukemic Spleen Female 8


title: IBC-BRC_28_rep1

description: miRNA profile of human whole invasive breast cancer. This sample was flagged as possibly poor technical quality, and was not included in our analyses.

tag: tissue type

tag: er (ihc)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

value: Normal

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type


title: Normal-AmbionCTRL_rep2

description: Gene expression profile of human whole normal breast tissue control.

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source

value: Ambion Human Breast Total RNA


title: DCIS-FW06_5

description: Gene expression profile of human whole ductal carcinoma in situ.

tag: tissue type

value: Ductal carcinoma in situ (DCIS)

tag: er (ihc)

value: contra invasive then liver +skeleton

value: Invasive

value: Oslo


title: Mouse Leukemic Spleen Female 7

description: Log base 2 expression value derived via RMA normalization in R

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

tag: biomaterial collected by


title: LLC1 control replicate 1

description: Biological replicate 1 of 3. Total RNA isolated from untreated LLC1 cells.

tag: treatment

value: Control

tag: cell line


title: DCIS-FW06_1

tag: pr (ihc)

tag: her2 (ihc)

tag: grade (combined)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

value: LumB

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type


title: DCIS-FW06_8

tag: tissue type

tag: er (ihc)

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: IBC-FW06_57_rep2

description: miRNA profile of human whole invasive breast cancer.

value: Invasive breast cancer (IBC)

tag: pr (ihc)

tag: her2 (ihc)

value: LumA


title: Mouse Leukemic Spleen Female 6

tag: tumorid

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

value: terminal

tag: biomaterial collected by

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA

value: N


title: IBC-BRC_233

tag: grade (combined)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type

value: Trondheim


title: Mouse Leukemic Spleen Female 5

tag: tumorid

tag: genotype

value: F


title: Mouse Leukemic Spleen Male 4

tag: Sex

value: M

tag: age

value: Spleen, tumor


title: EGS_44_MoGene

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Mouse Gene 1.0 ST arrays and scanned at the IGBMC Biopuces Plateform Facility.

data_processing: Raw data were processed with the Expression Console Software (Affymetrix). The Robust Multichip Analysis (RMA) algorithm was used to normalize the array signal data across chips and generate transcript level values. We used the Partek Genomics Suite software to obtain exon levels values from the CEL files. Student t-test was performed to obtain transcript (genes) which are significantly differentially expressed between experimental groups. We used the Benjamini & Hochberg procedure for controlling the False Discovery Rate (FDR) due to the multiple testing. We used Ingenuity Pathway Analysis (IPA) for recovering links between selected genes.

source_name: rectal mucosa (10 weeks)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: We used 10 week-old control and α6ΔIEC-TAM  mice raised in conventional facilities. Mice were killed by cervical dislocation. The rectal mucosa were rapidly excised, flushed with PBS and quickly frozen in liquid nitrogen. All samples were stored at -80°C until RNA extraction.

extract_protocol: RNA was isolated from rectal mucosa with the RNeasy® Midi Kit (QIAGEN), according to the manufacturer’s instructions. Quantification and quality control of RNA were assessed on Agilent 2100 Bioanalyzer.

treatment_protocol: To induce the specific Itga6 deletion in the α6ΔIEC-TAM mice, tamoxifen (dissolved in 0.9 % NaCl and homogenized by sonication) was administered by gavage (2 doses of 10 mg/day, 1 day/2, during 5 days) to 8 week-old α6ΔIEC-TAM mutant (n=4) and control (n=3) mice. In a control experiment mutant animals (n=4) receive NaCl instead of tamoxifen. The animals were analyzed 15 days after the first tamoxifen (or NaCl) gavage.

value: Female

tag: genotype/variaion

value: mutant

tag: treatment

value: NaCl


title: EGS_50_MoGene

value: Male


title: IBC-BRC_233

description: Gene expression profile of human whole invasive breast cancer.

tag: tissue type

tag: er (ihc)

tag: pr (ihc)

tag: her2 (ihc)

tag: iPSilateral event

tag: dmfs event

tag: follow-up time

tag: source


title: EGS_47_MoGene


title: EGS_42_MoGene

value: wild type

value: tamoxifen


title: EGS_35_MoGene


title: EGS_62_MoGene


title: EGS_56_MoGene


title: Mouse Leukemic Spleen Male 5

tag: tissue

tag: diagnosis

value: Myeloid Leukemia, Undifferentiated

tag: disease stage

tag: biomaterial collected by


title: EGS_46_MoGene


title: Mouse Leukemic Spleen Male 2

tag: tumorid

tag: genotype


title: Mouse Leukemic Spleen Male 3

tag: Sex

tag: age


title: Mouse Leukemic Spleen Female 4


title: EGS_38_MoGene

tag: genotype/variaion

tag: treatment


title: DCIS_FW08_429_rep2

tag: tissue type

value: Ductal carcinoma in situ (DCIS)

tag: er (ihc)

tag: grade (combined)

tag: grade (elston)

tag: grade (eortc)

tag: lymph node

tag: age (years)

tag: size (mm)

value: LumB

tag: death event

tag: recurrence event

tag: recurrence location

tag: recurrence type

value: Uppsala


title: Striatal tissue 6-week, Wild Type Male Mouse, biol rep 2

first: Andrew

last: Pitsilides

address: Royal College Street

department: Comparative Biomedical Sciences

institute: The Royal Veterinary College

description: Gene expression data from brain striatal tissue at 6 weeks

hyb_protocol: Hybridisation was performed according to the manufacturer's instructions

scan_protocol: Scanning of arrays was performed according to the manufacturer's instructions

data_processing: The data were analyzed with R/Bioconductor, RMA normalized values were obtained with the affy() package

source_name: Striatal Tissue at 6 weeks

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

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

value: 6 weeks

tag: genotype

value: Wild Type

tag: gender


title: Mouse Leukemic Spleen Female 3

tag: tumorid

tag: Sex

tag: age

tag: tissue

tag: diagnosis

tag: disease stage

value: terminal

tag: biomaterial collected by

value: Karen M. Mann, Ph.D. and Michael B. Mann, Ph.D., Houston Methodist Research Institute, Houton, TX, USA

value: N


title: Striatal tissue 6-week, Wild Type Male Mouse, biol rep 1


title: EGS_34_MoGene

tag: genotype/variaion

tag: treatment


title: Striatal tissue 6-week, YAC 128 Male Mouse, biol rep 3

value: YAC 128


title: EGS_43_MoGene


title: Striatal tissue 6-week, Wild Type Female Mouse, biol rep 2


title: Striatal tissue 6-week, YAC 128 Male Mouse, biol rep 2


title: Striatal tissue 6-week, Wild Type Female Mouse, biol rep 1


title: Mouse Leukemic Spleen Female 2

value: F

value: Spleen, tumor


title: Striatal tissue 18-week, YAC 128 Male Mouse, biol rep 2

description: Gene expression data from brain striatal tissue at 18 weeks

source_name: Striatal Tissue at 18 weeks

value: 18 weeks


title: Striatal tissue 18-week, YAC 128 Male Mouse, biol rep 1


title: Striatal tissue 18-week, YAC 128 Male Mouse, biol rep 3


title: Striatal tissue 18-week, YAC 128 Female Mouse, biol rep 2

value: Female


title: Striatal tissue 18-week, Wild Type Male Mouse, biol rep 2

value: Male


title: Striatal tissue 18-week, Wild Type Male Mouse, biol rep 1


title: Striatal tissue 6-week, YAC 128 Male Mouse, biol rep 1


title: Striatal tissue 6-week, YAC 128 Female Mouse, biol rep 1


title: Mouse Leukemic Spleen Male 1

value: M


title: Striatal tissue 18-week, Wild Type Female Mouse, biol rep 1


title: Striatal tissue 12-week, Wild Type Male Mouse, biol rep. 3

description: Gene expression data from brain striatal tissue at 12 weeks

source_name: Striatal Tissue at 12 weeks

value: 12 weeks


title: Mouse Leukemic Spleen Female 1

value: Myeloid Leukemia, Undifferentiated


title: Striatal tissue 18-week, YAC 128 Female Mouse, biol rep 1


title: Striatal tissue 12-week, Wild Type Male Mouse, biol rep. 2


title: Striatal tissue 12-week, Wild Type Female Mouse, biol rep. 1


title: Striatal tissue 12-week, Wild Type Female Mouse, biol rep. 2


title: Striatal tissue 12-week, YAC 128 Male Mouse, biol rep. 2


title: Striatal tissue 12-week, YAC 128 Male Mouse, biol rep. 1


title: Striatal tissue 12-week, YAC 128 Female Mouse, biol rep. 3


title: Striatal tissue 12-week, YAC 128 Female Mouse, biol rep. 2


title: Striatal tissue 12-week, YAC 128 Female Mouse, biol rep. 1


title: Spneumoniae_ R6_SECO_t30_rep_2

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

country: Spain

institute: Instituto de Salud Carlos III

hyb_protocol: 250 ng of labelled cDNA were used for hybridization. Arrays were hybridized at 65ºC for 40 hours.

scan_protocol: Scanning was done on a Roche MS200 scanner

data_processing: Raw data were extracted and normalized using Agilent Feature extraction 11.5.1.1 software. The median expression of every probeset was obtained, scaled to log2 and normalized by quantile using Bioconductor.

organism: Streptococcus pneumoniae R6

source_name: RNA extracted from S. pneumoniae R6

label_protocol: 25 ng of RNA were used to obtain cDNA with WTA2 from Sigma. This cDNA was labelled with Cy3 with ULS kit following Agilent's instructions

growth_protocol: Bacteria were grown in AGCH + 0.2% yeast extract + 0.3% sucrose medium until OD620=0.4

extract_protocol: RNA was extracted with Mini Rneasy columns from Quiagen and treated with DNAse I

treatment_protocol: Seconeolitsine was added to the culture (8 µM; 0.5 x MIC) and samples were taken at 0, 5, 15 and 30 min

tag: growth phase

value: Exponential

tag: medium

value: AGCH + 0.5% yeast extract + 0.3% sucrose


title: EGS_R4_MoGene

source_name: male, mutant, 64 weeks

growth_protocol: We used 53-80 week-old control and α6fl/fl Villin-Cre matched mice raised in conventional facilities. Mice were killed by cervical dislocation. The rectal prolapses developed in α6fl/fl Villin-Cre mutant mice were rapidly excised, flushed with PBS and quickly frozen in methyl butane cooled in liquid nitrogen. Transverse 5 µm-thick cryosections of prolapses were extemporaneously stained with haematoxilin-eosin and a pathologist defined the presence and the localization of adenocarcinomas. After identification, adenocarcinomas were macrodissected from 50 to 100 µm-thick cryosections. Adjacent non-tumoral rectal mucosa (corresponding to inflamed mucosa) was similarly macrodissected and recovered. The normal rectal mucosa used as reference was obtained from matched control mice. After sacrifice, the recto-anal region was excised, longitudinally opened and flushed with PBS. The rectal mucosa was recovered by scraping and directly frozen in liquid nitrogen. All samples were stored at -80°C until RNA extraction.

extract_protocol: RNA was isolated from scraped control normal mucosa and cryosections of mutant adenocarcinomas and inflamed rectal mucosa with the RNeasy® Micro Kit (QIAGEN), according to the manufacturer’s instructions. Quantification and quality control of RNA were assessed on Agilent 2100 Bioanalyzer.

tag: tissue type

value: inflamed rectal mucosa

tag: age (weeks)

value: 64 weeks

tag: genotype/variation

value: α6fl/fl Villin-Cre


title: EGS_T6_MoGene

source_name: female, control, 70 weeks

value: normal rectal mucosa

value: 70 weeks


title: EGS_R3_MoGene

source_name: male, mutant, 60 weeks

value: 60 weeks


title: Spneumoniae_ R6_SECO_t30_rep_1


title: EGS_T4_MoGene

source_name: male, control, 64 weeks


title: Striatal tissue 12-week, Wild Type Male Mouse, biol rep. 1

value: Wild Type


title: EGS_R2_MoGene


title: Spneumoniae_ R6_SECO_t15_rep_1


title: EGS_T1_MoGene

source_name: female, control, 53 weeks

value: 53 weeks


title: EGS_T2_MoGene

source_name: male, control, 60 weeks


title: EGS_A4_MoGene

value: Adenocarcinoma


title: EGS_R1_MoGene

source_name: female, mutant, 53 weeks


title: p.putida (mt2)-succinate_vs_control-R1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

address: Darwin 3

institute: CNB, CSIC

description:
p.putida (mt-2)-succinate_vs_control-R1
Pseudomonas putida (mt-2)

hyb_protocol: Samples were placed on ice and rapidly loaded onto arrays, hybridized (65ºC, 17 h), then washed once in GE Wash Buffer 1 (room temperature, 1 min) and once in GE Wash Buffer 2 (37ºC, 1 min). Arrays were drained by centrifugation (2000 rpm, 2 min).

scan_protocol: Images from Cy3 and Hyper 5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were quantified using GenePix software (Axon) for tiling array data sets (m-xylene VS succinate). For other tiling array data sets that are reference condition-based comparisons, we used the Agilent DNA Microarray Scanner and quantified images using Agilent Feature Extraction software.

data_processing: Raw intensities were background-corrected by the normexp method with an offset of 50. Background-corrected intensities were converted to log2 scale and normalized by adjusting the quantiles of all replicates. After normalization, differential expression for each probe was calculated as log2Ratios = log2Intensity (experimental condition) - log2Intensity (control condition).

organism: Pseudomonas putida

source_name: P. putida mt-2 culture, succinate, 96h (C-runout)

label_protocol: Total RNA (20 μg each) was retrotranscribed and aminoallyl-labeled using the SuperScript Indirect cDNA Labeling System (Invitrogen) and 5-(3-aminoallyl)-2'deoxyuridine-5'-triphosphate (aa-dUTP, Ambion) following manufacturers' protocols. To avoid antisense artifacts from second-strand cDNA during reverse transcription, actinomycin D was added after the denaturing step at 70°C to a final concentration of 6 μg/ml. For each sample, aminoallyl-labeled cDNA was resuspended in 0.1 M Na2CO3 (pH 9.0) and conjugated with Cy3 or Hyper 5 Mono NHS Ester (CyTMDye Post-labelling Reactive Dye Pack, Amersham), following a dye-swap strategy. Samples were purified with Megaclear (Ambion) following the manufacturer's instructions. Cy3 and Hyper 5 incorporation was measured in a NanoDrop spectrophotometer (NanoDrop Technologies). Probe preparation and hybridizations were performed as described (Two-Color Microarray-Based Prokaryote Analysis, Agilent Technologies).

growth_protocol: P. putida cultures were routinely grown at 30°C in M9 minimal medium including 6 g/l Na2HPO4, 3 g/l KH2PO4, 1.4 g/l (NH4)2SO4, 0.5 g/l NaCl, 0.2 g/l MgSO4·7H2O and 2.5 ml/l of a trace element solution, with a carbon source as described in treatment protocol.

extract_protocol: Cell cultures were transferred to 1/10 sample volume of ice-cold ethanol/phenol solution (5% water-saturated phenol in ethanol) to protect RNA from degradation and harvested by centrifugation (3,800 rpm, 15 min, 4°C). After supernatant aspiration, pellets were frozen in liquid nitrogen and stored at -80°C until required. Total RNA was extracted by using the miRNeasy kit (Qiagen) with some modifications. The collected pellets were resuspended into 0.3 ml Tris-HCl (pH 7.5) containing 2 mg/ml lysozyme and incubated (10 min, 37°C). Lysate (0.1 ml) was used according to manufacturer's instructions. RNase-free DNase (Qiagen) treatment was performed during the isolation procedure to eliminate residual DNA and quality was evaluated on Model 2100 Bioanalyzer (Agilent).

treatment_protocol: For induction of TOL catabolic genes during transcriptomics experiments, the P. putida mt-2 strain was precultured overnight in M9 medium with succinate, and bacterial cultures were then diluted 100-fold in the same medium and grown to the exponential phase (OD600 = 0.3-0.5). Samples were then cultured further without additional substrate or exposed to vaporous m-xylene, toluene or o-xylene (1/2 dilution in dibutylphthalate, which is a non-effector for TOL genes) in a flask (2 h). For soluble substrates, benzoate (5 mM) or 3MBz (5 mM) was added to the culture medium once growth had reached OD600c~ 0.3. For the C-runout condition, the cells were cultured for 96 h in succinate-supplemented minimal medium. The antibiotics kanamycin (Km) 50 μg/ml, ampicillin (Amp) 150 μg/ml, streptomycin (Sm) 100 μg/ml, chloramphenicol (Cm) 30 μg/ml and gentamycin (Gm) 10 μg/ml were added to bacterial cultures when necessary.

tag: strain/background

value: succinate-96h (C-runout)

source_name: P. putida mt-2 culture, succinate

value: succinate


title: p.putida (mt2)-succinate_vs_control-R2

description:
p.putida (mt-2)-succinate_vs_control-R2
Pseudomonas putida (mt-2)


title: EGS_A1_MoGene


title: p.putida (mt2)-succinate_vs_control-R4

description:
p.putida (mt-2)-benzoate_vs_control-R4
Pseudomonas putida (mt-2)


title: Spneumoniae_ R6_SECO_t15_rep_2


title: p.putida (mt2)-succinate_vs_control-R3

description:
p.putida (mt-2)-succinate_vs_control-R3
Pseudomonas putida (mt-2)


title: EGS_A3_MoGene


title: EGS_A6_MoGene

source_name: female, mutant, 80 weeks

value: 80 weeks


title: p.putida (mt2)-benzoate_vs_control-R4

source_name: P. putida mt-2 culture, benzoate

value: benzoate


title: EGS_A2_MoGene


title: Spneumoniae_ R6_SECO_t5_rep_2


title: Spneumoniae_ R6_SECO_t0_rep_2


title: Spneumoniae_ R6_SECO_t5_rep_1


title: p.putida (mt2)-benzoate_vs_control-R3

description:
p.putida (mt-2)-benzoate_vs_control-R3
Pseudomonas putida (mt-2)


title: p.putida (mt2)-benzoate_vs_control-R2

description:
p.putida (mt-2)-benzoate_vs_control-R2
Pseudomonas putida (mt-2)


title: p.putida (mt2)-toluene_vs_control-R2

description:
p.putida (mt-2)-toluene_vs_control-R2
Pseudomonas putida (mt-2)

source_name: P. putida mt-2 culture, toluene

value: toluene


title: p.putida (mt2)-toluene_vs_control-R4

description:
p.putida (mt-2)-toluene_vs_control-R4
Pseudomonas putida (mt-2)


title: p.putida (mt2)-toluene_vs_control-R3

description:
p.putida (mt-2)-toluene_vs_control-R3
Pseudomonas putida (mt-2)


title: Spneumoniae_ R6_SECO_t0_rep_1


title: p.putida (mt2)-3MBz_vs_control-R4

description:
p.putida (mt-2)-3MBz_vs_control-R4
Pseudomonas putida (mt-2)

source_name: P. putida mt-2 culture, 3MBz


title: p.putida (mt2)-toluene_vs_control-R1

description:
p.putida (mt-2)-toluene_vs_control-R1
Pseudomonas putida (mt-2)


title: p.putida (mt2)-3MBz_vs_control-R3

description:
p.putida (mt-2)-3MBz_vs_control-R3
Pseudomonas putida (mt-2)


title: p.putida (mt2)-3MBz_vs_control-R2

description:
p.putida (mt-2)-3MBz_vs_control-R2
Pseudomonas putida (mt-2)


title: p.putida (mt2)-benzoate_vs_control-R1

description:
p.putida (mt-2)-benzoate_vs_control-R1
Pseudomonas putida (mt-2)


title: p.putida (mt2)-3MBz_vs_control-R1

description:
p.putida (mt-2)-3MBz_vs_control-R1
Pseudomonas putida (mt-2)


title: normal progenitor sample (16wf)

first: Shiyuan

last: Cheng

address: 303 E. Superior Street

department: Neurology

hyb_protocol: All hybridization reactions were incubated at 65 °C for a minimum of 12 h. Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions.

scan_protocol: According to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA).

data_processing: For each assay, a high-density scan was performed. For platform validation using synthetic oligonucleotides, NanoString nCounter microRNA raw data was normalized for lane-to-lane variation with a dilution series of six spikein positive controls. The sum of the six positive controls for a given lane was divided by the average sum across lanes to yield a normalization factor, which was then multiplied by the raw counts in each lane to give normalized values. All microrna (or global microRNA expression data from the three type of cell) were used for visualization in a heat map and was analyzed by Principal component analysis (PCA) [Johnson, R.a.W., D. Applied multivariate statistical   analysis. (New Jersey; 1998).] Using the d Chip software with Statistical R package. Array was perform at the Ohio State University Comprehensive Cancer Center Microarray, Nucleic Acids, Proteomic Shared Facilities with their technical assistance.

source_name: progenitor sample

label_protocol: Using 225 ng total RNA, 734 miRNA levels were assayed using Nanostring miRNA assay kit by direct digital detection following the manufacturer’s guidelines (NanoString Technologies, Seattle, WA).

growth_protocol: GSCs were cultured in DMEM/F12 (Invitrogen) supplemented with B27 (1:50), heparin (5 mg/mL), basic FGF (bFGF) (20 ng/mL), and EGF (20 ng/mL). All the cells were maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol: Cells were collected in the exponential phase of growth by 200xg centrifigation and then washed twice with 1x PBS. Followed, the cells were lysed with 1 mL Qiazol lysis reagent. Total RNA was then extracted and purified using the Qiagen RNeasy Mini kit (catalog no. 217004) according to the manufacturer’s instructions.

tag: disease state


title: LLC1 5x2Gy irradiation replicate 3

description: LLC1 cells were irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Whole Mouse Genome 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C  using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned  using Tecan LS Reloaded scanner.

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized.

source_name: Untreated LLC1 cells

label_protocol: 1µg of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion).  cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Apllied Biosystems).

growth_protocol: Cells were cultured in DMEM cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2nM glutamine (Gibco), 100 UI/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated from harvested cells using mirVana miRNA Isolation Kit (Ambion) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

value: Control

tag: cell line

tag: origin

value: C57BL/6 mouse lung cancer

source_name: LLC1 cells irradiated with 5x2Gy

value: fractionated dose of 5x2Gy


title: p.putida (mt2)-m-xylene_vs_control-R3

description:
p.putida (mt-2)-m-xylene_vs_control-R3
Pseudomonas putida (mt-2)

source_name: P. putida mt-2 culture, m-xylene

value: m-xylene


title: 816 GBM

source_name: High grade glioma

value: High grade glioma


title: p.putida (mt2)-o-xylene_vs_control-R2

description:
p.putida (mt-2)-o-xylene_vs_control-R2
Pseudomonas putida (mt-2)

source_name: P. putida mt-2 culture, o-xylene

value: o-xylene


title: p.putida (mt2)-m-xylene_vs_control-R2

description:
p.putida (mt-2)-m-xylene_vs_control-R2
Pseudomonas putida (mt-2)


title: p.putida (mt2)-o-xylene_vs_control-R3

description:
p.putida (mt-2)-o-xylene_vs_control-R3
Pseudomonas putida (mt-2)


title: p.putida (mt2)-o-xylene_vs_control-R4

description:
p.putida (mt-2)-o-xylene_vs_control-R4
Pseudomonas putida (mt-2)


title: 528 GBM


title: p.putida (mt2)-m-xylene_vs_control-R1

description:
p.putida (mt-2)-m-xylene_vs_control-R1
Pseudomonas putida (mt-2)


title: LLC1 10Gy irradiation replicate 2

description: LLC1 cells were irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.

source_name: LLC1 cells irradiated with 10Gy

value: single dose of 10Gy


title: LLC1 5x2Gy irradiation replicate 2

description: LLC1 cells were irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.


title: LLC1 2Gy irradiation replicate 3

description: LLC1 cells were irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

source_name: LLC1 cells irradiated with 2Gy

value: single dose of 2Gy


title: LLC1 5x2Gy irradiation replicate 1

description: LLC1 cells were irradiated with fractionated 5x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: LLC1 2Gy irradiation replicate 2

description: LLC1 cells were irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.


title: p.putida (mt2)-o-xylene_vs_control-R1

description:
p.putida (mt-2)-o-xylene_vs_control-R1
Pseudomonas putida (mt-2)


title: p.putida (mt2)-m-xylene_vs_control-R4

description:
p.putida (mt-2)-m-xylene_vs_control-R4
Pseudomonas putida (mt-2)


title: LLC1 10Gy irradiation replicate 1

description: LLC1 cells were irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: p.putida (mt2)-m-xylene_vs_control-R4 (GenePix)

description:
p.putida (mt-2)-m-xylene_vs_control-R4 (GenePix)
Pseudomonas putida (mt-2)


title: 1123  high-grade glioma


title: 718 GBM


title: LLC1 2Gy irradiation replicate 1

description: LLC1 cells were irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: 83 GBM


title: 20 high-grade glioma


title: 17 high-grade glioma


title: 84 GBM


title: p.putida (mt2)-m-xylene_vs_control-R3 (GenePix)

description:
p.putida (mt-2)-m-xylene_vs_control-R3 (GenePix)
Pseudomonas putida (mt-2)


title: p.putida (mt2)-m-xylene_vs_control-R2 (GenePix)

description:
p.putida (mt-2)-m-xylene_vs_control-R2 (GenePix)
Pseudomonas putida (mt-2)


title: p.putida (mt2)-m-xylene_vs_control-R1 (GenePix)

description:
p.putida (mt-2)-m-xylene_vs_control-R1 (GenePix)
Pseudomonas putida (mt-2)


title: CUL4B

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

country: China

institute: Tianjin Medical University

description: Chip-chip MDA-MB-231 cells CUL4B

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Raw data were extracted as pair files by NimbleScan software. We performed Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma and MEDME. After normalization, a normalized log2-ratio data was created for each sample. From the normalized log2-ratio data, a permutation-based peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) was applied to find peaks which represent significant positive enrichment. NimbleScan detects peaks by searching for 4 or more probes whose signals were above the specified cutoff values, ranging from 90% to 15%, using a 500bp sliding window. The cutoff values are a percentage of a hypothetical maximum, which is the mean + 6[standard deviation]. The ratio data is then randomized 20 times to evaluate the probability of “false positives”.

source_name: CUL4B ChIP DNA from MDA-MB-231 cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: MDA-MB-231 cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Invitrogen). All media contained 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin (Gibco BRL).

extract_protocol: 1x10E7 cells were washed twice with PBS and cross-linked with 1% formaldehyde at room temperature for 10 min. Cells then were rinsed with ice-cold PBS twice and collected into 100 mM Tris-HCl (pH 9.4), 10 mM DTT and incubated for 15 min at 30°C and centrifuged for 5 min at 2000 g. Cells were washed sequentially with 1 ml of ice-cold PBS, buffer I (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5), and buffer II (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5). Cells were then resuspended in 0.3 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.1, 1× protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN) and sonicated three times for 10 s each at the maximum setting (Fisher Sonic Dismembrator, Model 300) followed by centrifugation for 10 min. Supernatants were collected and diluted in buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1) followed by immunoclearing with 2 μg sheared salmon sperm DNA, 20 μl preimmune serum and protein A-sepharose (45 μl of 50% slurry in 10 mM Tris-HCl, pH 8.1, 1 mM EDTA) for 2 hr at 4°C. Immunoprecipitation was performed for 6 hr or overnight at 4°C with specific antibodies. After immunoprecipitation, 45 μl protein A-Sepharose and 2 μg of salmon sperm DNA were added and the incubation was continued for another 1 hr. Precipitates were washed sequentially for 10 min each in TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), and buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1). Precipitates were then washed three times with TE buffer and extracted three times with 1% SDS, 0.1 M NaHCO3. Eluates were pooled and heated at 65°C for at least 6 hr to reverse the formaldehyde cross-linking. DNA fragments were purified with a QIAquick Spin Kit (Qiagen, CA). For PCR, 1 μl from a 50 μl DNA extraction and 21–25 cycles of amplification were used.

treatment_protocol: 1x10E7 cells were collected for ChIP assay per antibody

tag: chip antibody

tag: chip antibody vendor

value: sigma-aldrich

tag: chip antibody cat. #

tag: chip antibody lot #

source_name: Input DNA from MDA-MB-231 cells

value: none, input DNA


title: PRMT5

description: Chip-chip MDA-MB-231 cells PRMT5

source_name: PRMT5 ChIP DNA from MDA-MB-231 cells

value: abcam